Starting qr.refine on Mon May 20 18:52:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1wl3.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/1wl3.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1wl3.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 Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 288": "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: 8905 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4443 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 270} Chain: "B" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4462 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 271} Time building chain proxies: 1.03, per 1000 atoms: 0.12 Number of scatterers: 8905 At special positions: 0 Unit cell: (149.548, 149.548, 68.031, 90, 90, 90) Space group: P 4 21 2 (No. 90) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 823 8.00 N 729 7.00 C 2831 6.00 H 4498 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: 1.78 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Time building geometry restraints manager: 2.06 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: 4496 1.14 - 1.31: 769 1.31 - 1.48: 1658 1.48 - 1.64: 2005 1.64 - 1.81: 46 Bond restraints: 8974 Sorted by residual: bond pdb=" C LYS B 238 " pdb=" N PHE B 239 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 9.49e-01 bond pdb=" N PRO B 178 " pdb=" CA PRO B 178 " ideal model delta sigma weight residual 1.466 1.478 -0.012 1.50e-02 4.44e+03 6.00e-01 bond pdb=" C GLN B 26 " pdb=" N PHE B 27 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 5.79e-01 bond pdb=" C PHE A 230 " pdb=" O PHE A 230 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.72e-01 bond pdb=" N PRO B 37 " pdb=" CA PRO B 37 " ideal model delta sigma weight residual 1.466 1.477 -0.011 1.50e-02 4.44e+03 5.46e-01 ... (remaining 8969 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.06: 130 107.06 - 113.82: 10884 113.82 - 120.58: 3191 120.58 - 127.33: 2063 127.33 - 134.09: 26 Bond angle restraints: 16294 Sorted by residual: angle pdb=" C PHE B 27 " pdb=" N PHE B 28 " pdb=" CA PHE B 28 " ideal model delta sigma weight residual 121.70 116.07 5.63 1.80e+00 3.09e-01 9.79e+00 angle pdb=" CA PHE A 230 " pdb=" C PHE A 230 " pdb=" N PRO A 231 " ideal model delta sigma weight residual 116.90 121.42 -4.52 1.50e+00 4.44e-01 9.10e+00 angle pdb=" CA LEU B 177 " pdb=" C LEU B 177 " pdb=" N PRO B 178 " ideal model delta sigma weight residual 116.90 121.39 -4.49 1.50e+00 4.44e-01 8.95e+00 angle pdb=" CA PHE B 230 " pdb=" C PHE B 230 " pdb=" N PRO B 231 " ideal model delta sigma weight residual 116.90 121.32 -4.42 1.50e+00 4.44e-01 8.69e+00 angle pdb=" CA LEU A 177 " pdb=" C LEU A 177 " pdb=" N PRO A 178 " ideal model delta sigma weight residual 116.90 121.10 -4.20 1.50e+00 4.44e-01 7.85e+00 ... (remaining 16289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 3732 14.34 - 28.69: 254 28.69 - 43.03: 71 43.03 - 57.37: 57 57.37 - 71.71: 18 Dihedral angle restraints: 4132 sinusoidal: 2289 harmonic: 1843 Sorted by residual: dihedral pdb=" N ASP A 204 " pdb=" CA ASP A 204 " pdb=" CB ASP A 204 " pdb=" CG ASP A 204 " ideal model delta sinusoidal sigma weight residual -180.00 -120.40 -59.60 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB ARG B 46 " pdb=" CG ARG B 46 " pdb=" CD ARG B 46 " pdb=" NE ARG B 46 " ideal model delta sinusoidal sigma weight residual 60.00 118.55 -58.55 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLU A 184 " pdb=" CA GLU A 184 " pdb=" CB GLU A 184 " pdb=" CG GLU A 184 " ideal model delta sinusoidal sigma weight residual -60.00 -118.12 58.12 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 443 0.023 - 0.046: 132 0.046 - 0.069: 52 0.069 - 0.092: 36 0.092 - 0.115: 10 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA PHE B 27 " pdb=" N PHE B 27 " pdb=" C PHE B 27 " pdb=" CB PHE B 27 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.19e-01 chirality pdb=" CA ILE A 59 " pdb=" N ILE A 59 " pdb=" C ILE A 59 " pdb=" CB ILE A 59 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 670 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 28 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 29 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 28 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO B 29 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 29 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 29 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 79 " 0.005 2.00e-02 2.50e+03 9.42e-03 8.88e-01 pdb=" C LEU A 79 " -0.016 2.00e-02 2.50e+03 pdb=" O LEU A 79 " 0.006 2.00e-02 2.50e+03 pdb=" N HIS A 80 " 0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 492 2.05 - 2.69: 12754 2.69 - 3.32: 28743 3.32 - 3.96: 36367 3.96 - 4.60: 54353 Nonbonded interactions: 132709 Sorted by model distance: nonbonded pdb=" O LEU B 24 " pdb=" H PHE B 28 " model vdw 1.411 1.800 nonbonded pdb=" O LEU A 24 " pdb=" H PHE A 28 " model vdw 1.498 1.800 nonbonded pdb=" OD1 ASP A 82 " pdb="HH21 ARG A 90 " model vdw 1.522 1.800 nonbonded pdb=" OE1 GLU B 157 " pdb=" H GLU B 157 " model vdw 1.549 1.800 nonbonded pdb=" H GLY B 216 " pdb=" O PHE B 220 " model vdw 1.595 1.800 ... (remaining 132704 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 24 15.96 2 O 823 7.97 2 N 729 6.97 2 C 2831 5.97 2 H 4498 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: 0.87 clash: 2.0 rota: 1.49 rama: f: 94.74 o: 0.91 Z: 0.76 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1579.430179 -1682.317015 101 cycle 0: bond: 0.008 angle: 1.34 clash: 0.1 rota: 1.06 rama: f: 97.10 o: 0.36 Z: -0.63 cb: 0.00 shift start/prev: 0.197 0.197 LBFGS: function start/end, n_calls: -1682.317015 -1689.773136 102 cycle 1: bond: 0.008 angle: 1.30 clash: 0.0 rota: 0.64 rama: f: 97.10 o: 0.36 Z: -0.64 cb: 0.00 shift start/prev: 0.270 0.117 LBFGS: function start/end, n_calls: -1689.773136 -1693.310970 102 cycle 2: bond: 0.008 angle: 1.33 clash: 0.0 rota: 0.64 rama: f: 97.28 o: 0.18 Z: -0.83 cb: 0.00 shift start/prev: 0.320 0.084 calculator(opt), total_time (target_and_gradients) 84.60902571678162 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 1wl3_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 318.07 seconds wall clock time: 5 minutes 25.06 seconds (325.06 seconds total) /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)