Starting qr.refine on Sun May 19 15:34:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7k9i_22749.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7k9i_22749.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 { real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7k9i_22749.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7k9i_22749.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7k9i_22749.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7k9i_22749.pdb" } 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 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: 6441 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3007 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1835 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1599 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Time building chain proxies: 0.77, per 1000 atoms: 0.12 Number of scatterers: 6441 At special positions: 0 Unit cell: (67.1, 88, 89.1, 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 14 16.00 O 630 8.00 N 553 7.00 C 2087 6.00 H 3157 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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: 1.20 Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Time building geometry restraints manager: 1.38 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: 3157 1.15 - 1.32: 530 1.32 - 1.49: 1488 1.49 - 1.66: 1334 1.66 - 1.83: 16 Bond restraints: 6525 Sorted by residual: bond pdb=" C LEU L 75 " pdb=" N THR L 76 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 9.88e-01 bond pdb=" N GLY H 106 " pdb=" CA GLY H 106 " ideal model delta sigma weight residual 1.451 1.438 0.013 1.60e-02 3.91e+03 6.84e-01 bond pdb=" C LYS A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.54e-01 bond pdb=" C TYR A 505 " pdb=" N GLN A 506 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.47e-01 bond pdb=" C ILE H 20 " pdb=" N THR H 21 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.08e-01 ... (remaining 6520 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.39: 282 107.39 - 114.07: 7372 114.07 - 120.75: 2255 120.75 - 127.43: 1758 127.43 - 134.10: 39 Bond angle restraints: 11706 Sorted by residual: angle pdb=" C GLY L 52 " pdb=" N THR L 53 " pdb=" CA THR L 53 " ideal model delta sigma weight residual 121.70 130.28 -8.58 1.80e+00 3.09e-01 2.27e+01 angle pdb=" C PRO H 14 " pdb=" N SER H 15 " pdb=" CA SER H 15 " ideal model delta sigma weight residual 121.70 126.21 -4.51 1.80e+00 3.09e-01 6.28e+00 angle pdb=" CA CYS H 95 " pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " ideal model delta sigma weight residual 114.40 119.71 -5.31 2.30e+00 1.89e-01 5.33e+00 angle pdb=" C GLU L 40 " pdb=" N LYS L 41 " pdb=" CA LYS L 41 " ideal model delta sigma weight residual 121.70 125.62 -3.92 1.80e+00 3.09e-01 4.73e+00 angle pdb=" C THR H 21 " pdb=" N CYS H 22 " pdb=" CA CYS H 22 " ideal model delta sigma weight residual 121.70 125.09 -3.39 1.80e+00 3.09e-01 3.54e+00 ... (remaining 11701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 2873 17.73 - 35.46: 199 35.46 - 53.20: 51 53.20 - 70.93: 13 70.93 - 88.66: 4 Dihedral angle restraints: 3140 sinusoidal: 1656 harmonic: 1484 Sorted by residual: dihedral pdb=" CA TRP L 93 " pdb=" C TRP L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 123.27 -30.27 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 90 " pdb=" CB CYS L 90 " ideal model delta sinusoidal sigma weight residual 93.00 67.28 25.72 1 1.00e+01 1.00e-02 9.51e+00 ... (remaining 3137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 295 0.031 - 0.061: 129 0.061 - 0.092: 41 0.092 - 0.122: 29 0.122 - 0.153: 4 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA VAL A 401 " pdb=" N VAL A 401 " pdb=" C VAL A 401 " pdb=" CB VAL A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE L 77 " pdb=" N ILE L 77 " pdb=" C ILE L 77 " pdb=" CB ILE L 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 