Starting qr.refine on Sat Apr 6 12:19:52 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1u9o.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/1u9o.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1u9o.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 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 148": "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: 5976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain: "B" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Time building chain proxies: 0.72, per 1000 atoms: 0.12 Number of scatterers: 5976 At special positions: 0 Unit cell: (140.5, 140.5, 76.69, 90, 90, 120) Space group: R 3 :H (No. 146) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 586 8.00 N 520 7.00 C 1908 6.00 H 2954 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: 1.14 Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Time building geometry restraints manager: 1.33 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: 2954 1.14 - 1.31: 528 1.31 - 1.47: 1238 1.47 - 1.64: 1302 1.64 - 1.81: 16 Bond restraints: 6038 Sorted by residual: bond pdb=" C ALA A 161 " pdb=" N ALA A 162 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.26e+00 bond pdb=" CG2 ILE B 146 " pdb="HG22 ILE B 146 " ideal model delta sigma weight residual 1.090 1.073 0.017 2.00e-02 2.50e+03 7.59e-01 bond pdb=" CA THR A 89 " pdb=" C THR A 89 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.41e-01 bond pdb=" C TRP B 138 " pdb=" N SER B 139 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.29e-01 bond pdb=" C ALA A 31 " pdb=" N THR A 32 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.48e-01 ... (remaining 6033 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 126 107.08 - 113.81: 7045 113.81 - 120.54: 2120 120.54 - 127.27: 1561 127.27 - 134.00: 38 Bond angle restraints: 10890 Sorted by residual: angle pdb=" CA TYR B 62 " pdb=" C TYR B 62 " pdb=" N PHE B 63 " ideal model delta sigma weight residual 116.20 121.92 -5.72 2.00e+00 2.50e-01 8.18e+00 angle pdb=" CA ARG B 58 " pdb=" C ARG B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 116.90 121.07 -4.17 1.50e+00 4.44e-01 7.71e+00 angle pdb=" CA ARG A 58 " pdb=" C ARG A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 116.90 120.86 -3.96 1.50e+00 4.44e-01 6.96e+00 angle pdb=" CA THR A 89 " pdb=" C THR A 89 " pdb=" N LEU A 90 " ideal model delta sigma weight residual 116.20 120.64 -4.44 2.00e+00 2.50e-01 4.92e+00 angle pdb=" CA TYR B 62 " pdb=" C TYR B 62 " pdb=" O TYR B 62 " ideal model delta sigma weight residual 120.80 117.17 3.63 1.70e+00 3.46e-01 4.57e+00 ... (remaining 10885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 2610 14.80 - 29.60: 155 29.60 - 44.40: 56 44.40 - 59.20: 22 59.20 - 74.00: 3 Dihedral angle restraints: 2846 sinusoidal: 1524 harmonic: 1322 Sorted by residual: dihedral pdb=" CA ARG A 25 " pdb=" CB ARG A 25 " pdb=" CG ARG A 25 " pdb=" CD ARG A 25 " ideal model delta sinusoidal sigma weight residual 180.00 125.61 54.39 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ARG B 128 " pdb=" CB ARG B 128 " pdb=" CG ARG B 128 " pdb=" CD ARG B 128 " ideal model delta sinusoidal sigma weight residual -180.00 -139.02 -40.98 3 1.50e+01 4.44e-03 7.32e+00 dihedral pdb=" CA LEU B 87 " pdb=" CB LEU B 87 " pdb=" CG LEU B 87 " pdb=" CD1 LEU B 87 " ideal model delta sinusoidal sigma weight residual 180.00 141.82 38.18 3 1.50e+01 4.44e-03 6.71e+00 ... (remaining 2843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 353 0.029 - 0.059: 86 0.059 - 0.088: 35 0.088 - 0.117: 9 0.117 - 0.146: 1 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA VAL B 194 " pdb=" N VAL B 194 " pdb=" C VAL B 194 " pdb=" CB VAL B 194 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL A 194 " pdb=" N VAL A 194 " pdb=" C VAL A 194 " pdb=" CB VAL A 194 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.26e-01 chirality pdb=" CA ILE A 45 " pdb=" N ILE A 45 " pdb=" C ILE A 45 " pdb=" CB ILE A 45 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 481 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 120 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C VAL A 120 " 0.019 2.00e-02 2.50e+03 pdb=" O VAL A 120 " -0.007 2.00e-02 2.50e+03 pdb=" N THR A 121 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 93 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO B 94 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " -0.005 2.00e-02 2.50e+03 9.43e-03 8.90e-01 pdb=" C THR A 173 " 0.016 2.00e-02 2.50e+03 pdb=" O THR A 173 " -0.006 2.00e-02 2.50e+03 pdb=" N ALA A 174 " -0.005 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 348 2.01 - 2.66: 7373 2.66 - 3.31: 19336 3.31 - 3.95: 24181 3.95 - 4.60: 36365 Nonbonded interactions: 87603 Sorted by model distance: nonbonded pdb=" O ASP A 23 " pdb=" H LEU A 27 " model vdw 1.365 1.800 nonbonded pdb=" O HIS B 169 " pdb=" HG1 THR B 173 " model vdw 1.518 1.800 nonbonded pdb=" OE2 GLU A 34 " pdb=" HD1 HIS A 117 " model vdw 1.532 1.800 nonbonded pdb=" O GLU B 112 " pdb=" HG SER B 116 " model vdw 1.547 1.800 nonbonded pdb=" O ALA A 172 " pdb="HD22 ASN A 176 " model vdw 1.547 1.800 ... (remaining 87598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary----------