Starting phenix.real_space_refine on Fri Sep 27 16:22:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/09_2024/7q62_13850.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/09_2024/7q62_13850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/09_2024/7q62_13850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/09_2024/7q62_13850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/09_2024/7q62_13850.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/09_2024/7q62_13850.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 10356 2.51 5 N 2653 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16186 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9560 Classifications: {'peptide': 1223} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1159} Chain breaks: 3 Chain: "B" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6486 Classifications: {'peptide': 822} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 772} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.99, per 1000 atoms: 0.68 Number of scatterers: 16186 At special positions: 0 Unit cell: (106.108, 122.93, 142.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 3102 8.00 N 2653 7.00 C 10356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.02 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.11 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.02 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 78 " distance=2.02 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 291 " distance=2.04 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 589 " - pdb=" SG CYS B 769 " distance=2.02 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 694 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B 845 " - pdb=" SG CYS B 881 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A1501 " - " ASN A 120 " " NAG A1502 " - " ASN A 328 " " NAG A1503 " - " ASN A 609 " " NAG A1504 " - " ASN A 857 " " NAG A1505 " - " ASN A 867 " " NAG B1501 " - " ASN B 120 " " NAG B1502 " - " ASN B 328 " " NAG B1503 " - " ASN B 609 " " NAG B1504 " - " ASN B 857 " " NAG B1505 " - " ASN B 867 " Time building additional restraints: 4.39 Conformation dependent library (CDL) restraints added in 2.4 seconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 34 sheets defined 12.2% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 406 through 409 removed outlier: 4.133A pdb=" N ASN A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 597 through 602 removed outlier: 4.008A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 597 through 602' Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 670 through 679 removed outlier: 3.674A pdb=" N VAL A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 963 removed outlier: 3.704A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 removed outlier: 4.343A pdb=" N VAL A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 990 removed outlier: 4.265A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 990 " --> pdb=" O GLN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1010 Processing helix chain 'A' and resid 1011 through 1014 Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1056 through 1070 removed outlier: 3.845A pdb=" N LYS A1064 " --> pdb=" O GLN A1060 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TRP A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1104 removed outlier: 3.612A pdb=" N LEU A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 4.294A pdb=" N MET A1108 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 4.331A pdb=" N ASN A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A1127 " --> pdb=" O CYS A1123 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1129 " --> pdb=" O LYS A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1148 removed outlier: 3.796A pdb=" N ILE A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1162 removed outlier: 3.946A pdb=" N LYS A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN A1159 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A1162 " --> pdb=" O LYS A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1207 removed outlier: 3.702A pdb=" N LYS A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1227 removed outlier: 4.039A pdb=" N LYS A1227 " --> pdb=" O ALA A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 removed outlier: 3.552A pdb=" N ALA A1255 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 removed outlier: 3.824A pdb=" N ALA B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 481' Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.807A pdb=" N LYS B 511 " --> pdb=" O ASN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 602 removed outlier: 3.719A pdb=" N LEU B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 624 through 628 removed outlier: 3.697A pdb=" N ALA B 628 " --> pdb=" O TYR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 removed outlier: 8.244A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.797A pdb=" N PHE A 52 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 54 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.759A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 346 removed outlier: 4.038A pdb=" N GLU A 345 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 