495 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 41 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO L 42 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 39 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO H 40 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO H 40 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 40 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 355 " -0.075 9.50e-02 1.11e+02 2.54e-02 9.74e-01 pdb=" NE ARG A 355 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 355 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 355 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 355 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 355 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 355 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 355 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG A 355 " 0.000 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 356 2.07 - 2.70: 9329 2.70 - 3.33: 17564 3.33 - 3.97: 24837 3.97 - 4.60: 35797 Nonbonded interactions: 87883 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" HG1 THR A 523 " model vdw 1.436 1.800 nonbonded pdb=" HZ2 LYS H 64 " pdb=" O SER H 84 " model vdw 1.478 1.800 nonbonded pdb="HH12 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 1.506 1.800 nonbonded pdb=" O THR H 53 " pdb=" HZ3 LYS H 71 " model vdw 1.515 1.800 nonbonded pdb=" HE1 TRP H 52 " pdb=" OD1 ASN H 58 " model vdw 1.523 1.800 ... (remaining 87878 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 630 7.97 2 N 553 6.97 2 C 2087 5.97 2 H 3157 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 0.026 3368 Z= 0.198 ANGLE : 0.971 8.576 4588 Z= 0.448 CHIRALITY : 0.044 0.153 498 PLANARITY : 0.004 0.037 593 DIHEDRAL : 11.937 88.662 1181 MIN NONBONDED DISTANCE : 2.227 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 3.57 RAMACHANDRAN PLOT: OUTLIERS : 0.24 % ALLOWED : 6.00 % FAVORED : 93.76 % ROTAMER: OUTLIERS : 0.85 % ALLOWED : 3.94 % FAVORED : 95.21 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % 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: -1.60 (0.38), RESIDUES: 417 HELIX: -2.37 (0.67), RESIDUES: 32 SHEET: -0.54 (0.42), RESIDUES: 143 LOOP : -1.19 (0.37), RESIDUES: 242 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.005 0.001 ARG A 355 TYR 0.009 0.001 TYR A 423 PHE 0.008 0.001 PHE A 400 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 Resolution of map is: 3.4033 Map-model correlation coefficient (CC) CC_mask : 0.8160 weight= None bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 Initial weight estimate from ratio of grad norms: 0.4417619505444195 cycle: 0 start: weight= 0.4418 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.4418 bond: 0.026 angle: 2.58 clash: 25.9 rota: 3.66 rama: f: 82.97 o: 2.40 Z: -5.23 cb: 3.92 shift=0.3583 cc_mask=0.8521 cycle: 1 start: weight= 0.3092 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.3092 bond: 0.021 angle: 2.22 clash: 14.3 rota: 3.10 rama: f: 86.81 o: 0.96 Z: -4.53 cb: 0.78 shift=0.3219 cc_mask=0.8466 cycle: 2 start: weight= 0.2165 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.2165 bond: 0.017 angle: 1.97 clash: 7.5 rota: 1.41 rama: f: 90.17 o: 0.48 Z: -3.71 cb: 0.52 shift=0.2885 cc_mask=0.8409 cycle: 3 start: weight= 0.1082 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.1082 bond: 0.013 angle: 1.72 clash: 2.5 rota: 1.13 rama: f: 94.48 o: 0.00 Z: -2.48 cb: 0.26 shift=0.2319 cc_mask=0.8301 cycle: 4 start: weight= 0.0758 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.0758 bond: 0.011 angle: 1.67 clash: 1.4 rota: 1.13 rama: f: 94.00 o: 0.00 Z: -2.19 cb: 0.26 shift=0.2223 cc_mask=0.8256 cycle: 5 start: weight= 0.0530 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.0530 bond: 0.010 angle: 1.65 clash: 0.9 rota: 1.13 rama: f: 94.72 o: 0.00 Z: -1.97 cb: 0.26 shift=0.2207 cc_mask=0.8219 cycle: 6 start: weight= 0.0265 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.0265 bond: 0.010 angle: 1.64 clash: 0.6 rota: 1.41 rama: f: 94.72 o: 0.00 Z: -1.75 cb: 0.26 shift=0.2287 cc_mask=0.8164 cycle: 7 start: weight= 0.0186 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.0186 bond: 0.010 angle: 1.64 clash: 0.6 rota: 1.41 rama: f: 94.96 o: 0.00 Z: -1.70 cb: 0.26 shift=0.2307 cc_mask=0.8146 cycle: 8 start: weight= 0.0130 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.0130 bond: 0.009 angle: 1.64 clash: 0.6 rota: 1.69 rama: f: 94.96 o: 0.00 Z: -1.67 cb: 0.26 shift=0.2371 cc_mask=0.8131 cycle: 9 start: weight= 0.0065 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.0065 bond: 0.009 angle: 1.64 clash: 0.6 rota: 1.69 rama: f: 95.20 o: 0.00 Z: -1.59 cb: 0.26 shift=0.2337 cc_mask=0.8118 cycle: 10 start: weight= 0.0045 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.0045 bond: 0.009 angle: 1.64 clash: 0.6 rota: 1.69 rama: f: 94.96 o: 0.00 Z: -1.59 cb: 0.26 shift=0.2398 cc_mask=0.8111 cycle: 11 start: weight= 0.0032 bond: 0.004 angle: 0.97 clash: 3.6 rota: 0.85 rama: f: 93.76 o: 0.24 Z: -1.60 cb: 0.00 shift=0.0000 cc_mask=0.8160 final: weight= 0.0032 bond: 0.009 angle: 1.64 clash: 0.6 rota: 1.69 rama: f: 94.96 o: 0.00 Z: -1.58 cb: 0.26 shift=0.2389 cc_mask=0.8109 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0031833371678255257 start: weight= 0.0032 bond: 0.009 angle: 1.64 clash: 0.6 rota: 1.69 rama: f: 94.96 o: 0.00 Z: -1.58 cb: 0.26 shift=0.0000 cc_mask=0.8160 final: weight= 0.0032 bond: 0.009 angle: 1.64 clash: 0.6 rota: 1.69 rama: f: 94.96 o: 0.00 Z: -1.60 cb: 0.26 shift=0.2418 cc_mask=0.8108 start: weight= 0.0032 bond: 0.009 angle: 1.64 clash: 0.6 rota: 1.69 rama: f: 94.96 o: 0.00 Z: -1.60 cb: 0.26 shift=0.2418 cc_mask=0.8108 final: weight= 0.0032 bond: 0.009 angle: 1.61 clash: 0.3 rota: 1.41 rama: f: 95.20 o: 0.00 Z: -1.52 cb: 0.26 shift=0.3189 cc_mask=0.8044 start: weight= 0.0032 bond: 0.009 angle: 1.61 clash: 0.3 rota: 1.41 rama: f: 95.20 o: 0.00 Z: -1.52 cb: 0.26 shift=0.3189 cc_mask=0.8044 final: weight= 0.0032 bond: 0.009 angle: 1.62 clash: 0.0 rota: 1.13 rama: f: 95.44 o: 0.00 Z: -1.58 cb: 0.26 shift=0.3853 cc_mask=0.7988 start: weight= 0.0032 bond: 0.009 angle: 1.62 clash: 0.0 rota: 1.13 rama: f: 95.44 o: 0.00 Z: -1.58 cb: 0.26 shift=0.3853 cc_mask=0.7988 final: weight= 0.0032 bond: 0.009 angle: 1.61 clash: 0.3 rota: 1.41 rama: f: 95.92 o: 0.00 Z: -1.55 cb: 0.26 shift=0.4350 cc_mask=0.7942 start: weight= 0.0032 bond: 0.009 angle: 1.61 clash: 0.3 rota: 1.41 rama: f: 95.92 o: 0.00 Z: -1.55 cb: 0.26 shift=0.4350 cc_mask=0.7942 final: weight= 0.0032 bond: 0.009 angle: 1.62 clash: 0.2 rota: 1.13 rama: f: 95.68 o: 0.00 Z: -1.56 cb: 0.26 shift=0.4702 cc_mask=0.7904 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.030 3368 Z= 0.474 ANGLE : 1.624 9.190 4588 Z= 0.836 CHIRALITY : 0.116 0.522 498 PLANARITY : 0.014 0.096 593 DIHEDRAL : 13.735 146.844 1181 MIN NONBONDED DISTANCE : 2.575 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.16 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.32 % FAVORED : 95.68 % ROTAMER: OUTLIERS : 1.13 % ALLOWED : 5.07 % FAVORED : 93.80 % CBETA DEVIATIONS : 0.26 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % 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: -1.56 (0.39), RESIDUES: 417 HELIX: -3.81 (0.55), RESIDUES: 34 SHEET: -0.77 (0.45), RESIDUES: 136 LOOP : -0.69 (0.37), RESIDUES: 247 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.021 0.005 ARG H 66 TYR 0.084 0.013 TYR A 449 PHE 0.049 0.010 PHE H 79 TRP 0.181 0.029 TRP H 47 HIS 0.003 0.001 HIS L 97 Resolution of map is: 3.4033 Map-model correlation coefficient (CC) CC_mask : 0.7904 =============================================================================== Job complete usr+sys time: 648.81 seconds wall clock time: 11 minutes 47.60 seconds (707.60 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)