Starting qr.refine on Mon May 20 18:37:40 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1w60.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/1w60.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1w60.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 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 239": "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: 7874 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Time building chain proxies: 0.92, per 1000 atoms: 0.12 Number of scatterers: 7874 At special positions: 0 Unit cell: (82.892, 82.892, 70.859, 90, 90, 120) Space group: P 3 (No. 143) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 786 8.00 N 644 7.00 C 2466 6.00 H 3946 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: 1.47 Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Time building geometry restraints manager: 1.72 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: 3934 1.14 - 1.31: 712 1.31 - 1.48: 1450 1.48 - 1.64: 1778 1.64 - 1.81: 52 Bond restraints: 7926 Sorted by residual: bond pdb=" CB VAL B 70 " pdb=" CG2 VAL B 70 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" C ILE A 23 " pdb=" N ASN A 24 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 8.96e-01 bond pdb=" C LEU A 251 " pdb=" N ALA A 252 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.70e-01 bond pdb=" CB GLU A 192 " pdb=" CG GLU A 192 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.49e-01 bond pdb=" C MET B 229 " pdb=" N SER B 230 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.26e-01 ... (remaining 7921 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.93: 115 106.93 - 113.69: 9896 113.69 - 120.45: 2246 120.45 - 127.21: 2095 127.21 - 133.97: 22 Bond angle restraints: 14374 Sorted by residual: angle pdb=" CA THR A 219 " pdb=" C THR A 219 " pdb=" N PRO A 220 " ideal model delta sigma weight residual 116.90 121.57 -4.67 1.50e+00 4.44e-01 9.69e+00 angle pdb=" CA THR B 219 " pdb=" C THR B 219 " pdb=" N PRO B 220 " ideal model delta sigma weight residual 116.90 121.09 -4.19 1.50e+00 4.44e-01 7.82e+00 angle pdb=" CA SER B 230 " pdb=" C SER B 230 " pdb=" N ALA B 231 " ideal model delta sigma weight residual 116.20 119.83 -3.63 2.00e+00 2.50e-01 3.30e+00 angle pdb=" C GLN A 38 " pdb=" N SER A 39 " pdb=" CA SER A 39 " ideal model delta sigma weight residual 121.70 118.51 3.19 1.80e+00 3.09e-01 3.15e+00 angle pdb=" CA ILE A 128 " pdb=" C ILE A 128 " pdb=" N PRO A 129 " ideal model delta sigma weight residual 116.90 119.52 -2.62 1.50e+00 4.44e-01 3.06e+00 ... (remaining 14369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 3330 16.45 - 32.89: 241 32.89 - 49.34: 86 49.34 - 65.79: 49 65.79 - 82.23: 6 Dihedral angle restraints: 3712 sinusoidal: 2056 harmonic: 1656 Sorted by residual: dihedral pdb=" CG ARG B 91 " pdb=" CD ARG B 91 " pdb=" NE ARG B 91 " pdb=" CZ ARG B 91 " ideal model delta sinusoidal sigma weight residual -90.00 -132.05 42.05 2 1.50e+01 4.44e-03 9.57e+00 dihedral pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " pdb=" CG LYS B 80 " pdb=" CD LYS B 80 " ideal model delta sinusoidal sigma weight residual -60.00 -119.95 59.95 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS B 110 " pdb=" CB LYS B 110 " pdb=" CG LYS B 110 " pdb=" CD LYS B 110 " ideal model delta sinusoidal sigma weight residual -180.00 -120.39 -59.61 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 340 0.028 - 0.057: 190 0.057 - 0.085: 51 0.085 - 0.113: 25 0.113 - 0.141: 30 Chirality restraints: 636 Sorted by residual: chirality pdb=" CA ILE A 87 " pdb=" N ILE A 87 " pdb=" C ILE A 87 " pdb=" CB ILE A 87 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 180 " pdb=" N ILE B 180 " pdb=" C ILE B 180 " pdb=" CB ILE B 180 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE A 180 " pdb=" N ILE A 180 " pdb=" C ILE A 180 " pdb=" CB ILE A 180 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 633 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 252 " 0.016 5.00e-02 4.00e+02 2.44e-02 9.56e-01 pdb=" N PRO B 253 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 233 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.14e-01 pdb=" N PRO B 234 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 252 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.05e-01 pdb=" N PRO A 253 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.013 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 567 2.13 - 2.75: 13601 2.75 - 3.37: 22095 3.37 - 3.98: 31236 3.98 - 4.60: 45844 Nonbonded interactions: 113343 Sorted by model distance: nonbonded pdb=" H ARG A 53 " pdb=" O MET A 244 " model vdw 1.514 1.800 nonbonded pdb="HE22 GLN A 49 " pdb=" OG1 THR A 51 " model vdw 1.516 1.800 nonbonded pdb=" H ARG B 53 " pdb=" O MET B 244 " model vdw 1.519 1.800 nonbonded pdb=" O CYS B 148 " pdb=" HG SER B 152 " model vdw 1.579 1.800 nonbonded pdb=" HZ2 LYS A 190 " pdb=" OE1 GLU A 192 " model vdw 1.614 1.800 ... (remaining 113338 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 32 15.96 2 O 786 7.97 2 N 644 6.97 2 C 2466 5.97 2 H 3946 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: 0.95 clash: 2.2 rota: 10.09 rama: f: 90.91 o: 1.78 Z: -2.81 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1324.543115 -1431.853096 101 cycle 0: bond: 0.009 angle: 1.63 clash: 0.4 rota: 4.04 rama: f: 94.66 o: 0.79 Z: -2.33 cb: 0.21 shift start/prev: 0.237 0.237 LBFGS: function start/end, n_calls: -1431.853096 -1441.487774 102 cycle 1: bond: 0.009 angle: 1.62 clash: 0.4 rota: 3.59 rama: f: 95.65 o: 0.59 Z: -2.04 cb: 0.21 shift start/prev: 0.326 0.139 LBFGS: function start/end, n_calls: -1441.487774 -1446.226293 102 cycle 2: bond: 0.009 angle: 1.63 clash: 0.4 rota: 2.47 rama: f: 96.25 o: 0.59 Z: -1.84 cb: 0.21 shift start/prev: 0.388 0.103 calculator(opt), total_time (target_and_gradients) 81.08070135116577 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 1w60_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 271.62 seconds wall clock time: 4 minutes 38.45 seconds (278.45 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)