Starting qr.refine on Sun May 19 23:49:52 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8fsj_29419.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8fsj_29419.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=refine restraints=qm engine=aimnet2 clustering=false minimizer=lbfgsb max_bond_rmsd=0.0001 gradient_only=false Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8fsj_29419.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8fsj_29419.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8fsj_29419.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8fsj_29419.map" } cluster { clustering = false } quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { max_bond_rmsd = 0.0001 minimizer = lbfgs *lbfgsb } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = False debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = True cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 10 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 = 50 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 50 max_iterations_refine = 50 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = False refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.0001 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 "E PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 18915 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4331 Classifications: {'peptide': 284} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 260} Chain: "H" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3307 Inner-chain residues flagged as termini: ['pdbres="SER H 127 "', 'pdbres="SER H 132 "'] Classifications: {'peptide': 225} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3244 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1225 Inner-chain residues flagged as termini: ['pdbres="THR A 255 "', 'pdbres="PRO A 295 "'] Classifications: {'peptide': 82} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain breaks: 1 Chain: "B" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3191 Inner-chain residues flagged as termini: ['pdbres="GLY B 128 "'] Classifications: {'peptide': 211} Modifications used: {'COO': 1, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain: "C" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3617 Classifications: {'peptide': 242} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Time building chain proxies: 2.09, per 1000 atoms: 0.11 Number of scatterers: 18915 At special positions: 0 Unit cell: (72.009, 139.573, 139.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 O 1884 8.00 N 1646 7.00 C 6044 6.00 H 9288 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 429 " - pdb=" SG CYS E 503 " distance=2.03 Simple disulfide: pdb=" SG CYS E 452 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS E 486 " distance=2.04 Simple disulfide: pdb=" SG CYS E 494 " - pdb=" SG CYS E 564 " distance=2.04 Simple disulfide: pdb=" SG CYS E 508 " - pdb=" SG CYS E 552 " distance=2.03 Simple disulfide: pdb=" SG CYS E 569 " - pdb=" SG CYS E 597 " distance=2.03 Simple disulfide: pdb=" SG CYS E 581 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 607 " - pdb=" SG CYS E 644 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 677 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 304 " distance=2.04 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.05 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: 3.38 Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.15: 9288 1.15 - 1.33: 1699 1.33 - 1.50: 4305 1.50 - 1.68: 3808 1.68 - 1.86: 64 Bond restraints: 19164 Sorted by residual: bond pdb=" CG TYR L 49 " pdb=" CD2 TYR L 49 " ideal model delta sigma weight residual 1.389 1.330 0.059 