Starting qr.refine on Sun May 19 16:53:50 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8idn_35369.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8idn_35369.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/8idn_35369.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8idn_35369.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8idn_35369.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8idn_35369.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 Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "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: 6370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3010 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1770 Classifications: {'peptide': 116} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1590 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 0.77, per 1000 atoms: 0.12 Number of scatterers: 6370 At special positions: 0 Unit cell: (69.01, 75.04, 89.11, 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 627 8.00 N 540 7.00 C 2064 6.00 H 3125 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 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 109 " distance=2.04 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: 1.33 Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Time building geometry restraints manager: 1.52 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: 3125 1.15 - 1.31: 531 1.31 - 1.48: 1421 1.48 - 1.65: 1358 1.65 - 1.82: 16 Bond restraints: 6451 Sorted by residual: bond pdb=" C VAL L 79 " pdb=" O VAL L 79 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 5.22e-01 bond pdb=" C ARG A 509 " pdb=" N VAL A 510 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.95e-01 bond pdb=" C THR A 376 " pdb=" N PHE A 377 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.64e-01 bond pdb=" CA ARG A 346 " pdb=" CB ARG A 346 " ideal model delta sigma weight residual 1.530 1.544 -0.014 2.00e-02 2.50e+03 4.59e-01 bond pdb=" C TRP H 55 " pdb=" N VAL H 56 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 3.97e-01 ... (remaining 6446 not shown) Histogram of bond angle deviations from ideal: 100.80 - 107.46: 286 107.46 - 114.11: 7414 114.11 - 120.76: 2115 120.76 - 127.41: 1738 127.41 - 134.07: 38 Bond angle restraints: 11591 Sorted by residual: angle pdb=" CA ASN A 440 " pdb=" C ASN A 440 " pdb=" N LEU A 441 " ideal model delta sigma weight residual 116.20 122.09 -5.89 2.00e+00 2.50e-01 8.66e+00 angle pdb=" CA ASN A 440 " pdb=" C ASN A 440 " pdb=" O ASN A 440 " ideal model delta sigma weight residual 120.80 116.94 3.86 1.70e+00 3.46e-01 5.16e+00 angle pdb=" CA ASN L 73 " pdb=" C ASN L 73 " pdb=" N SER L 74 " ideal model delta sigma weight residual 116.20 119.95 -3.75 2.00e+00 2.50e-01 3.52e+00 angle pdb=" CA GLN A 498 " pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 116.90 119.63 -2.73 1.50e+00 4.44e-01 3.31e+00 angle pdb=" CA VAL L 79 " pdb=" C VAL L 79 " pdb=" N PRO L 80 " ideal model delta sigma weight residual 116.90 119.52 -2.62 1.50e+00 4.44e-01 3.04e+00 ... (remaining 11586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 2791 14.81 - 29.61: 207 29.61 - 44.42: 64 44.42 - 59.23: 32 59.23 - 74.04: 4 Dihedral angle restraints: 3098 sinusoidal: 1639 harmonic: 1459 Sorted by residual: dihedral pdb=" N LYS A 356 " pdb=" CA LYS A 356 " pdb=" CB LYS A 356 " pdb=" CG LYS A 356 " ideal model delta sinusoidal sigma weight residual -60.00 -109.61 49.61 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA TYR H 113 " pdb=" C TYR H 113 " pdb=" N CYS H 114 " pdb=" CA CYS H 114 " ideal model delta harmonic sigma weight residual 180.00 166.08 13.92 0 5.00e+00 4.00e-02 7.75e+00 dihedral pdb=" CA CYS H 41 " pdb=" CB CYS H 41 " pdb=" SG CYS H 41 " pdb=" SG CYS H 114 " ideal model delta sinusoidal sigma weight residual 79.00 125.84 -46.84 1 2.00e+01 2.50e-03 7.58e+00 ... (remaining 3095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 300 0.032 - 0.064: 