Starting qr.refine on Sun May 19 19:05:23 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgt_40467.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgt_40467.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/8sgt_40467.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgt_40467.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgt_40467.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgt_40467.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 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 102": "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: 14174 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 10724 Inner-chain residues flagged as termini: ['pdbres="SER A 73 "', 'pdbres="GLU A 97 "', 'pdbres="PHE A 223 "', 'pdbres="PRO A 370 "', 'pdbres="SER A 467 "', 'pdbres="THR A 482 "', 'pdbres="ALA A 644 "', 'pdbres="LEU A 653 "', 'pdbres="GLU A 683 "', 'pdbres="ASN A 707 "', 'pdbres="THR A 718 "', 'pdbres="SER A 737 "'] Classifications: {'peptide': 687} Modifications used: {'COO': 7, 'NH2': 1, 'NH3': 6} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 663} Chain breaks: 6 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1609 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1841 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 1.61, per 1000 atoms: 0.11 Number of scatterers: 14174 At special positions: 0 Unit cell: (121.18, 97.11, 146.91, 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 30 16.00 O 1347 8.00 N 1145 7.00 C 4608 6.00 H 7044 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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: 2.60 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 7033 1.14 - 1.31: 1178 1.31 - 1.48: 3024 1.48 - 1.65: 3062 1.65 - 1.81: 43 Bond restraints: 14340 Sorted by residual: bond pdb=" C ALA H 12 " pdb=" N ARG H 13 " ideal model delta sigma weight residual 1.329 1.344 -0.015 1.40e-02 5.10e+03 1.15e+00 bond pdb=" CB PRO A 635 " pdb=" CG PRO A 635 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.13e+00 bond pdb=" C PHE A 207 " pdb=" O PHE A 207 " ideal model delta sigma weight residual 1.231 1.250 -0.019 2.00e-02 2.50e+03 8.81e-01 bond pdb=" C PHE A 206 " pdb=" N PHE A 207 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.30e-01 bond pdb=" C PHE A 456 " pdb=" N LEU A 457 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 6.83e-01 ... (remaining 14335 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.04: 291 107.04 - 113.80: 16895 113.80 - 120.56: 4717 120.56 - 127.32: 3877 127.32 - 134.07: 82 Bond angle restraints: 25862 Sorted by residual: angle pdb=" C ILE A 636 " pdb=" N LEU A 637 " pdb=" CA LEU A 637 " ideal model delta sigma weight residual 121.70 127.88 -6.18 1.80e+00 3.09e-01 1.18e+01 angle pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 116.90 121.24 -4.34 1.50e+00 4.44e-01 8.38e+00 angle pdb=" CA VAL A 812 " pdb=" C VAL A 812 " pdb=" N PRO A 813 " ideal model delta sigma weight residual 116.90 120.85 -3.95 1.50e+00 4.44e-01 6.92e+00 angle pdb=" C GLU A 559 " pdb=" N LEU A 560 " pdb=" CA LEU A 560 " ideal model delta sigma weight residual 121.70 117.11 4.59 1.80e+00 3.09e-01 6.49e+00 angle pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " ideal model delta sigma weight residual 116.90 120.71 -3.81 1.50e+00 4.44e-01 6.45e+00 ... (remaining 25857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 6190 16.74 - 33.49: 383 33.49 - 50.23: 130 50.23 - 66.98: 59 66.98 - 83.72: 14 Dihedral angle restraints: 6776 sinusoidal: 3565 harmonic: 3211 Sorted by residual: dihedral pdb=" CA GLU A 566 " pdb=" C GLU A 566 " pdb=" N ILE A 567 " pdb=" CA ILE A 567 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR H 60 " pdb=" C TYR H 60 " pdb=" N THR H 61 " pdb=" CA THR H 61 