Starting qr.refine on Sat Apr 6 09:33:50 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/2h1g.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- debug_rss=true expansion=true mode=opt restraints=qm engine=aimnet2 clustering=false minimizer=lbfgs gradient_only=true use_reduce=False select_within_radius=7 number_of_micro_cycles=100 max_iterations_refine=100 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/2h1g.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/2h1g.pdb" } debug_rss = true use_reduce = False cluster { clustering = false select_within_radius = 7 } expansion = true quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { mode = *opt refine gtest number_of_micro_cycles = 100 max_iterations_refine = 100 gradient_only = true } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = True debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = False cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 7 clustering_method = gnc *bcc altloc_method = average *subtract save_clusters = True bond_with_altloc = True re_calculate_rmsd_tolerance = 0.5 } restraints = cctbx *qm expansion = True quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server basis = Auto charge = None method = Auto memory = None nproc = 1 server_url = "http://127.0.0.1:8000" qm_addon = gcp dftd3 gcp-d3 qm_addon_method = None } refine { dry_run = False sf_algorithm = *direct fft refinement_target_name = *ml ls_wunit_k1 mode = *opt refine gtest number_of_macro_cycles = 1 number_of_weight_search_cycles = 50 number_of_refine_cycles = 5 number_of_micro_cycles = 100 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 50 max_iterations_refine = 100 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = True refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.03 max_r_work_r_free_gap = 5 r_tolerance = 0.001 rmsd_tolerance = 0.01 opt_log = False pre_opt = False pre_opt_stpmax = 0.1 pre_opt_iter = 10 pre_opt_switch = 2 pre_opt_gconv = 3000 minimizer = *lbfgs lbfgsb shift_evaluation = max *mean } parallel { method = *multiprocessing slurm pbs sge lsf threading nproc = 1 qsub_command = None } output_file_name_prefix = None output_folder_name = "pdb" rst_file = None dump_gradients = None output { filename = None file_name = None prefix = None suffix = None serial = 0 serial_format = "%03d" target_output_format = None *pdb mmcif overwrite = False } ------------------------------------------------------------------------------- Extracting model **************** Symmetric amino acids flipped Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 4293 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2139 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 127} Chain: "B" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2154 Classifications: {'peptide': 137} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Time building chain proxies: 0.57, per 1000 atoms: 0.13 Number of scatterers: 4293 At special positions: 0 Unit cell: (47.031, 59.522, 109.562, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 405 8.00 N 349 7.00 C 1391 6.00 H 2138 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Adding C-beta torsion restraints... Number of C-beta restraints generated: 506 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 2138 1.14 - 1.31: 365 1.31 - 1.48: 864 1.48 - 1.64: 960 1.64 - 1.81: 20 Bond restraints: 4347 Sorted by residual: bond pdb=" CB PRO B 139 " pdb=" CG PRO B 139 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.37e-01 bond pdb=" C VAL A 137 " pdb=" N SER A 138 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.68e-01 bond pdb=" C ASP A 41 " pdb=" N ALA A 42 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.52e-01 bond pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 1.466 1.478 -0.012 1.50e-02 4.44e+03 6.27e-01 bond pdb=" C ASP B 41 " pdb=" N ALA B 42 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.26e-01 ... (remaining 4342 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.04: 112 107.04 - 113.77: 5243 113.77 - 120.50: 1369 