2.10e-02 2.27e+03 7.85e+00 bond pdb=" CG ARG B 141 " pdb=" CD ARG B 141 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.13e+00 bond pdb=" N GLY B 128 " pdb=" CA GLY B 128 " ideal model delta sigma weight residual 1.491 1.449 0.042 2.10e-02 2.27e+03 4.05e+00 bond pdb=" CD1 TYR L 49 " pdb=" HD1 TYR L 49 " ideal model delta sigma weight residual 1.080 1.045 0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" CA CYS C 140 " pdb=" CB CYS C 140 " ideal model delta sigma weight residual 1.530 1.563 -0.033 2.00e-02 2.50e+03 2.79e+00 ... (remaining 19159 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.16: 256 105.16 - 112.38: 21756 112.38 - 119.60: 4758 119.60 - 126.82: 7576 126.82 - 134.03: 190 Bond angle restraints: 34536 Sorted by residual: angle pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " pdb=" CG TYR H 99 " ideal model delta sigma weight residual 113.90 107.19 6.71 1.80e+00 3.09e-01 1.39e+01 angle pdb=" CA CYS E 452 " pdb=" C CYS E 452 " pdb=" N PRO E 453 " ideal model delta sigma weight residual 116.90 121.75 -4.85 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C ARG E 587 " pdb=" N LYS E 588 " pdb=" CA LYS E 588 " ideal model delta sigma weight residual 121.70 127.36 -5.66 1.80e+00 3.09e-01 9.88e+00 angle pdb=" N CYS C 140 " pdb=" CA CYS C 140 " pdb=" CB CYS C 140 " ideal model delta sigma weight residual 110.50 115.56 -5.06 1.70e+00 3.46e-01 8.85e+00 angle pdb=" C SER C 156 " pdb=" CA SER C 156 " pdb=" CB SER C 156 " ideal model delta sigma weight residual 110.10 115.46 -5.36 1.90e+00 2.77e-01 7.97e+00 ... (remaining 34531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 8380 18.40 - 36.81: 617 36.81 - 55.21: 225 55.21 - 73.61: 30 73.61 - 92.02: 11 Dihedral angle restraints: 9263 sinusoidal: 4989 harmonic: 4274 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -138.44 52.44 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS E 569 " pdb=" SG CYS E 569 " pdb=" SG CYS E 597 " pdb=" CB CYS E 597 " ideal model delta sinusoidal sigma weight residual 93.00 143.64 -50.64 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS E 452 " pdb=" SG CYS E 452 " pdb=" SG CYS E 620 " pdb=" CB CYS E 620 " ideal model delta sinusoidal sigma weight residual -86.00 -130.46 44.46 1 1.00e+01 1.00e-02 2.75e+01 ... (remaining 9260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 933 0.034 - 0.068: 381 0.068 - 0.102: 104 0.102 - 0.136: 71 0.136 - 0.170: 10 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CA VAL C 181 " pdb=" N VAL C 181 " pdb=" C VAL C 181 " pdb=" CB VAL C 181 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ILE C 50 " pdb=" N ILE C 50 " pdb=" C ILE C 50 " pdb=" CB ILE C 50 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA VAL H 11 " pdb=" N VAL H 11 " pdb=" C VAL H 11 " pdb=" CB VAL H 11 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1496 not shown) Planarity restraints: 2906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 99 " -0.022 2.00e-02 2.50e+03 1.60e-02 7.65e+00 pdb=" CG TYR H 99 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 99 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR H 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR H 99 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 99 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR H 99 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR H 99 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 TYR H 99 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR H 99 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TYR H 99 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 TYR H 99 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.028 2.00e-02 