Starting qr.refine on Sat Apr 6 08:38:23 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1u87.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/1u87.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1u87.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 ASP 39": "OD1" <-> "OD2" 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: 3506 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3471 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.50, per 1000 atoms: 0.14 Number of scatterers: 3506 At special positions: 0 Unit cell: (123.05, 123.05, 72.51, 90, 90, 120) Space group: P 63 2 2 (No. 182) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 316 8.00 N 282 7.00 C 1138 6.00 H 1756 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: 0.89 Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Time building geometry restraints manager: 1.01 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: 1751 1.14 - 1.31: 293 1.31 - 1.48: 702 1.48 - 1.64: 781 1.64 - 1.81: 23 Bond restraints: 3550 Sorted by residual: bond pdb=" CA1 GSH A 500 " pdb=" N1 GSH A 500 " ideal model delta sigma weight residual 1.472 1.438 0.034 2.00e-02 2.50e+03 2.86e+00 bond pdb=" CB1 GSH A 500 " pdb=" CA1 GSH A 500 " ideal model delta sigma weight residual 1.526 1.512 0.014 1.20e-02 6.94e+03 1.34e+00 bond pdb=" C LYS A 78 " pdb=" N HIS A 79 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.23e+00 bond pdb=" C1 GSH A 500 " pdb=" CA1 GSH A 500 " ideal model delta sigma weight residual 1.535 1.517 0.018 1.80e-02 3.09e+03 9.61e-01 bond pdb=" C TRP A 41 " pdb=" N ARG A 42 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 5.89e-01 ... (remaining 3545 not shown) Histogram of bond angle deviations from ideal: 92.54 - 100.97: 7 100.97 - 109.39: 2382 109.39 - 117.81: 2381 117.81 - 126.24: 1632 126.24 - 134.66: 42 Bond angle restraints: 6444 Sorted by residual: angle pdb=" C1 GSH A 500 " pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 124.92 92.54 32.38 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CB1 GSH A 500 " pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 124.92 93.17 31.75 3.00e+00 1.11e-01 1.12e+02 angle pdb=" CB1 GSH A 500 " pdb=" CA1 GSH A 500 " pdb=" C1 GSH A 500 " ideal model delta sigma weight residual 109.47 134.66 -25.19 3.00e+00 1.11e-01 7.05e+01 angle pdb=" N1 GSH A 500 " pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 124.92 106.32 18.60 3.00e+00 1.11e-01 3.84e+01 angle pdb=" N2 GSH A 500 " pdb=" CA2 GSH A 500 " pdb=" HA2 GSH A 500 " ideal model delta sigma weight residual 124.87 110.05 14.82 3.00e+00 1.11e-01 2.44e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.67: 1460 13.67 - 27.33: 142 27.33 - 41.00: 39 41.00 - 54.67: 24 54.67 - 68.33: 7 Dihedral angle restraints: 1672 sinusoidal: 918 harmonic: 754 Sorted by residual: dihedral pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N THR A 66 " pdb=" CA THR A 66 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP A 60 " pdb=" C ASP A 60 " pdb=" N GLY A 61 " pdb=" CA GLY A 61 " ideal model delta harmonic sigma weight residual 180.00 -164.46 -15.54 0 5.00e+00 4.00e-02 9.65e+00 dihedral pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " pdb=" CG LYS A 113 " ideal model delta sinusoidal sigma weight residual -60.00 -117.62 57.62 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.721: 254 0.721 - 1.441: 0 1.441 - 2.161: 0 2.161 - 2.882: 0 2.882 - 3.602: 1 Chirality restraints: 255 Sorted by residual: chirality pdb=" CA1 GSH A 500 " pdb=" CB1 GSH A 500 " pdb=" C1 GSH A 500 " pdb=" N1 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.66 0.95 -3.60 2.00e-01 2.50e+01 3.24e+02 chirality pdb=" CA2 GSH A 500 " pdb=" CB2 GSH A 500 " pdb=" C2 GSH A 500 " pdb=" N2 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 252 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 166 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO A 167 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 126 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 127 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 201 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 202 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " -0.016 5.00e-02 4.00e+02 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 289 2.15 - 2.76: 6310 2.76 - 3.37: 10169 3.37 - 3.99: 13700 3.99 - 4.60: 20430 Nonbonded interactions: 50898 Sorted by model distance: nonbonded pdb=" O ILE A 10 " pdb="HH12 ARG A 18 " model vdw 1.533 1.800 nonbonded pdb=" O ASP A 114 " pdb=" H LEU A 118 " model vdw 1.618 1.800 nonbonded pdb=" HZ3 LYS A 180 " pdb=" OE2 GLU A 184 " model vdw 1.622 1.800 nonbonded pdb=" O GLY A 205 " pdb=" H ALA A 208 " model vdw 1.643 1.800 nonbonded pdb=" HE ARG A 136 " pdb=" O LEU A 143 " model vdw 1.646 1.800 ... (remaining 50893 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 14 15.96 2 O 316 7.97 2 N 282 6.97 2 C 1138 5.97 2 H 1756 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 10 242.53992438316345 Trying rss 9 196.25725054740906 Trying rss 8 188.70154356956482 Trying rss 7 153.78658366203308 Trying rss 6 131.9504144191742 Trying rss 5 108.17731070518494 Trying rss 4 95.50847816467285 Trying rss 3 85.8723304271698 Trying rss 2 65.26337552070618 Trying rss 1 59.060691833496094 STOP: /net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/qrefine/refine.py(128)