**********************************************************************
*                                                                    *
*                        M   A   P   L   E                           *
*                                                                    *
*      MAchine-learning Potential for Landscape Exploration          *
*                                                                    *
*                                                                    *
*      © 2025 University of Pittsburgh. All rights reserved.         *
*      Licensed under CC BY 4.0 for academic use.                    *
*                                                                    *
*      Principal Developer:  Xujian Wang                             *
*                                                                    *
**********************************************************************


Parsing # commands...
Global parameter: model = uma with options {'size': 'uma-s-1p1'}
Task set to 'parmfit'
Global parameter: device = gpu0
Parsed configuration:
----------------------------------------
Task: parmfit
model          : uma(size=uma-s-1p1)
method         : metalaa
input          : MetalAA1.in
device         : gpu0

                             Coordinates                              
**********************************************************************

Group 1 (PDB File)
Resolved PDB: /home/hungn/Desktop/MyRepo/MLP/MAPLE/examples/parmfit_tutorial/4ZF6.pdb
PDB coordinates are parsed by the parmfit route at runtime.
--------------------

======================================================================
                           Parmfit MetalAA                            
======================================================================
Target: A462:FE (ion)
  PDB residue templates: matched=460, backbone_only=0, unmatched=1
    not matched (seemingly not protein): A461:HEM
    declare them via lig_resids (or ncaa_resids) to build parameters as small molecules
  ion_resids: A462
  add_resid: []
  cluster_cutoff: 3.00 A
  donor_cutoff: 2.70 A
  water ff: tip3p
  protein ff: ff14SB
  ion ff: 12_6
  ion_charges: 3
  ion_mults: 6
  ncaa_resids: []
  large model charge/mult: -2 6
  chgmod: 1
  fixchg_resids: []
  QM method: PBE1PBE/def2SV
  [MetalAA] large-model input written.
  [MetalAA] MLIP large-model optimization ...
  [MetalAA] large-model RESP ...
  [MetalAA] site files written.
  [MetalAA] MLIP Hessian + Seminario + final frcmod ...
  [MetalAA] final parameter files written.
  [MetalAA] running tleap validation ...
  [MetalAA] route completed; final summary follows.

======================================================================
                        PARMFIT METALAA RESULT                        
======================================================================
Status: completed
Route: MetalAA
Target: A462:FE
Protein ff: ff14SB
Ions charge: 3
Large model charge/mult: -2 6
Core residues: _400:CYM, A461:HEM, A462:FE

Main products:
  final frcmod: MetalAA1_work/MetalAA1_metal.frcmod
  tleap input: MetalAA1_work/MetalAA1_metal_tleap.in
  tleap PDB:   MetalAA1_work/MetalAA1_metal_tleap.pdb
  mol2 files:  MetalAA1_work/CM1.mol2, MetalAA1_work/HM1.mol2, MetalAA1_work/FE1.mol2

Renamed atom types:
  residue      atom  old   new   charge
  _400:CYM     SG    SH    Z1    -0.329172
  A461:HEM     NA    nc    Z2    -0.129187
  A461:HEM     NB    nd    Z3    -0.181075
  A461:HEM     ND    nc    Z4    -0.152740
  A461:HEM     NC    nd    Z5    -0.118203
  A462:FE      FE    FE    M1     0.439642

Stage timing:
  RESP fitting           27m 22s
  ligand building         3m 29s
  Hessian + Seminario        59s
  model optimization         29s
  tleap validation            5s
  site export                 0s
  model build                 0s
  site selection              0s
  ncaa building               0s

Next step:
  cd MetalAA1_work
  tleap -s -f MetalAA1_metal_tleap.in |tee MetalAA1_metal_tleap.out

Tleap status:
  Errors: 0
  Warnings: 8
  Notes: 1

Warnings:
  Potentially charged standard residues within 8 Å of the metal but outside the large model: _398:ARG
======================================================================



Program started: 2026-09-30 05:23:43

======================================================================
                      TIMING SUMMARY
======================================================================
Input Reading.......................................   0.022 s  (   0.0 %)
  Settings Parsing....................................   0.020 s  (  91.5 %)
  Coordinate Section Parsing..........................   0.001 s  (   3.8 %)
  Post-Processing Expansion...........................   0.000 s  (   0.0 %)
MLP Initialization..................................  10.457 s  (   0.5 %)
Job Dispatching..................................... 1946.612 s  (  99.5 %)
  Parmfit optimization................................ 1946.611 s  ( 100.0 %)
    Parmfit MetalAA..................................... 1946.543 s  ( 100.0 %)
======================================================================
Total wall time: 1957.092 s
Total CPU time: 104.376 s
======================================================================

Program ended: 2026-09-30 05:56:20
TOTAL RUN TIME: 0 days 0 hours 32 minutes 37 seconds 91 msec