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 6773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 675 0.030 - 0.060: 314 0.060 - 0.090: 84 0.090 - 0.121: 51 0.121 - 0.151: 16 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CA ILE A 542 " pdb=" N ILE A 542 " pdb=" C ILE A 542 " pdb=" CB ILE A 542 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE A 641 " pdb=" N ILE A 641 " pdb=" C ILE A 641 " pdb=" CB ILE A 641 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 374 " pdb=" N ILE A 374 " pdb=" C ILE A 374 " pdb=" CB ILE A 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1137 not shown) Planarity restraints: 2129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 133 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 111 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 112 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 488 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 489 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.018 5.00e-02 4.00e+02 ... (remaining 2126 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 960 2.09 - 2.72: 21992 2.72 - 3.35: 39877 3.35 - 3.97: 55194 3.97 - 4.60: 80232 Nonbonded interactions: 198255 Sorted by model distance: nonbonded pdb=" O VAL A 430 " pdb=" HZ2 LYS A 438 " model vdw 1.468 1.800 nonbonded pdb=" OE1 GLU A 113 " pdb=" H GLU A 113 " model vdw 1.513 1.800 nonbonded pdb=" O THR A 135 " pdb=" HG SER A 139 " model vdw 1.517 1.800 nonbonded pdb=" O LEU A 55 " pdb=" HG SER A 58 " model vdw 1.526 1.800 nonbonded pdb=" O SER A 35 " pdb=" HZ2 LYS A 39 " model vdw 1.530 1.800 ... (remaining 198250 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 30 15.96 2 O 1347 7.97 2 N 1145 6.97 2 C 4608 5.97 2 H 7044 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 0.053 7296 Z= 0.198 ANGLE : 0.927 6.324 9920 Z= 0.442 CHIRALITY : 0.042 0.151 1140 PLANARITY : 0.004 0.041 1249 DIHEDRAL : 12.725 82.505 2534 MIN NONBONDED DISTANCE : 2.131 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.48 RAMACHANDRAN PLOT: OUTLIERS : 0.11 % ALLOWED : 3.44 % FAVORED : 96.44 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 1.17 % FAVORED : 98.83 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 6.90 % 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: -0.92 (0.26), RESIDUES: 900 HELIX: -0.14 (0.27), RESIDUES: 314 SHEET: -0.53 (0.32), RESIDUES: 251 LOOP : -0.92 (0.31), RESIDUES: 335 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.001 ARG A 595 TYR 0.012 0.001 TYR A 180 PHE 0.016 0.002 PHE A 553 TRP 0.007 0.001 TRP A 198 HIS 0.002 0.001 HIS A 744 Resolution of map is: 3.8874 Map-model correlation coefficient (CC) CC_mask : 0.6781 weight= None bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 Initial weight estimate from ratio of grad norms: 0.4934577033778076 cycle: 0 start: weight= 0.4935 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.4935 bond: 0.030 angle: 3.05 clash: 52.9 rota: 5.72 rama: f: 79.33 o: 4.89 Z: -6.08 cb: 9.30 shift=0.6435 cc_mask=0.7877 cycle: 1 start: weight= 0.3454 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.3454 bond: 0.023 angle: 2.52 clash: 29.6 rota: 4.03 rama: f: 85.78 o: 2.89 Z: -5.20 cb: 4.05 shift=0.5579 cc_mask=0.7756 cycle: 2 start: weight= 0.2418 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.2418 bond: 0.019 angle: 2.14 clash: 16.5 rota: 1.56 rama: f: 90.22 o: 1.56 Z: -4.30 cb: 2.15 shift=0.4755 cc_mask=0.7631 cycle: 3 start: weight= 0.1209 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.1209 bond: 0.013 angle: 1.73 clash: 4.9 rota: 0.13 rama: f: 94.67 o: 0.44 Z: -2.76 cb: 0.60 shift=0.3502 cc_mask=0.7400 cycle: 4 start: weight= 0.0846 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.0846 bond: 0.012 angle: 1.64 clash: 2.8 rota: 0.13 rama: f: 96.11 o: 0.33 Z: -2.30 