Starting qr.refine on Mon May 20 17:55:43 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1yab.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=opt restraints=qm engine=aimnet2 clustering=false minimizer=lbfgs gradient_only=true use_reduce=False select_within_radius=7 number_of_micro_cycles=3 max_iterations_refine=100 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1yab.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1yab.pdb" } use_reduce = False cluster { clustering = false select_within_radius = 7 } quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { mode = *opt refine gtest number_of_micro_cycles = 3 max_iterations_refine = 100 gradient_only = true } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = False 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 = False 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 = 3 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_angle_rmsd = 1.7 stop_one_found_first_good_weight = True 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 None 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: 2831 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1401 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "B" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1430 Classifications: {'peptide': 87} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Time building chain proxies: 0.39, per 1000 atoms: 0.14 Number of scatterers: 2831 At special positions: 0 Unit cell: (100.173, 100.173, 87.853, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 257 8.00 N 229 7.00 C 865 6.00 H 1476 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: 0.56 Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Time building geometry restraints manager: 0.65 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: 1476 1.14 - 1.31: 241 1.31 - 1.47: 433 1.47 - 1.64: 681 1.64 - 1.80: 8 Bond restraints: 2839 Sorted by residual: bond pdb=" C ILE A 123 " pdb=" O ILE A 123 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.27e-01 bond pdb=" C ASN B 153 " pdb=" N GLU B 154 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.87e-01 bond pdb=" N GLU B 154 " pdb=" CA GLU B 154 " ideal model delta sigma weight residual 1.458 1.471 -0.013 1.90e-02 2.77e+03 4.45e-01 bond pdb=" C GLU A 112 " pdb=" N PRO A 113 " ideal model delta sigma weight residual 1.341 1.331 0.010 1.60e-02 3.91e+03 4.23e-01 bond pdb=" CB LYS B 70 " pdb=" CG LYS B 70 " ideal model delta sigma weight residual 1.520 1.538 -0.018 3.00e-02 1.11e+03 3.56e-01 ... (remaining 2834 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.29: 35 106.29 - 112.54: 3680 112.54 - 118.79: 581 118.79 - 125.04: 891 125.04 - 131.29: 34 Bond angle restraints: 5221 Sorted by residual: angle pdb=" C ASN B 153 " pdb=" N GLU B 154 " pdb=" CA GLU B 154 " ideal model delta sigma weight residual 121.70 127.43 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA ILE A 123 " pdb=" C ILE A 123 " pdb=" N ALA A 124 " ideal model delta sigma weight residual 116.20 120.93 -4.73 2.00e+00 2.50e-01 5.59e+00 angle pdb=" CA ASN B 153 " pdb=" C ASN B 153 " pdb=" N GLU B 154 " ideal model delta sigma weight residual 116.20 119.92 -3.72 2.00e+00 2.50e-01 3.45e+00 angle pdb=" C ILE B 123 " pdb=" N ALA B 124 " pdb=" CA ALA B 124 " ideal model delta sigma weight residual 121.70 118.41 3.29 1.80e+00 3.09e-01 3.35e+00 angle pdb=" O ILE A 123 " pdb=" C ILE A 123 " pdb=" N ALA A 124 " ideal model delta sigma weight residual 123.00 120.08 2.92 1.60e+00 3.91e-01 3.33e+00 ... (remaining 5216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1111 16.70 - 33.41: 105 33.41 - 50.11: 34 50.11 - 66.82: 17 66.82 - 83.52: 3 Dihedral angle restraints: 1270 sinusoidal: 764 harmonic: 506 Sorted by residual: dihedral pdb=" CA ASP B 107 " pdb=" C ASP B 107 " pdb=" N LYS B 108 " pdb=" CA LYS B 108 " ideal model delta harmonic sigma weight residual -180.00 -164.57 -15.43 0 5.00e+00 4.00e-02 9.52e+00 dihedral pdb=" CA GLU B 150 " pdb=" CB GLU B 150 " pdb=" CG GLU B 150 " pdb=" CD GLU B 150 " ideal model delta sinusoidal sigma weight residual 60.00 118.71 -58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB GLU A 84 " pdb=" CG GLU A 84 " pdb=" CD GLU A 84 " pdb=" OE1 GLU A 84 " ideal model delta sinusoidal sigma weight residual 0.00 -83.52 83.52 1 3.00e+01 1.11e-03 9.46e+00 ... (remaining 1267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 145 0.031 - 0.061: 54 0.061 - 0.092: 14 0.092 - 0.123: 19 0.123 - 0.153: 6 Chirality restraints: 238 Sorted by residual: chirality pdb=" CA ILE A 116 " pdb=" N ILE A 116 " pdb=" C ILE A 116 " pdb=" CB ILE A 116 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE B 116 " pdb=" N ILE B 116 " pdb=" C ILE B 116 " pdb=" CB ILE B 116 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA VAL B 83 " pdb=" N VAL B 83 " pdb=" C VAL B 83 " pdb=" CB VAL B 83 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 235 not shown) Planarity restraints: 394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 94 " -0.130 9.50e-02 1.11e+02 4.35e-02 2.09e+00 pdb=" NE ARG B 94 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 94 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 94 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 94 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG B 94 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 94 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 94 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 94 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 77 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 78 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 94 " -0.079 9.50e-02 1.11e+02 2.63e-02 7.65e-01 pdb=" NE ARG A 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 94 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 94 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 94 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG A 94 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 94 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 94 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 94 " -0.001 2.00e-02 2.50e+03 ... (remaining 391 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 235 2.13 - 2.74: 5213 2.74 - 3.36: 8264 3.36 - 3.98: 11492 3.98 - 4.60: 16701 Nonbonded interactions: 41905 Sorted by model distance: nonbonded pdb=" O VAL B 143 " pdb=" HE ARG B 148 " model vdw 1.508 1.800 nonbonded pdb=" OD1 ASP B 115 " pdb=" H ASP B 115 " model vdw 1.518 1.800 nonbonded pdb=" O VAL B 129 " pdb=" H GLY B 136 " model vdw 1.582 1.800 nonbonded pdb=" O SER B 144 " pdb=" H ARG B 148 " model vdw 1.641 1.800 nonbonded pdb=" O LEU B 152 " pdb="HD22 ASN B 153 " model vdw 1.653 1.800 ... (remaining 41900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 4 15.96 2 O 257 7.97 2 N 229 6.97 2 C 865 5.97 2 H 1476 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 start: bond: 0.004 angle: 0.97 clash: 4.2 rota: 15.82 rama: f: 88.10 o: 2.98 Z: -4.05 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -561.478467 -604.451324 102 cycle 0: bond: 0.008 angle: 1.74 clash: 0.0 rota: 10.76 rama: f: 94.64 o: 1.19 Z: -1.60 cb: 1.88 shift start/prev: 0.250 0.250 LBFGS: function start/end, n_calls: -604.451324 -608.535898 102 cycle 1: bond: 0.008 angle: 1.72 clash: 0.0 rota: 8.23 rama: f: 95.24 o: 0.60 Z: -1.59 cb: 2.50 shift start/prev: 0.353 0.159 LBFGS: function start/end, n_calls: -608.535898 -610.259654 102 cycle 2: bond: 0.008 angle: 1.71 clash: 0.0 rota: 5.06 rama: f: 96.43 o: 0.60 Z: -2.33 cb: 1.88 shift start/prev: 0.411 0.101 calculator(opt), total_time (target_and_gradients) 36.778817653656006 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 306 See 1yab_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 83.67 seconds wall clock time: 88.42 seconds /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)