2.50e+03 1.53e-02 6.98e+00 pdb=" CG TYR L 49 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR L 49 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR L 49 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR L 49 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR L 49 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 99 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C TYR H 99 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR H 99 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS H 100 " 0.014 2.00e-02 2.50e+03 ... (remaining 2903 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1071 2.08 - 2.71: 28299 2.71 - 3.34: 51424 3.34 - 3.97: 69438 3.97 - 4.60: 101113 Nonbonded interactions: 251345 Sorted by model distance: nonbonded pdb=" O ALA A 251 " pdb=" HG1 THR A 255 " model vdw 1.452 1.800 nonbonded pdb=" O ASN E 540 " pdb="HD21 ASN E 548 " model vdw 1.455 1.800 nonbonded pdb=" O SER B 127 " pdb=" H1 GLY B 128 " model vdw 1.479 1.920 nonbonded pdb=" O ASP E 658 " pdb=" HG SER E 678 " model vdw 1.490 1.800 nonbonded pdb=" OD1 ASP L 170 " pdb=" HG1 THR L 172 " model vdw 1.507 1.800 ... (remaining 251340 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 53 15.96 2 O 1884 7.97 2 N 1646 6.97 2 C 6044 5.97 2 H 9288 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 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.004 0.061 9876 Z= 0.227 ANGLE : 1.058 6.709 13471 Z= 0.484 CHIRALITY : 0.045 0.170 1499 PLANARITY : 0.005 0.057 1739 DIHEDRAL : 12.887 92.017 3532 MIN NONBONDED DISTANCE : 1.990 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 8.09 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 8.70 % FAVORED : 91.30 % ROTAMER: OUTLIERS : 0.65 % ALLOWED : 2.21 % FAVORED : 97.14 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 11.11 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -1.83 (0.23), RESIDUES: 1241 HELIX: -3.01 (0.56), RESIDUES: 48 SHEET: -0.60 (0.25), RESIDUES: 444 LOOP : -1.50 (0.22), RESIDUES: 749 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.009 0.001 ARG B 77 TYR 0.039 0.002 TYR H 99 PHE 0.009 0.001 PHE E 509 TRP 0.016 0.001 TRP C 154 HIS 0.006 0.001 HIS C 95 Resolution of map is: 3.8552 Map-model correlation coefficient (CC) CC_mask : 0.7373 weight= None bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 Initial weight estimate from ratio of grad norms: 0.33682137459769934 cycle: 0 start: weight= 0.3368 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.3368 bond: 0.032 angle: 3.05 clash: 33.1 rota: 6.92 rama: f: 75.71 o: 5.33 Z: -5.25 cb: 7.19 shift=0.4785 cc_mask=0.8078 cycle: 1 start: weight= 0.1684 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.1684 bond: 0.026 angle: 2.26 clash: 13.0 rota: 2.58 rama: f: 84.18 o: 2.10 Z: -3.97 cb: 1.65 shift=0.3885 cc_mask=0.7901 cycle: 2 start: weight= 0.1179 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.1179 bond: 0.025 angle: 2.07 clash: 8.5 rota: 1.48 rama: f: 87.41 o: 0.89 Z: -3.39 cb: 0.78 shift=0.3467 cc_mask=0.7803 cycle: 3 start: weight= 0.0825 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.0825 bond: 0.024 angle: 1.91 clash: 5.1 rota: 1.38 rama: f: 90.07 o: 0.65 Z: -2.83 cb: 0.26 shift=0.2948 cc_mask=0.7703 cycle: 4 start: weight= 0.0413 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.0413 bond: 0.021 angle: 1.77 clash: 2.8 rota: 0.83 rama: f: 93.06 o: 0.32 Z: -1.98 cb: 0.26 shift=0.2350 cc_mask=0.7531 cycle: 5 start: weight= 0.0289 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.0289 bond: 0.021 angle: 1.77 clash: 2.0 rota: 0.92 rama: f: 93.70 o: 0.32 Z: -1.80 cb: 0.26 shift=0.2359 cc_mask=0.7466 cycle: 6 start: weight= 0.0202 