Starting qr.refine on Mon May 20 19:09:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/4yei.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/4yei.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/4yei.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 TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 225": "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: 9333 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "B" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "C" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Time building chain proxies: 1.15, per 1000 atoms: 0.12 Number of scatterers: 9333 At special positions: 0 Unit cell: (110.36, 115.96, 164.12, 90, 90, 90) Space group: I 2 2 2 (No. 23) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 966 8.00 N 909 7.00 C 2865 6.00 H 4584 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: 1.76 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Time building geometry restraints manager: 2.03 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: 4581 1.14 - 1.31: 903 1.31 - 1.48: 1833 1.48 - 1.64: 2049 1.64 - 1.81: 15 Bond restraints: 9381 Sorted by residual: bond pdb=" C VAL A 223 " pdb=" N ALA A 224 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.78e-01 bond pdb=" C VAL C 205 " pdb=" N LEU C 206 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.77e-01 bond pdb=" C TYR B 30 " pdb=" N ALA B 31 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.63e-01 bond pdb=" CA THR C 188 " pdb=" CB THR C 188 " ideal model delta sigma weight residual 1.540 1.526 0.014 2.70e-02 1.37e+03 2.58e-01 bond pdb=" C ALA A 227 " pdb=" N ALA A 228 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.47e-01 ... (remaining 9376 not shown) Histogram of bond angle deviations from ideal: 101.04 - 107.63: 572 107.63 - 114.22: 10933 114.22 - 120.81: 2564 120.81 - 127.40: 2737 127.40 - 133.98: 39 Bond angle restraints: 16845 Sorted by residual: angle pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N ALA A 234 " ideal model delta sigma weight residual 116.20 119.85 -3.65 2.00e+00 2.50e-01 3.34e+00 angle pdb=" C GLU C 98 " pdb=" N ALA C 99 " pdb=" CA ALA C 99 " ideal model delta sigma weight residual 121.70 124.85 -3.15 1.80e+00 3.09e-01 3.06e+00 angle pdb=" C GLN B 43 " pdb=" N GLU B 44 " pdb=" CA GLU B 44 " ideal model delta sigma weight residual 121.70 124.82 -3.12 1.80e+00 3.09e-01 3.01e+00 angle pdb=" C ASP B 193 " pdb=" N ASP B 194 " pdb=" CA ASP B 194 " ideal model delta sigma weight residual 121.70 124.78 -3.08 1.80e+00 3.09e-01 2.94e+00 angle pdb=" C GLN A 118 " pdb=" N GLU A 119 " pdb=" CA GLU A 119 " ideal model delta sigma weight residual 121.70 124.73 -3.03 1.80e+00 3.09e-01 2.83e+00 ... (remaining 16840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.12: 4080 13.12 - 26.23: 174 26.23 - 39.35: 105 39.35 - 52.47: 22 52.47 - 65.58: 2 Dihedral angle restraints: 4383 sinusoidal: 2373 harmonic: 2010 Sorted by residual: dihedral pdb=" CA LEU A 117 " pdb=" CB LEU A 117 " pdb=" CG LEU A 117 " pdb=" CD1 LEU A 117 " ideal model delta sinusoidal sigma weight residual 180.00 130.99 49.01 3 1.50e+01 4.44e-03 8.72e+00 dihedral pdb=" CA LEU B 117 " pdb=" CB LEU B 117 " pdb=" CG LEU B 117 " pdb=" CD1 LEU B 117 " ideal model delta sinusoidal sigma weight residual 180.00 132.41 47.59 3 1.50e+01 4.44e-03 8.52e+00 dihedral pdb=" CA LEU C 117 " pdb=" CB LEU C 117 " pdb=" CG LEU C 117 " pdb=" CD1 LEU C 117 " ideal model delta sinusoidal sigma weight residual 180.00 134.27 45.73 3 1.50e+01 4.44e-03 8.22e+00 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 303 0.022 - 0.044: 336 0.044 - 0.065: 92 0.065 - 0.087: 19 0.087 - 0.109: 15 Chirality restraints: 765 Sorted by residual: chirality pdb=" CA VAL C 151 " pdb=" N VAL C 151 " pdb=" C VAL C 151 " pdb=" CB VAL C 151 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.97e-01 chirality pdb=" CA VAL A 151 " pdb=" N VAL A 151 " pdb=" C VAL A 151 " pdb=" CB VAL A 151 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.82e-01 chirality pdb=" CA VAL A 213 " pdb=" N VAL A 213 " pdb=" C VAL A 213 " pdb=" CB VAL A 213 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.77e-01 ... (remaining 762 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 203 " 0.012 5.00e-02 4.00e+02 1.80e-02 5.18e-01 pdb=" N PRO C 204 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO C 204 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 204 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 225 " -0.007 2.00e-02 2.50e+03 3.65e-03 3.99e-01 pdb=" CG PHE B 225 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 225 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 225 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 225 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 225 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 225 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 225 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE B 225 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE B 225 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE B 225 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 225 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 225 " 0.006 2.00e-02 2.50e+03 3.37e-03 3.40e-01 pdb=" CG PHE C 225 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE C 225 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 225 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 225 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE C 225 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE C 225 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE C 225 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE C 225 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE C 225 " 0.000 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 614 2.11 - 2.73: 15451 2.73 - 3.35: 28528 3.35 - 3.98: 39979 3.98 - 4.60: 56738 Nonbonded interactions: 141310 Sorted by model distance: nonbonded pdb=" OD1 ASN C 161 " pdb="HD22 ASN C 163 " model vdw 1.486 1.800 nonbonded pdb=" OD1 ASN B 161 " pdb="HD22 ASN B 163 " model vdw 1.503 1.800 nonbonded pdb=" OE1 GLN C 38 " pdb=" HD1 HIS C 39 " model vdw 1.505 1.800 nonbonded pdb=" OD1 ASN A 161 " pdb="HD22 ASN A 163 " model vdw 1.506 1.800 nonbonded pdb=" OE1 GLN A 38 " pdb=" HD1 HIS A 39 " model vdw 1.517 1.800 ... (remaining 141305 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 9 15.96 2 O 966 7.97 2 N 909 6.97 2 C 2865 5.97 2 H 4584 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: 0.003 angle: 0.82 clash: 0.6 rota: 0.00 rama: f: 99.22 o: 0.00 Z: -2.28 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1694.709239 -1806.101750 102 cycle 0: bond: 0.009 angle: 1.53 clash: 0.0 rota: 0.00 rama: f: 99.84 o: 0.00 Z: -1.74 cb: 0.00 shift start/prev: 0.179 0.179 LBFGS: function start/end, n_calls: -1806.101750 -1811.575847 102 cycle 1: bond: 0.009 angle: 1.52 clash: 0.0 rota: 0.00 rama: f: 99.22 o: 0.00 Z: -1.64 cb: 0.00 shift start/prev: 0.233 0.088 LBFGS: function start/end, n_calls: -1811.575847 -1813.975080 102 cycle 2: bond: 0.009 angle: 1.53 clash: 0.0 rota: 0.00 rama: f: 99.22 o: 0.00 Z: -1.67 cb: 0.00 shift start/prev: 0.270 0.061 calculator(opt), total_time (target_and_gradients) 88.51191234588623 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 306 See 4yei_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 341.57 seconds wall clock time: 5 minutes 49.00 seconds (349.00 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)