Starting qr.refine on Mon May 20 18:20:44 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2a8z.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/2a8z.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2a8z.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 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 386": "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: 6280 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6280 Classifications: {'peptide': 404} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 388} Time building chain proxies: 0.77, per 1000 atoms: 0.12 Number of scatterers: 6280 At special positions: 0 Unit cell: (77.779, 77.779, 149.634, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 612 8.00 N 555 7.00 C 2066 6.00 H 3035 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 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: 1.31 Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Time building geometry restraints manager: 1.50 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: 3035 1.14 - 1.31: 539 1.31 - 1.48: 1463 1.48 - 1.64: 1316 1.64 - 1.81: 22 Bond restraints: 6375 Sorted by residual: bond pdb=" C ASN A 68 " pdb=" O ASN A 68 " ideal model delta sigma weight residual 1.231 1.251 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CB GLU A 363 " pdb=" CG GLU A 363 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.75e-01 bond pdb=" C GLY A 140 " pdb=" N PRO A 141 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.70e-01 bond pdb=" C GLN A 373 " pdb=" O GLN A 373 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.23e-01 bond pdb=" C ALA A 220 " pdb=" N ASP A 221 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 3.97e-01 ... (remaining 6370 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.60: 98 106.60 - 113.45: 6847 113.45 - 120.29: 2387 120.29 - 127.14: 2013 127.14 - 133.98: 44 Bond angle restraints: 11389 Sorted by residual: angle pdb=" C GLU A 279 " pdb=" CA GLU A 279 " pdb=" CB GLU A 279 " ideal model delta sigma weight residual 110.10 114.58 -4.48 1.90e+00 2.77e-01 5.56e+00 angle pdb=" CA TYR A 50 " pdb=" CB TYR A 50 " pdb=" CG TYR A 50 " ideal model delta sigma weight residual 113.90 117.83 -3.93 1.80e+00 3.09e-01 4.77e+00 angle pdb=" C TYR A 53 " pdb=" N THR A 54 " pdb=" CA THR A 54 " ideal model delta sigma weight residual 121.70 124.96 -3.26 1.80e+00 3.09e-01 3.27e+00 angle pdb=" CA TRP A 124 " pdb=" C TRP A 124 " pdb=" N LYS A 125 " ideal model delta sigma weight residual 116.20 119.81 -3.61 2.00e+00 2.50e-01 3.26e+00 angle pdb=" CA ASP A 200 " pdb=" C ASP A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 116.90 119.61 -2.71 1.50e+00 4.44e-01 3.26e+00 ... (remaining 11384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 2798 15.92 - 31.83: 184 31.83 - 47.75: 56 47.75 - 63.67: 30 63.67 - 79.59: 2 Dihedral angle restraints: 3070 sinusoidal: 1572 harmonic: 1498 Sorted by residual: dihedral pdb=" CA ARG A 190 " pdb=" C ARG A 190 " pdb=" N PHE A 191 " pdb=" CA PHE A 191 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA TRP A 249 " pdb=" C TRP A 249 " pdb=" N ASN A 250 " pdb=" CA ASN A 250 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA THR A 46 " pdb=" C THR A 46 " pdb=" N GLN A 47 " pdb=" CA GLN A 47 " ideal model delta harmonic sigma weight residual 180.00 164.09 15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 244 0.024 - 0.048: 136 0.048 - 0.072: 39 0.072 - 0.096: 16 0.096 - 0.121: 13 Chirality restraints: 448 Sorted by residual: chirality pdb=" CA ILE A 205 " pdb=" N ILE A 205 " pdb=" C ILE A 205 " pdb=" CB ILE A 205 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE A 188 " pdb=" N ILE A 188 " pdb=" C ILE A 188 " pdb=" CB ILE A 188 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA VAL A 9 " pdb=" N VAL A 9 " pdb=" C VAL A 9 " pdb=" CB VAL A 9 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 445 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 31 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C GLN A 31 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 31 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS A 32 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 348 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C ASN A 348 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN A 348 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA A 349 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 50 " 0.013 2.00e-02 2.50e+03 7.08e-03 1.50e+00 pdb=" CG TYR A 50 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 50 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 50 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR A 50 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 50 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 50 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 50 " 0.001 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 534 2.12 - 2.74: 10539 2.74 - 3.36: 19877 3.36 - 3.98: 27662 3.98 - 4.60: 40324 Nonbonded interactions: 98936 Sorted by model distance: nonbonded pdb=" O VAL A 216 " pdb=" HZ3 LYS A 222 " model vdw 1.498 1.800 nonbonded pdb=" OE2 GLU A 147 " pdb=" HH TYR A 209 " model vdw 1.545 1.800 nonbonded pdb=" H2 ALA A 1 " pdb=" O GLU A 23 " model vdw 1.570 1.800 nonbonded pdb=" OE1 GLU A 95 " pdb=" H GLU A 95 " model vdw 1.572 1.800 nonbonded pdb=" O GLY A 245 " pdb=" H TRP A 249 " model vdw 1.572 1.800 ... (remaining 98931 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 12 15.96 2 O 612 7.97 2 N 555 6.97 2 C 2066 5.97 2 H 3035 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: 0.92 clash: 2.7 rota: 1.50 rama: f: 94.53 o: 0.00 Z: -1.42 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -865.187236 -948.566414 101 cycle 0: bond: 0.009 angle: 1.43 clash: 0.5 rota: 0.30 rama: f: 97.76 o: 0.00 Z: -0.74 cb: 0.00 shift start/prev: 0.217 0.217 LBFGS: function start/end, n_calls: -948.566414 -952.700010 102 cycle 1: bond: 0.009 angle: 1.41 clash: 0.0 rota: 0.30 rama: f: 97.76 o: 0.00 Z: -0.65 cb: 0.00 shift start/prev: 0.270 0.096 LBFGS: function start/end, n_calls: -952.700010 -954.928875 102 cycle 2: bond: 0.009 angle: 1.43 clash: 0.0 rota: 0.30 rama: f: 97.51 o: 0.00 Z: -0.73 cb: 0.00 shift start/prev: 0.311 0.073 calculator(opt), total_time (target_and_gradients) 65.73221850395203 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 2a8z_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 200.69 seconds wall clock time: 3 minutes 27.99 seconds (207.99 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)