Starting qr.refine on Sat Apr 6 11:59:15 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1fb5.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- debug_rss=true expansion=true mode=opt restraints=qm engine=aimnet2 clustering=false minimizer=lbfgs gradient_only=true use_reduce=False select_within_radius=7 number_of_micro_cycles=100 max_iterations_refine=100 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1fb5.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1fb5.pdb" } debug_rss = true use_reduce = False cluster { clustering = false select_within_radius = 7 } expansion = true quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { mode = *opt refine gtest number_of_micro_cycles = 100 max_iterations_refine = 100 gradient_only = true } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = True 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 = True 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 = 100 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_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 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 271": "OE1" <-> "OE2" 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: 5100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5082 Classifications: {'peptide': 320} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Time building chain proxies: 0.68, per 1000 atoms: 0.13 Number of scatterers: 5100 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 476 8.00 N 427 7.00 C 1617 6.00 H 2569 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: 1.03 Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 544 1.04 - 1.23: 2057 1.23 - 1.42: 1017 1.42 - 1.62: 1513 1.62 - 1.81: 20 Bond restraints: 5151 Sorted by residual: bond pdb=" C HIS A 107 " pdb=" O HIS A 107 " ideal model delta sigma weight residual 1.231 1.247 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C GLU A 98 " pdb=" N THR A 99 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.24e-01 bond pdb=" C TYR A 345 " pdb=" N SER A 346 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.10e-01 bond pdb=" C GLY A 162 " pdb=" N LEU A 163 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.97e-01 bond pdb=" N PRO A 75 " pdb=" CA PRO A 75 " ideal model delta sigma weight residual 1.466 1.476 -0.010 1.50e-02 4.44e+03 4.75e-01 ... (remaining 5146 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 181 107.23 - 113.91: 6261 113.91 - 120.59: 1572 120.59 - 127.27: 1301 127.27 - 133.95: 29 Bond angle restraints: 9344 Sorted by residual: angle pdb=" C GLY A 162 " pdb=" N LEU A 163 " pdb=" CA LEU A 163 " ideal model delta sigma weight residual 121.70 126.26 -4.56 1.80e+00 3.09e-01 6.43e+00 angle pdb=" C LEU A 186 " pdb=" N LYS A 187 " pdb=" CA LYS A 187 " ideal model delta sigma weight residual 121.70 125.38 -3.68 1.80e+00 3.09e-01 4.18e+00 angle pdb=" C TYR A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta sigma weight residual 121.70 125.24 -3.54 1.80e+00 3.09e-01 3.86e+00 angle pdb=" CA ASP A 249 " pdb=" C ASP A 249 " pdb=" N PRO A 250 " ideal model delta sigma weight residual 116.90 119.83 -2.93 1.50e+00 4.44e-01 3.83e+00 angle pdb=" N ARG A 141 " pdb=" CA ARG A 141 " pdb=" C ARG A 141 " ideal model delta sigma weight residual 111.00 105.99 5.01 2.80e+00 1.28e-01 3.20e+00 ... (remaining 9339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.81: 2219 18.81 - 37.61: 146 37.61 - 56.42: 32 56.42 - 75.22: 11 75.22 - 94.03: 2 Dihedral angle restraints: 2410 sinusoidal: 1325 harmonic: 1085 Sorted by residual: dihedral pdb=" CG NVA A 900 " pdb=" CA NVA A 900 " pdb=" CB NVA A 900 " pdb=" HA NVA A 900 " ideal model delta sinusoidal sigma weight residual -62.82 31.21 -94.03 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CB GLU A 271 " pdb=" CG GLU A 271 " pdb=" CD GLU A 271 " pdb=" OE1 GLU A 271 " ideal model delta sinusoidal sigma weight residual 0.00 -84.62 84.62 1 3.00e+01 1.11e-03 9.67e+00 dihedral pdb=" CA GLU A 149 " pdb=" CB GLU A 149 " pdb=" CG GLU A 149 " pdb=" CD GLU A 149 " ideal model delta sinusoidal sigma weight residual 60.00 118.34 -58.34 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 255 0.028 - 0.056: 95 0.056 - 0.085: 33 0.085 - 0.113: 9 0.113 - 0.141: 5 Chirality restraints: 397 Sorted by residual: chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE A 261 " pdb=" N ILE A 261 " pdb=" C ILE A 261 " pdb=" CB ILE A 261 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE A 157 " pdb=" N ILE A 157 " pdb=" C ILE A 157 " pdb=" CB ILE A 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 394 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 304 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 305 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 107 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 108 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 324 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 325 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.018 5.00e-02 4.00e+02 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 375 2.11 - 2.73: 8805 2.73 - 3.35: 15748 3.35 - 3.98: 21478 3.98 - 4.60: 31867 Nonbonded interactions: 78273 Sorted by model distance: nonbonded pdb=" OG1 THR A 178 " pdb="HD22 ASN A 329 " model vdw 1.484 1.800 nonbonded pdb=" O ALA A 140 " pdb=" H GLY A 162 " model vdw 1.540 1.800 nonbonded pdb="HH22 ARG A 94 " pdb=" O PHE A 110 " model vdw sym.op. 1.566 1.800 y,z,x nonbonded pdb=" HG1 THR A 299 " pdb=" O ARG A 320 " model vdw 1.582 1.800 nonbonded pdb=" OE1 GLN A 114 " pdb=" H GLN A 114 " model vdw 1.606 1.800 ... (remaining 78268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary----------