139 0.064 - 0.096: 34 0.096 - 0.128: 23 0.128 - 0.160: 3 Chirality restraints: 499 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 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA ILE L 106 " pdb=" N ILE L 106 " pdb=" C ILE L 106 " pdb=" CB ILE L 106 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE L 88 " pdb=" N ILE L 88 " pdb=" C ILE L 88 " pdb=" CB ILE L 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 496 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 58 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.33e-01 pdb=" N PRO H 59 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO H 59 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 59 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.013 5.00e-02 4.00e+02 2.02e-02 6.52e-01 pdb=" N PRO A 463 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 400 " -0.008 2.00e-02 2.50e+03 4.42e-03 5.85e-01 pdb=" CG PHE A 400 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 400 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 400 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 400 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 400 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 400 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 400 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 400 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 400 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 400 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 400 " -0.001 2.00e-02 2.50e+03 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 489 2.15 - 2.76: 11058 2.76 - 3.38: 16333 3.38 - 3.99: 22883 3.99 - 4.60: 33337 Nonbonded interactions: 84100 Sorted by model distance: nonbonded pdb=" OE1 GLN A 493 " pdb="HD21 ASN L 73 " model vdw 1.540 1.800 nonbonded pdb=" OD1 ASN A 439 " pdb=" HG SER A 443 " model vdw 1.549 1.800 nonbonded pdb=" OE1 GLU L 104 " pdb=" H GLU L 104 " model vdw 1.584 1.800 nonbonded pdb="HH12 ARG A 408 " pdb=" OD1 ASP H 119 " model vdw 1.598 1.800 nonbonded pdb=" O TYR H 120 " pdb=" HG SER L 74 " model vdw 1.606 1.800 ... (remaining 84095 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 627 7.97 2 N 540 6.97 2 C 2064 5.97 2 H 3125 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 0.015 3326 Z= 0.182 ANGLE : 0.915 5.885 4533 Z= 0.425 CHIRALITY : 0.043 0.160 499 PLANARITY : 0.003 0.029 585 DIHEDRAL : 11.207 74.036 1166 MIN NONBONDED DISTANCE : 2.010 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.89 RAMACHANDRAN PLOT: OUTLIERS : 0.24 % ALLOWED : 6.30 % FAVORED : 93.46 % ROTAMER: OUTLIERS : 0.28 % ALLOWED : 1.98 % FAVORED : 97.74 % 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: -1.16 (0.39), RESIDUES: 413 HELIX: -2.00 (0.97), RESIDUES: 27 SHEET: 0.28 (0.42), RESIDUES: 146 LOOP : -1.32 (0.37), RESIDUES: 240 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.001 ARG H 116 TYR 0.008 0.001 TYR H 113 PHE 0.013 0.001 PHE A 400 TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 Resolution of map is: 3.4328 Map-model correlation coefficient (CC) CC_mask : 0.7459 weight= None bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 Initial weight estimate from ratio of grad norms: 0.2916131421076683 cycle: 0 start: weight= 0.2916 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.2916 bond: 0.023 angle: 2.61 clash: 24.1 rota: 5.08 rama: f: 79.18 o: 4.84 Z: -4.79 cb: 3.68 shift=0.4802 cc_mask=0.8004 cycle: 1 start: weight= 0.2041 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.2041 bond: 0.019 angle: 2.20 clash: 13.8 rota: 2.82 rama: f: 85.47 o: 2.66 Z: -3.94 cb: 1.05 shift=0.4135 cc_mask=0.7925 cycle: 2 start: weight= 0.1429 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.1429 bond: 0.015 angle: 1.95 clash: 6.4 rota: 1.13 rama: f: 88.38 o: 1.69 Z: -3.12 cb: 0.53 shift=0.3576 cc_mask=0.7843 cycle: 3 start: weight= 0.0714 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.0714 bond: 0.012 angle: 1.68 