Starting qr.refine on Mon May 20 18:12:07 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1x24.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/1x24.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1x24.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 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 126": "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: 4962 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2481 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2481 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Time building chain proxies: 0.65, per 1000 atoms: 0.13 Number of scatterers: 4962 At special positions: 0 Unit cell: (146.891, 146.891, 146.891, 90, 90, 90) Space group: I 21 3 (No. 199) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 434 8.00 N 424 7.00 C 1580 6.00 H 2510 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 104 " 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: 0.96 Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2506 1.15 - 1.31: 402 1.31 - 1.48: 984 1.48 - 1.64: 1104 1.64 - 1.81: 20 Bond restraints: 5016 Sorted by residual: bond pdb=" C ALA A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.49e-01 bond pdb=" C ALA A 74 " pdb=" O ALA A 74 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 5.06e-01 bond pdb=" C ASN B 24 " pdb=" N PRO B 25 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.43e-01 bond pdb=" C TRP B 68 " pdb=" N PRO B 69 " ideal model delta sigma weight residual 1.341 1.331 0.010 1.60e-02 3.91e+03 4.21e-01 bond pdb=" C ALA B 74 " pdb=" O ALA B 74 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.19e-01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 149 107.23 - 113.91: 6054 113.91 - 120.60: 1635 120.60 - 127.28: 1246 127.28 - 133.96: 26 Bond angle restraints: 9110 Sorted by residual: angle pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 116.90 121.27 -4.37 1.50e+00 4.44e-01 8.50e+00 angle pdb=" C LYS A 15 " pdb=" CA LYS A 15 " pdb=" CB LYS A 15 " ideal model delta sigma weight residual 110.10 115.64 -5.54 1.90e+00 2.77e-01 8.49e+00 angle pdb=" C LYS B 15 " pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " ideal model delta sigma weight residual 110.10 115.55 -5.45 1.90e+00 2.77e-01 8.22e+00 angle pdb=" CA ALA B 111 " pdb=" C ALA B 111 " pdb=" N PRO B 112 " ideal model delta sigma weight residual 116.90 121.03 -4.13 1.50e+00 4.44e-01 7.58e+00 angle pdb=" CA ARG A 153 " pdb=" C ARG A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 116.90 119.63 -2.73 1.50e+00 4.44e-01 3.31e+00 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.68: 2018 11.68 - 23.35: 210 23.35 - 35.02: 74 35.02 - 46.70: 16 46.70 - 58.37: 24 Dihedral angle restraints: 2342 sinusoidal: 1294 harmonic: 1048 Sorted by residual: dihedral pdb=" CA ILE A 90 " pdb=" C ILE A 90 " pdb=" N LYS A 91 " pdb=" CA LYS A 91 " ideal model delta harmonic sigma weight residual 180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" N LEU B 85 " pdb=" CA LEU B 85 " pdb=" CB LEU B 85 " pdb=" CG LEU B 85 " ideal model delta sinusoidal sigma weight residual -60.00 -118.37 58.37 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU A 158 " pdb=" CA LEU A 158 " pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " ideal model delta sinusoidal sigma weight residual -60.00 -117.31 57.31 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 223 0.026 - 0.052: 90 0.052 - 0.078: 43 0.078 - 0.104: 12 0.104 - 0.130: 12 Chirality restraints: 380 Sorted by residual: chirality pdb=" CA ILE B 100 " pdb=" N ILE B 100 " pdb=" C ILE B 100 " pdb=" CB ILE B 100 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE A 100 " pdb=" N ILE A 100 " pdb=" C ILE A 100 " pdb=" CB ILE A 100 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 377 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 111 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 112 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 111 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 112 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 74 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.10e-01 pdb=" N PRO A 75 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.012 5.00e-02 4.00e+02 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 508 2.18 - 2.78: 9637 2.78 - 3.39: 14597 3.39 - 3.99: 20021 3.99 - 4.60: 29339 Nonbonded interactions: 74102 Sorted by model distance: nonbonded pdb=" OE2 GLU A 127 " pdb="HH22 ARG B 157 " model vdw 1.574 1.800 nonbonded pdb=" O PHE A 70 " pdb="HH12 ARG A 110 " model vdw 1.577 1.800 nonbonded pdb="HH22 ARG A 157 " pdb=" OE2 GLU B 127 " model vdw 1.591 1.800 nonbonded pdb=" HE ARG A 47 " pdb=" OD1 ASP A 67 " model vdw 1.602 1.800 nonbonded pdb=" HE ARG B 47 " pdb=" OD1 ASP B 67 " model vdw 1.632 1.800 ... (remaining 74097 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 14 15.96 2 O 434 7.97 2 N 424 6.97 2 C 1580 5.97 2 H 2510 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: 0.90 clash: 4.2 rota: 7.14 rama: f: 91.67 o: 2.33 Z: -1.80 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -799.122305 -862.570517 101 cycle 0: bond: 0.009 angle: 1.52 clash: 0.2 rota: 5.26 rama: f: 94.67 o: 1.00 Z: -2.26 cb: 0.35 shift start/prev: 0.200 0.200 LBFGS: function start/end, n_calls: -862.570517 -867.091624 102 cycle 1: bond: 0.009 angle: 1.52 clash: 0.2 rota: 4.51 rama: f: 93.33 o: 1.00 Z: -2.33 cb: 0.00 shift start/prev: 0.278 0.123 LBFGS: function start/end, n_calls: -867.091624 -869.183374 102 cycle 2: bond: 0.009 angle: 1.53 clash: 0.2 rota: 3.76 rama: f: 93.67 o: 1.00 Z: -2.44 cb: 0.00 shift start/prev: 0.313 0.067 calculator(opt), total_time (target_and_gradients) 51.975738286972046 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 1x24_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 151.20 seconds wall clock time: 2 minutes 36.67 seconds (156.67 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)