120.50 - 127.23: 1134 127.23 - 133.96: 31 Bond angle restraints: 7889 Sorted by residual: angle pdb=" C VAL A 137 " pdb=" N SER A 138 " pdb=" CA SER A 138 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C ILE A 172 " pdb=" N LYS A 173 " pdb=" CA LYS A 173 " ideal model delta sigma weight residual 121.70 115.74 5.96 1.80e+00 3.09e-01 1.09e+01 angle pdb=" CA GLU B 75 " pdb=" C GLU B 75 " pdb=" N PRO B 76 " ideal model delta sigma weight residual 116.90 121.27 -4.37 1.50e+00 4.44e-01 8.50e+00 angle pdb=" CA SER A 138 " pdb=" C SER A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 116.90 120.20 -3.30 1.50e+00 4.44e-01 4.85e+00 angle pdb=" CA SER B 138 " pdb=" C SER B 138 " pdb=" N PRO B 139 " ideal model delta sigma weight residual 116.90 120.12 -3.22 1.50e+00 4.44e-01 4.60e+00 ... (remaining 7884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 1877 15.60 - 31.21: 112 31.21 - 46.81: 46 46.81 - 62.42: 16 62.42 - 78.02: 4 Dihedral angle restraints: 2055 sinusoidal: 1106 harmonic: 949 Sorted by residual: dihedral pdb=" CA LYS A 79 " pdb=" C LYS A 79 " pdb=" N GLU A 80 " pdb=" CA GLU A 80 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" N ASN B 170 " pdb=" CA ASN B 170 " pdb=" CB ASN B 170 " pdb=" CG ASN B 170 " ideal model delta sinusoidal sigma weight residual -60.00 -112.35 52.35 3 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" N LYS B 61 " pdb=" CA LYS B 61 " pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sinusoidal sigma weight residual -60.00 -109.85 49.85 3 1.50e+01 4.44e-03 8.83e+00 ... (remaining 2052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 199 0.027 - 0.054: 66 0.054 - 0.081: 32 0.081 - 0.107: 13 0.107 - 0.134: 21 Chirality restraints: 331 Sorted by residual: chirality pdb=" CA ILE B 55 " pdb=" N ILE B 55 " pdb=" C ILE B 55 " pdb=" CB ILE B 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE A 55 " pdb=" N ILE A 55 " pdb=" C ILE A 55 " pdb=" CB ILE A 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL A 123 " pdb=" N VAL A 123 " pdb=" C VAL A 123 " pdb=" CB VAL A 123 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 328 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 81 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 82 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 81 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.31e-01 pdb=" N PRO B 82 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 75 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.92e-01 pdb=" N PRO B 76 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.012 5.00e-02 4.00e+02 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 358 2.16 - 2.77: 7982 2.77 - 3.38: 12827 3.38 - 3.99: 17463 3.99 - 4.60: 25799 Nonbonded interactions: 64429 Sorted by model distance: nonbonded pdb=" OD1 ASP A 41 " pdb=" HZ3 LYS A 151 " model vdw 1.556 1.800 nonbonded pdb=" OD1 ASN A 102 " pdb=" H GLU A 105 " model vdw 1.566 1.800 nonbonded pdb=" HH TYR A 88 " pdb=" OE1 GLU A 97 " model vdw 1.566 1.800 nonbonded pdb=" O MET B 84 " pdb=" H TYR B 88 " model vdw 1.571 1.800 nonbonded pdb=" OD1 ASP B 41 " pdb=" HZ3 LYS B 151 " model vdw 1.607 1.800 ... (remaining 64424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/ase/__init__.py:21: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(np.__version__) < '1.9': /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. other = LooseVersion(other) Number of scattering types: 5 Type Number sf(0) Gaussians S 10 15.96 2 O 405 7.97 2 N 349 6.97 2 C 1391 5.97 2 H 2138 1.00 3 sf(0) = scattering factor at diffraction angle 0. Setting QM defaults Setting QM method to HF Setting QM basis to 6-31g Trying rss 10 376.88574600219727 Trying rss 9 308.6005837917328 Trying rss 8 276.093065738678 Trying rss 7 235.56049394607544 Trying rss 6 193.14752054214478 Trying rss 5 151.64590859413147 Trying rss 4 127.5043113231659 Trying rss 3 121.43244814872742 Trying rss 2 90.88911962509155 Trying rss 1 87.43357253074646 STOP: /net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/qrefine/refine.py(128)