clash: 2.4 rota: 0.28 rama: f: 92.49 o: 1.21 Z: -1.97 cb: 0.26 shift=0.2803 cc_mask=0.7705 cycle: 4 start: weight= 0.0500 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.0500 bond: 0.011 angle: 1.61 clash: 1.6 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.75 cb: 0.26 shift=0.2546 cc_mask=0.7636 cycle: 5 start: weight= 0.0350 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.0350 bond: 0.010 angle: 1.58 clash: 0.9 rota: 0.56 rama: f: 94.19 o: 0.24 Z: -1.56 cb: 0.26 shift=0.2424 cc_mask=0.7579 cycle: 6 start: weight= 0.0175 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.0175 bond: 0.009 angle: 1.57 clash: 0.3 rota: 0.56 rama: f: 94.92 o: 0.24 Z: -1.36 cb: 0.26 shift=0.2308 cc_mask=0.7499 cycle: 7 start: weight= 0.0123 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.0123 bond: 0.009 angle: 1.57 clash: 0.2 rota: 0.56 rama: f: 94.92 o: 0.24 Z: -1.25 cb: 0.26 shift=0.2284 cc_mask=0.7469 cycle: 8 start: weight= 0.0086 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.0086 bond: 0.009 angle: 1.57 clash: 0.2 rota: 0.56 rama: f: 95.16 o: 0.24 Z: -1.27 cb: 0.26 shift=0.2251 cc_mask=0.7446 cycle: 9 start: weight= 0.0043 bond: 0.004 angle: 0.92 clash: 1.9 rota: 0.28 rama: f: 93.46 o: 0.24 Z: -1.16 cb: 0.00 shift=0.0000 cc_mask=0.7459 final: weight= 0.0043 bond: 0.009 angle: 1.58 clash: 0.2 rota: 0.28 rama: f: 95.16 o: 0.24 Z: -1.28 cb: 0.26 shift=0.2252 cc_mask=0.7417 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.004288499319478135 start: weight= 0.0043 bond: 0.009 angle: 1.58 clash: 0.2 rota: 0.28 rama: f: 95.16 o: 0.24 Z: -1.28 cb: 0.26 shift=0.0000 cc_mask=0.7459 final: weight= 0.0043 bond: 0.009 angle: 1.58 clash: 0.2 rota: 0.28 rama: f: 95.16 o: 0.24 Z: -1.28 cb: 0.26 shift=0.2251 cc_mask=0.7417 start: weight= 0.0043 bond: 0.009 angle: 1.58 clash: 0.2 rota: 0.28 rama: f: 95.16 o: 0.24 Z: -1.28 cb: 0.26 shift=0.2251 cc_mask=0.7417 final: weight= 0.0043 bond: 0.009 angle: 1.55 clash: 0.2 rota: 0.56 rama: f: 95.88 o: 0.24 Z: -1.40 cb: 0.26 shift=0.3295 cc_mask=0.7350 start: weight= 0.0043 bond: 0.009 angle: 1.55 clash: 0.2 rota: 0.56 rama: f: 95.88 o: 0.24 Z: -1.40 cb: 0.26 shift=0.3295 cc_mask=0.7350 final: weight= 0.0043 bond: 0.009 angle: 1.58 clash: 0.3 rota: 0.85 rama: f: 94.92 o: 0.24 Z: -1.69 cb: 0.26 shift=0.3898 cc_mask=0.7298 start: weight= 0.0043 bond: 0.009 angle: 1.58 clash: 0.3 rota: 0.85 rama: f: 94.92 o: 0.24 Z: -1.69 cb: 0.26 shift=0.3898 cc_mask=0.7298 final: weight= 0.0043 bond: 0.009 angle: 1.58 clash: 0.3 rota: 1.13 rama: f: 94.92 o: 0.24 Z: -1.73 cb: 0.26 shift=0.4504 cc_mask=0.7236 start: weight= 0.0043 bond: 0.009 angle: 1.58 clash: 0.3 rota: 1.13 rama: f: 94.92 o: 0.24 Z: -1.73 cb: 0.26 shift=0.4504 cc_mask=0.7236 final: weight= 0.0043 bond: 0.009 angle: 1.59 clash: 0.6 rota: 1.69 rama: f: 95.16 o: 0.24 Z: -1.88 cb: 0.26 shift=0.4853 cc_mask=0.7201 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.034 3326 Z= 0.476 ANGLE : 1.587 9.270 4533 Z= 0.819 CHIRALITY : 0.108 0.377 499 PLANARITY : 0.018 0.192 585 DIHEDRAL : 12.761 90.224 1166 MIN NONBONDED DISTANCE : 2.587 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.63 RAMACHANDRAN PLOT: OUTLIERS : 0.24 % ALLOWED : 4.60 % FAVORED : 95.16 % ROTAMER: OUTLIERS : 1.69 % ALLOWED : 3.67 % FAVORED : 94.63 % 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: -1.88 (0.36), RESIDUES: 413 HELIX: -3.49 (0.71), RESIDUES: 21 SHEET: -1.67 (0.36), RESIDUES: 146 LOOP : -0.65 (0.36), RESIDUES: 246 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.019 0.004 ARG A 509 TYR 0.103 0.016 TYR H 120 PHE 0.051 0.010 PHE A 497 TRP 0.120 0.027 TRP H 66 HIS 0.003 0.002 HIS L 63 Resolution of map is: 3.4328 Map-model correlation coefficient (CC) CC_mask : 0.7201 =============================================================================== Job complete usr+sys time: 674.49 seconds wall clock time: 12 minutes 4.80 seconds (724.80 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)