Starting qr.refine on Mon May 20 19:03:38 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2jcl.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/2jcl.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2jcl.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 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1276": "OD1" <-> "OD2" Residue "B TYR 2113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2277": "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: 9180 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4576 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 262} Chain: "B" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4579 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Unusual residues: {'SO4': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.11, per 1000 atoms: 0.12 Number of scatterers: 9180 At special positions: 0 Unit cell: (95.93, 103.26, 121.49, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 832 8.00 N 756 7.00 C 3022 6.00 H 4541 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: 1052 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: 4535 1.14 - 1.31: 742 1.31 - 1.48: 1982 1.48 - 1.64: 2018 1.64 - 1.81: 42 Bond restraints: 9319 Sorted by residual: bond pdb=" C ALA B2253 " pdb=" N ASP B2254 " ideal model delta sigma weight residual 1.329 1.367 -0.038 1.40e-02 5.10e+03 7.47e+00 bond pdb=" CA PHE B2234 " pdb=" CB PHE B2234 " ideal model delta sigma weight residual 1.530 1.560 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C GLU A1192 " pdb=" N LYS A1193 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.74e+00 bond pdb=" N LYS A1193 " pdb=" CA LYS A1193 " ideal model delta sigma weight residual 1.458 1.474 -0.016 1.90e-02 2.77e+03 7.27e-01 bond pdb=" CA PHE A1234 " pdb=" CB PHE A1234 " ideal model delta sigma weight residual 1.530 1.546 -0.016 2.00e-02 2.50e+03 6.76e-01 ... (remaining 9314 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.35: 174 106.35 - 113.27: 10674 113.27 - 120.19: 3077 120.19 - 127.11: 2829 127.11 - 134.03: 88 Bond angle restraints: 16842 Sorted by residual: angle pdb=" C GLU A1192 " pdb=" N LYS A1193 " pdb=" CA LYS A1193 " ideal model delta sigma weight residual 121.70 132.31 -10.61 1.80e+00 3.09e-01 3.47e+01 angle pdb=" CA GLU A1192 " pdb=" C GLU A1192 " pdb=" N LYS A1193 " ideal model delta sigma weight residual 116.20 124.69 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" C GLU A1192 " pdb=" CA GLU A1192 " pdb=" CB GLU A1192 " ideal model delta sigma weight residual 110.10 117.38 -7.28 1.90e+00 2.77e-01 1.47e+01 angle pdb=" O GLU A1192 " pdb=" C GLU A1192 " pdb=" N LYS A1193 " ideal model delta sigma weight residual 123.00 118.69 4.31 1.60e+00 3.91e-01 7.25e+00 angle pdb=" C HIS A1315 " pdb=" CA HIS A1315 " pdb=" CB HIS A1315 " ideal model delta sigma weight residual 110.10 114.85 -4.75 1.90e+00 2.77e-01 6.26e+00 ... (remaining 16837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3966 17.70 - 35.39: 292 35.39 - 53.09: 95 53.09 - 70.79: 28 70.79 - 88.48: 2 Dihedral angle restraints: 4383 sinusoidal: 2288 harmonic: 2095 Sorted by residual: dihedral pdb=" CA GLN A1196 " pdb=" C GLN A1196 " pdb=" N ASP A1197 " pdb=" CA ASP A1197 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ILE B2283 " pdb=" C ILE B2283 " pdb=" N PHE B2284 " pdb=" CA PHE B2284 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PHE B2234 " pdb=" C PHE B2234 " pdb=" N GLY B2235 " pdb=" CA GLY B2235 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 373 0.030 - 0.059: 197 0.059 - 0.089: 52 0.089 - 0.119: 41 0.119 - 0.148: 9 Chirality restraints: 672 Sorted by residual: chirality pdb=" CA PHE B2234 " pdb=" N PHE B2234 " pdb=" C PHE B2234 " pdb=" CB PHE B2234 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE B2283 " pdb=" N ILE B2283 " pdb=" C ILE B2283 " pdb=" CB ILE B2283 " 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 VAL A1107 " pdb=" N VAL A1107 " pdb=" C VAL A1107 " pdb=" CB VAL A1107 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 669 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B2190 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B2191 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B2191 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B2191 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B2318 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C SER B2318 " -0.024 2.00e-02 2.50e+03 pdb=" O SER B2318 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS B2319 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1254 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A1255 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A1255 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1255 " 0.019 5.00e-02 4.00e+02 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 884 2.14 - 2.75: 16539 2.75 - 3.37: 28502 3.37 - 3.98: 39942 3.98 - 4.60: 57658 Nonbonded interactions: 143525 Sorted by model distance: nonbonded pdb=" OD1 ASN B2152 " pdb=" H GLY B2179 " model vdw 1.519 1.800 nonbonded pdb=" O ASP B2197 " pdb=" H MET B2200 " model vdw 1.532 1.800 nonbonded pdb=" O GLU B2145 " pdb=" H THR B2149 " model vdw 1.539 1.800 nonbonded pdb=" OD1 ASN A1152 " pdb=" H GLY A1179 " model vdw 1.540 1.800 nonbonded pdb=" O TYR B2323 " pdb=" H ASN B2327 " model vdw 1.549 1.800 ... (remaining 143520 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 29 15.96 2 O 832 7.97 2 N 756 6.97 2 C 3022 5.97 2 H 4541 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: 0.98 clash: 4.1 rota: 6.05 rama: f: 91.27 o: 1.09 Z: -2.78 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1320.416284 -1455.585250 104 cycle 0: bond: 0.019 angle: 1.79 clash: 2.5 rota: 5.85 rama: f: 92.18 o: 0.91 Z: -2.39 cb: 0.00 shift start/prev: 0.064 0.064 LBFGS: function start/end, n_calls: -1455.585250 -1473.447628 104 cycle 1: bond: 0.019 angle: 1.86 clash: 2.3 rota: 5.24 rama: f: 93.82 o: 0.91 Z: -1.62 cb: 0.00 shift start/prev: 0.107 0.055 LBFGS: function start/end, n_calls: -1473.447628 -1461.613123 151 cycle 2: bond: 0.019 angle: 1.93 clash: 2.4 rota: 5.04 rama: f: 93.82 o: 0.91 Z: -1.58 cb: 0.00 shift start/prev: 0.109 0.005 calculator(opt), total_time (target_and_gradients) 102.7404944896698 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 359 See 2jcl_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 352.53 seconds wall clock time: 6 minutes 1.49 seconds (361.49 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)