cb: 0.48 shift=0.3076 cc_mask=0.7297 cycle: 5 start: weight= 0.0592 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.0592 bond: 0.011 angle: 1.57 clash: 1.5 rota: 0.13 rama: f: 96.56 o: 0.22 Z: -1.88 cb: 0.36 shift=0.2695 cc_mask=0.7196 cycle: 6 start: weight= 0.0296 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.0296 bond: 0.009 angle: 1.54 clash: 0.7 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -1.51 cb: 0.36 shift=0.2321 cc_mask=0.7034 cycle: 7 start: weight= 0.0207 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.0207 bond: 0.009 angle: 1.53 clash: 0.6 rota: 0.00 rama: f: 97.11 o: 0.00 Z: -1.40 cb: 0.24 shift=0.2223 cc_mask=0.6971 cycle: 8 start: weight= 0.0145 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.0145 bond: 0.009 angle: 1.54 clash: 0.7 rota: 0.00 rama: f: 97.22 o: 0.00 Z: -1.33 cb: 0.24 shift=0.2181 cc_mask=0.6920 cycle: 9 start: weight= 0.0073 bond: 0.004 angle: 0.93 clash: 1.5 rota: 0.00 rama: f: 96.44 o: 0.11 Z: -0.92 cb: 0.00 shift=0.0000 cc_mask=0.6781 final: weight= 0.0073 bond: 0.009 angle: 1.54 clash: 0.4 rota: 0.00 rama: f: 97.33 o: 0.00 Z: -1.27 cb: 0.24 shift=0.2124 cc_mask=0.6847 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.007256850668086961 start: weight= 0.0073 bond: 0.009 angle: 1.54 clash: 0.4 rota: 0.00 rama: f: 97.33 o: 0.00 Z: -1.27 cb: 0.24 shift=0.0000 cc_mask=0.6781 final: weight= 0.0073 bond: 0.009 angle: 1.53 clash: 0.4 rota: 0.00 rama: f: 97.22 o: 0.00 Z: -1.26 cb: 0.24 shift=0.2119 cc_mask=0.6846 start: weight= 0.0073 bond: 0.009 angle: 1.53 clash: 0.4 rota: 0.00 rama: f: 97.22 o: 0.00 Z: -1.26 cb: 0.24 shift=0.2119 cc_mask=0.6846 final: weight= 0.0073 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.13 rama: f: 97.33 o: 0.11 Z: -1.52 cb: 0.24 shift=0.2808 cc_mask=0.6862 start: weight= 0.0073 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.13 rama: f: 97.33 o: 0.11 Z: -1.52 cb: 0.24 shift=0.2808 cc_mask=0.6862 final: weight= 0.0073 bond: 0.009 angle: 1.52 clash: 0.5 rota: 0.39 rama: f: 97.11 o: 0.22 Z: -1.63 cb: 0.24 shift=0.3378 cc_mask=0.6870 start: weight= 0.0073 bond: 0.009 angle: 1.52 clash: 0.5 rota: 0.39 rama: f: 97.11 o: 0.22 Z: -1.63 cb: 0.24 shift=0.3378 cc_mask=0.6870 final: weight= 0.0073 bond: 0.009 angle: 1.51 clash: 0.5 rota: 0.39 rama: f: 96.78 o: 0.22 Z: -1.80 cb: 0.24 shift=0.3765 cc_mask=0.6870 start: weight= 0.0073 bond: 0.009 angle: 1.51 clash: 0.5 rota: 0.39 rama: f: 96.78 o: 0.22 Z: -1.80 cb: 0.24 shift=0.3765 cc_mask=0.6870 final: weight= 0.0073 bond: 0.009 angle: 1.52 clash: 0.4 rota: 0.65 rama: f: 96.67 o: 0.22 Z: -1.84 cb: 0.24 shift=0.3962 cc_mask=0.6869 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.041 7296 Z= 0.469 ANGLE : 1.520 9.438 9920 Z= 0.795 CHIRALITY : 0.109 0.405 1140 PLANARITY : 0.013 0.141 1249 DIHEDRAL : 12.937 112.466 2534 MIN NONBONDED DISTANCE : 2.583 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.42 RAMACHANDRAN PLOT: OUTLIERS : 0.22 % ALLOWED : 3.11 % FAVORED : 96.67 % ROTAMER: OUTLIERS : 0.65 % ALLOWED : 2.21 % FAVORED : 97.14 % CBETA DEVIATIONS : 0.24 % PEPTIDE PLANE: CIS-PROLINE : 6.90 % 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: -1.84 (0.25), RESIDUES: 900 HELIX: -0.99 (0.23), RESIDUES: 319 SHEET: -1.67 (0.30), RESIDUES: 256 LOOP : -0.71 (0.32), RESIDUES: 325 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.020 0.004 ARG A 894 TYR 0.112 0.016 TYR A 923 PHE 0.045 0.010 PHE A 145 TRP 0.115 0.017 TRP H 99 HIS 0.006 0.002 HIS A 674 Resolution of map is: 3.8874 Map-model correlation coefficient (CC) CC_mask : 0.6869 =============================================================================== Job complete usr+sys time: 2194.48 seconds wall clock time: 25 minutes 31.92 seconds (1531.92 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)