Starting qr.refine on Mon May 20 18:07:09 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1xgo.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/1xgo.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1xgo.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 None 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: 4719 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4719 Classifications: {'peptide': 295} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 280} Time building chain proxies: 0.58, per 1000 atoms: 0.12 Number of scatterers: 4719 At special positions: 0 Unit cell: (138.916, 138.916, 63.907, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 423 8.00 N 390 7.00 C 1490 6.00 H 2407 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: 0.96 Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Time building geometry restraints manager: 1.10 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: 2407 1.14 - 1.31: 392 1.31 - 1.47: 855 1.47 - 1.64: 1088 1.64 - 1.81: 18 Bond restraints: 4760 Sorted by residual: bond pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CG LYS A 14 " pdb=" CD LYS A 14 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CG LEU A 223 " pdb=" CD2 LEU A 223 " ideal model delta sigma weight residual 1.521 1.555 -0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" C VAL A 212 " pdb=" N PRO A 213 " ideal model delta sigma weight residual 1.341 1.357 -0.016 1.60e-02 3.91e+03 1.03e+00 bond pdb=" C MET A 244 " pdb=" N PRO A 245 " ideal model delta sigma weight residual 1.341 1.357 -0.016 1.60e-02 3.91e+03 1.01e+00 ... (remaining 4755 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.98: 80 105.98 - 112.96: 5839 112.96 - 119.95: 1245 119.95 - 126.93: 1503 126.93 - 133.92: 22 Bond angle restraints: 8689 Sorted by residual: angle pdb=" CA LEU A 223 " pdb=" CB LEU A 223 " pdb=" CG LEU A 223 " ideal model delta sigma weight residual 116.30 126.54 -10.24 3.50e+00 8.16e-02 8.55e+00 angle pdb=" C LYS A 22 " pdb=" N LEU A 23 " pdb=" CA LEU A 23 " ideal model delta sigma weight residual 121.70 126.52 -4.82 1.80e+00 3.09e-01 7.16e+00 angle pdb=" C ALA A 252 " pdb=" N LEU A 253 " pdb=" CA LEU A 253 " ideal model delta sigma weight residual 121.70 117.16 4.54 1.80e+00 3.09e-01 6.36e+00 angle pdb=" CA THR A 64 " pdb=" C THR A 64 " pdb=" N PRO A 65 " ideal model delta sigma weight residual 116.90 120.30 -3.40 1.50e+00 4.44e-01 5.15e+00 angle pdb=" CA LEU A 253 " pdb=" CB LEU A 253 " pdb=" CG LEU A 253 " ideal model delta sigma weight residual 116.30 124.16 -7.86 3.50e+00 8.16e-02 5.05e+00 ... (remaining 8684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 1828 16.45 - 32.89: 243 32.89 - 49.34: 88 49.34 - 65.79: 36 65.79 - 82.24: 3 Dihedral angle restraints: 2198 sinusoidal: 1234 harmonic: 964 Sorted by residual: dihedral pdb=" CA PHE A 90 " pdb=" C PHE A 90 " pdb=" N ILE A 91 " pdb=" CA ILE A 91 " ideal model delta harmonic sigma weight residual -180.00 -161.28 -18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LYS A 67 " pdb=" C LYS A 67 " pdb=" N GLY A 68 " pdb=" CA GLY A 68 " ideal model delta harmonic sigma weight residual -180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR A 63 " pdb=" C TYR A 63 " pdb=" N THR A 64 " pdb=" CA THR A 64 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 201 0.031 - 0.063: 92 0.063 - 0.094: 44 0.094 - 0.125: 23 0.125 - 0.156: 5 Chirality restraints: 365 Sorted by residual: chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA VAL A 290 " pdb=" N VAL A 290 " pdb=" C VAL A 290 " pdb=" CB VAL A 290 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA VAL A 126 " pdb=" N VAL A 126 " pdb=" C VAL A 126 " pdb=" CB VAL A 126 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 362 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 50 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO A 51 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 166 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 167 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 64 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 65 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.022 5.00e-02 4.00e+02 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 455 2.11 - 2.74: 8410 2.74 - 3.36: 14508 3.36 - 3.98: 20340 3.98 - 4.60: 29562 Nonbonded interactions: 73275 Sorted by model distance: nonbonded pdb=" HG1 THR A 97 " pdb=" O GLN A 278 " model vdw 1.492 1.800 nonbonded pdb=" HZ2 LYS A 269 " pdb=" O GLU A 270 " model vdw 1.499 1.800 nonbonded pdb=" H ALA A 60 " pdb=" O LEU A 268 " model vdw 1.532 1.800 nonbonded pdb=" O ASP A 93 " pdb=" HG1 THR A 282 " model vdw 1.532 1.800 nonbonded pdb=" O LYS A 47 " pdb=" H HIS A 86 " model vdw 1.624 1.800 ... (remaining 73270 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 423 7.97 2 N 390 6.97 2 C 1490 5.97 2 H 2407 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: 0.005 angle: 1.15 clash: 16.3 rota: 21.40 rama: f: 76.11 o: 5.80 Z: -5.87 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -789.812825 -877.125363 101 cycle 0: bond: 0.009 angle: 1.79 clash: 2.8 rota: 14.40 rama: f: 91.81 o: 2.05 Z: -3.50 cb: 0.73 shift start/prev: 0.299 0.299 LBFGS: function start/end, n_calls: -877.125363 -884.939163 102 cycle 1: bond: 0.009 angle: 1.73 clash: 1.3 rota: 12.76 rama: f: 92.15 o: 0.68 Z: -3.27 cb: 0.37 shift start/prev: 0.401 0.159 LBFGS: function start/end, n_calls: -884.939163 -889.089544 102 cycle 2: bond: 0.009 angle: 1.73 clash: 0.6 rota: 11.52 rama: f: 92.15 o: 0.68 Z: -2.73 cb: 0.37 shift start/prev: 0.484 0.133 calculator(opt), total_time (target_and_gradients) 49.199039936065674 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 1xgo_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 137.60 seconds wall clock time: 2 minutes 23.62 seconds (143.62 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)