Starting qr.refine on Mon May 20 18:58:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1jkt.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/1jkt.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1jkt.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 GLU 115": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ASP 250": "OD1" <-> "OD2" Residue "B PHE 251": "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: 8966 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4483 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4483 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Time building chain proxies: 1.01, per 1000 atoms: 0.11 Number of scatterers: 8966 At special positions: 0 Unit cell: (58.37, 58.37, 212.61, 90, 90, 90) Space group: P 41 (No. 76) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 850 8.00 N 744 7.00 C 2876 6.00 H 4488 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: 1.77 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 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: 0.97 - 1.14: 4486 1.14 - 1.31: 774 1.31 - 1.48: 1766 1.48 - 1.65: 2018 1.65 - 1.82: 14 Bond restraints: 9058 Sorted by residual: bond pdb=" CA PHE A 4 " pdb=" C PHE A 4 " ideal model delta sigma weight residual 1.525 1.496 0.029 2.10e-02 2.27e+03 1.84e+00 bond pdb=" CB PHE A 43 " pdb=" CG PHE A 43 " ideal model delta sigma weight residual 1.502 1.533 -0.031 2.30e-02 1.89e+03 1.80e+00 bond pdb=" C GLY B 179 " pdb=" N THR B 180 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.68e+00 bond pdb=" C GLN A 72 " pdb=" N HIS A 73 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.61e+00 bond pdb=" C HIS A 73 " pdb=" N PRO A 74 " ideal model delta sigma weight residual 1.341 1.360 -0.019 1.60e-02 3.91e+03 1.45e+00 ... (remaining 9053 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.54: 242 106.54 - 113.42: 10719 113.42 - 120.30: 2882 120.30 - 127.18: 2549 127.18 - 134.06: 36 Bond angle restraints: 16428 Sorted by residual: angle pdb=" CA ILE A 123 " pdb=" CB ILE A 123 " pdb=" CG1 ILE A 123 " ideal model delta sigma weight residual 110.40 116.11 -5.71 1.70e+00 3.46e-01 1.13e+01 angle pdb=" C PHE A 174 " pdb=" N LYS A 175 " pdb=" CA LYS A 175 " ideal model delta sigma weight residual 121.70 127.30 -5.60 1.80e+00 3.09e-01 9.67e+00 angle pdb=" CA THR B 180 " pdb=" C THR B 180 " pdb=" N PRO B 181 " ideal model delta sigma weight residual 116.90 121.27 -4.37 1.50e+00 4.44e-01 8.48e+00 angle pdb=" C GLY B 179 " pdb=" N THR B 180 " pdb=" CA THR B 180 " ideal model delta sigma weight residual 121.70 126.93 -5.23 1.80e+00 3.09e-01 8.43e+00 angle pdb=" C PHE A 4 " pdb=" CA PHE A 4 " pdb=" CB PHE A 4 " ideal model delta sigma weight residual 110.10 114.97 -4.87 1.90e+00 2.77e-01 6.56e+00 ... (remaining 16423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3578 17.77 - 35.55: 432 35.55 - 53.32: 147 53.32 - 71.10: 54 71.10 - 88.87: 15 Dihedral angle restraints: 4226 sinusoidal: 2310 harmonic: 1916 Sorted by residual: dihedral pdb=" CA PRO B 193 " pdb=" C PRO B 193 " pdb=" N LEU B 194 " pdb=" CA LEU B 194 " ideal model delta harmonic sigma weight residual -180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ILE A 177 " pdb=" C ILE A 177 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N LEU B 196 " pdb=" CA LEU B 196 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 4223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 409 0.038 - 0.076: 187 0.076 - 0.113: 68 0.113 - 0.151: 17 0.151 - 0.189: 5 Chirality restraints: 686 Sorted by residual: chirality pdb=" CB ILE A 177 " pdb=" CA ILE A 177 " pdb=" CG1 ILE A 177 " pdb=" CG2 ILE A 177 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CA LYS A 175 " pdb=" N LYS A 175 " pdb=" C LYS A 175 " pdb=" CB LYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 683 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 192 " 0.061 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO B 193 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 192 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO A 193 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 272 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO B 273 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " 0.027 5.00e-02 4.00e+02 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.98: 410 1.98 - 2.64: 11675 2.64 - 3.29: 27761 3.29 - 3.95: 36562 3.95 - 4.60: 54419 Nonbonded interactions: 130827 Sorted by model distance: nonbonded pdb=" O PHE A 24 " pdb=" H LYS A 45 " model vdw 1.330 1.800 nonbonded pdb=" OG SER B 52 " pdb=" H ARG B 53 " model vdw 1.378 1.800 nonbonded pdb=" O PHE A 174 " pdb=" H ASN A 176 " model vdw 1.410 1.800 nonbonded pdb=" O ILE B 209 " pdb=" H GLY B 213 " model vdw 1.424 1.800 nonbonded pdb=" O ASN B 8 " pdb=" H ASP B 11 " model vdw 1.439 1.800 ... (remaining 130822 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 8 15.96 2 O 850 7.97 2 N 744 6.97 2 C 2876 5.97 2 H 4488 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: 0.006 angle: 1.15 clash: 18.3 rota: 16.67 rama: f: 74.27 o: 6.93 Z: -6.28 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1377.160254 -1580.767154 102 cycle 0: bond: 0.009 angle: 1.71 clash: 1.6 rota: 7.11 rama: f: 90.69 o: 1.28 Z: -3.24 cb: 0.96 shift start/prev: 0.353 0.353 LBFGS: function start/end, n_calls: -1580.767154 -1598.552555 102 cycle 1: bond: 0.009 angle: 1.60 clash: 1.2 rota: 5.28 rama: f: 91.79 o: 1.28 Z: -2.91 cb: 1.15 shift start/prev: 0.469 0.190 LBFGS: function start/end, n_calls: -1598.552555 -1606.972948 102 cycle 2: bond: 0.009 angle: 1.60 clash: 0.9 rota: 4.47 rama: f: 91.79 o: 1.28 Z: -3.00 cb: 1.34 shift start/prev: 0.545 0.133 calculator(opt), total_time (target_and_gradients) 88.59173274040222 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 306 See 1jkt_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 325.35 seconds wall clock time: 5 minutes 32.68 seconds (332.68 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)