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.0202 bond: 0.020 angle: 1.76 clash: 1.9 rota: 0.74 rama: f: 93.79 o: 0.16 Z: -1.67 cb: 0.26 shift=0.2219 cc_mask=0.7413 cycle: 7 start: weight= 0.0101 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.0101 bond: 0.020 angle: 1.76 clash: 1.3 rota: 0.83 rama: f: 94.27 o: 0.16 Z: -1.60 cb: 0.26 shift=0.2366 cc_mask=0.7334 cycle: 8 start: weight= 0.0071 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.0071 bond: 0.028 angle: 1.75 clash: 1.3 rota: 1.01 rama: f: 93.95 o: 0.16 Z: -1.58 cb: 0.26 shift=0.2433 cc_mask=0.7307 cycle: 9 start: weight= 0.0050 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.0050 bond: 0.020 angle: 1.76 clash: 1.2 rota: 0.92 rama: f: 93.95 o: 0.16 Z: -1.55 cb: 0.26 shift=0.2389 cc_mask=0.7291 cycle: 10 start: weight= 0.0025 bond: 0.004 angle: 1.06 clash: 8.1 rota: 0.65 rama: f: 91.30 o: 0.00 Z: -1.83 cb: 0.00 shift=0.0000 cc_mask=0.7373 final: weight= 0.0025 bond: 0.020 angle: 1.78 clash: 1.2 rota: 1.01 rama: f: 94.03 o: 0.16 Z: -1.54 cb: 0.26 shift=0.2454 cc_mask=0.7264 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.002476668618752796 start: weight= 0.0025 bond: 0.020 angle: 1.78 clash: 1.2 rota: 1.01 rama: f: 94.03 o: 0.16 Z: -1.54 cb: 0.26 shift=0.0000 cc_mask=0.7373 final: weight= 0.0025 bond: 0.021 angle: 1.79 clash: 1.1 rota: 1.11 rama: f: 94.03 o: 0.16 Z: -1.54 cb: 0.26 shift=0.2543 cc_mask=0.7258 start: weight= 0.0025 bond: 0.021 angle: 1.79 clash: 1.1 rota: 1.11 rama: f: 94.03 o: 0.16 Z: -1.54 cb: 0.26 shift=0.2543 cc_mask=0.7258 final: weight= 0.0025 bond: 0.020 angle: 1.76 clash: 0.8 rota: 1.20 rama: f: 94.67 o: 0.16 Z: -1.35 cb: 0.17 shift=0.3287 cc_mask=0.7213 start: weight= 0.0025 bond: 0.020 angle: 1.76 clash: 0.8 rota: 1.20 rama: f: 94.67 o: 0.16 Z: -1.35 cb: 0.17 shift=0.3287 cc_mask=0.7213 final: weight= 0.0025 bond: 0.021 angle: 1.79 clash: 0.7 rota: 1.11 rama: f: 94.75 o: 0.24 Z: -1.28 cb: 0.17 shift=0.4000 cc_mask=0.7161 start: weight= 0.0025 bond: 0.021 angle: 1.79 clash: 0.7 rota: 1.11 rama: f: 94.75 o: 0.24 Z: -1.28 cb: 0.17 shift=0.4000 cc_mask=0.7161 final: weight= 0.0025 bond: 0.021 angle: 1.77 clash: 0.5 rota: 1.01 rama: f: 94.59 o: 0.24 Z: -1.29 cb: 0.17 shift=0.4385 cc_mask=0.7134 start: weight= 0.0025 bond: 0.021 angle: 1.77 clash: 0.5 rota: 1.01 rama: f: 94.59 o: 0.24 Z: -1.29 cb: 0.17 shift=0.4385 cc_mask=0.7134 final: weight= 0.0025 bond: 0.021 angle: 1.79 clash: 0.5 rota: 0.92 rama: f: 94.59 o: 0.40 Z: -1.37 cb: 0.09 shift=0.4886 cc_mask=0.7094 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.021 1.822 9876 Z= 1.048 ANGLE : 1.786 41.769 13471 Z= 0.938 CHIRALITY : 0.114 0.454 1499 PLANARITY : 0.020 0.267 1739 DIHEDRAL : 13.516 104.624 3532 MIN NONBONDED DISTANCE : 2.531 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.53 RAMACHANDRAN PLOT: OUTLIERS : 0.40 % ALLOWED : 5.00 % FAVORED : 94.59 % ROTAMER: OUTLIERS : 0.92 % ALLOWED : 3.97 % FAVORED : 95.11 % CBETA DEVIATIONS : 0.09 % PEPTIDE PLANE: CIS-PROLINE : 11.11 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -1.37 (0.23), RESIDUES: 1239 HELIX: -2.85 (0.49), RESIDUES: 54 SHEET: -0.77 (0.23), RESIDUES: 440 LOOP : -0.78 (0.22), RESIDUES: 745 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.022 0.004 ARG C 94 TYR 0.163 0.019 TYR H 99 PHE 0.064 0.012 PHE B 139 TRP 0.118 0.023 TRP E 529 HIS 0.008 0.002 HIS E 693 Resolution of map is: 3.8552 Map-model correlation coefficient (CC) CC_mask : 0.7094 =============================================================================== Job complete usr+sys time: 2982.46 seconds wall clock time: 39 minutes 44.69 seconds (2384.69 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)