455 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 507 removed outlier: 5.308A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 495 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 487 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB4, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB5, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB6, first strand: chain 'A' and resid 800 through 801 removed outlier: 7.081A pdb=" N VAL A 800 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB8, first strand: chain 'A' and resid 921 through 930 Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.599A pdb=" N TYR A1172 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 75 through 82 removed outlier: 8.101A pdb=" N LYS B 38 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.814A pdb=" N LEU B 56 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 64 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 121 through 126 Processing sheet with id=AC4, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.626A pdb=" N SER B 156 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU B 172 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN B 170 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 160 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 219 through 223 Processing sheet with id=AC6, first strand: chain 'B' and resid 229 through 230 removed outlier: 6.230A pdb=" N LEU B 229 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS B 310 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN B 311 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS B 261 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 340 through 346 removed outlier: 5.431A pdb=" N MET B 342 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ARG B 364 " --> pdb=" O MET B 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 344 " --> pdb=" O ARG B 362 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 362 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 346 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AC9, first strand: chain 'B' and resid 451 through 455 Processing sheet with id=AD1, first strand: chain 'B' and resid 498 through 507 removed outlier: 5.152A pdb=" N LEU B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY B 495 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER B 488 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE B 539 " --> pdb=" O SER B 488 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 563 through 567 Processing sheet with id=AD3, first strand: chain 'B' and resid 742 through 743 Processing sheet with id=AD4, first strand: chain 'B' and resid 592 through 595 Processing sheet with id=AD5, first strand: chain 'B' and resid 729 through 730 removed outlier: 5.938A pdb=" N VAL B 800 " --> pdb=" O LYS B 904 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD7, first strand: chain 'B' and resid 790 through 795 640 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.61 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5061 1.34 - 1.46: 4006 1.46 - 1.59: 7390 1.59 - 1.71: 0 1.71 - 1.84: 110 Bond restraints: 16567 Sorted by residual: bond pdb=" CD GLU B 596 " pdb=" OE1 GLU B 596 " ideal model delta sigma weight residual 1.249 1.326 -0.077 1.90e-02 2.77e+03 1.66e+01 bond pdb=" CD GLU A 596 " pdb=" OE1 GLU A 596 " ideal model delta sigma weight residual 1.249 1.321 -0.072 1.90e-02 2.77e+03 1.45e+01 bond pdb=" N ILE A1318 " pdb=" CA ILE A1318 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.61e+00 bond pdb=" N GLY A1031 " pdb=" CA GLY A1031 " ideal model delta sigma weight residual 1.449 1.478 -0.028 9.80e-03 1.04e+04 8.41e+00 bond pdb=" C1 NAG A1504 " pdb=" O5 NAG A1504 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.36e+00 ... (remaining 16562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 22455 7.50 - 15.00: 56 15.00 - 22.51: 1 22.51 - 30.01: 0 30.01 - 37.51: 2 Bond angle restraints: 22514 Sorted by residual: angle pdb=" CA CYS A 279 " pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " ideal model delta sigma weight residual 114.40 151.91 -37.51 2.30e+00 1.89e-01 2.66e+02 angle pdb=" CA CYS A 259 " pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " ideal model delta sigma weight residual 114.40 151.66 -37.26 2.30e+00 1.89e-01 2.62e+02 angle pdb=" N CYS A 259 " pdb=" CA CYS A 259 " pdb=" C CYS A 259 " ideal model delta sigma weight residual 108.99 122.76 -13.77 1.57e+00 4.06e-01 7.69e+01 angle pdb=" N CYS A 279 " pdb=" CA CYS A 279 " pdb=" C CYS A 279 " ideal model delta sigma weight residual 108.79 119.95 -11.16 1.53e+00 4.27e-01 5.32e+01 angle pdb=" C ASN B 103 " pdb=" N ASN B 104 " pdb=" CA ASN B 104 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 ... (remaining 22509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 9123 17.69 - 35.38: 733 35.38 - 53.07: 137 53.07 - 70.76: 39 70.76 - 88.45: 34 Dihedral angle restraints: 10066 sinusoidal: 4126 harmonic: 5940 Sorted by residual: dihedral pdb=" CB CYS A 633 " pdb=" SG CYS A 633 " pdb=" SG CYS A 694 " pdb=" CB CYS A 694 " ideal model delta sinusoidal sigma weight residual -86.00 -173.78 87.78 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual -86.00 -2.50 -83.50 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CA GLU A 835 " pdb=" C GLU A 835 " pdb=" N SER A 836 " pdb=" CA SER A 836 " ideal model delta harmonic sigma weight residual 180.00 140.64 39.36 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 10063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2446 0.139 - 0.277: 93 0.277 - 0.416: 10 0.416 - 0.554: 3 0.554 - 0.693: 1 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C1 NAG A1504 " pdb=" ND2 ASN A 857 " pdb=" C2 NAG A1504 " pdb=" O5 NAG A1504 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA CYS A 259 " pdb=" N CYS A 259 " pdb=" C CYS A 259 " pdb=" CB CYS A 259 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CA CYS A 279 " pdb=" N CYS A 279 " pdb=" C CYS A 279 " pdb=" CB CYS A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 2550 not shown) Planarity restraints: 2899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 837 " 0.029 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP A 837 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 837 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 837 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 837 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 837 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 837 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 837 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 837 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 837 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 44 " 0.057 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A 45 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 609 " 0.027 2.00e-02 2.50e+03 2.64e-02 8.73e+00 pdb=" CG ASN B 609 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 609 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 609 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG B1503 " 0.030 2.00e-02 2.50e+03 ... (remaining 2896 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4033 2.80 - 3.33: 13141 3.33 - 3.85: 26931 3.85 - 4.38: 29959 4.38 - 4.90: 52543 Nonbonded interactions: 126607 Sorted by model distance: nonbonded pdb=" OD1 ASP A 127 " pdb=" OH TYR A 131 " model vdw 2.276 3.040 nonbonded pdb=" O ALA B 827 " pdb=" OH TYR B 832 " model vdw 2.327 3.040 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.333 3.040 nonbonded pdb=" OD1 ASP B 127 " pdb=" OH TYR B 131 " model vdw 2.337 3.040 nonbonded pdb=" OG1 THR A1238 " pdb=" OE1 GLN A1239 " model vdw 2.341 3.040 ... (remaining 126602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 46.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 16567 Z= 0.372 Angle : 1.133 37.509 22514 Z= 0.569 Chirality : 0.067 0.693 2553 Planarity : 0.008 0.105 2889 Dihedral : 14.476 88.447 6200 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 0.06 % Allowed : 0.67 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.75 (0.17), residues: 2031 helix: -2.90 (0.26), residues: 204 sheet: -0.24 (0.17), residues: 917 loop : -1.65 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 837 HIS 0.007 0.001 HIS A 77 PHE 0.030 0.003 PHE A1286 TYR 0.049 0.003 TYR B 306 ARG 0.022 0.001 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.825 Fit side-chains REVERT: A 266 TRP cc_start: 0.6368 (m-10) cc_final: 0.6051 (m-90) REVERT: A 394 ASP cc_start: 0.7663 (p0) cc_final: 0.7412 (p0) REVERT: A 578 GLU cc_start: 0.7945 (tt0) cc_final: 0.7547 (tt0) REVERT: A 985 LEU cc_start: 0.9067 (mm) cc_final: 0.8834 (mm) REVERT: A 1015 MET cc_start: 0.7157 (pmm) cc_final: 0.6045 (tmm) REVERT: A 1065 TRP cc_start: 0.6221 (m100) cc_final: 0.5448 (m100) REVERT: A 1173 TRP cc_start: 0.6464 (m-90) cc_final: 0.5897 (m-90) REVERT: A 1297 MET cc_start: 0.7573 (pmm) cc_final: 0.7273 (pmm) REVERT: B 298 MET cc_start: 0.7019 (ppp) cc_final: 0.6725 (ppp) REVERT: B 306 TYR cc_start: 0.7928 (t80) cc_final: 0.7713 (t80) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2361 time to fit residues: 68.1039 Evaluate side-chains 133 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 chunk 185 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 506 HIS ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 164 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 855 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16567 Z= 0.190 Angle : 0.655 16.877 22514 Z= 0.328 Chirality : 0.046 0.521 2553 Planarity : 0.005 0.055 2889 Dihedral : 6.141 57.151 2402 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 0.56 % Allowed : 6.88 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.18 (0.18), residues: 2031 helix: -1.63 (0.30), residues: 217 sheet: -0.11 (0.17), residues: 905 loop : -1.17 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 837 HIS 0.002 0.001 HIS A 366 PHE 0.038 0.001 PHE A1286 TYR 0.016 0.001 TYR B 491 ARG 0.005 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6371 (m-10) cc_final: 0.6012 (m-90) REVERT: A 394 ASP cc_start: 0.7714 (p0) cc_final: 0.7410 (p0) REVERT: A 578 GLU cc_start: 0.7976 (tt0) cc_final: 0.7448 (tt0) REVERT: A 619 TRP cc_start: 0.5838 (p90) cc_final: 0.5459 (p-90) REVERT: A 985 LEU cc_start: 0.9053 (mm) cc_final: 0.8767 (mm) REVERT: A 1065 TRP cc_start: 0.5975 (m100) cc_final: 0.5326 (m100) REVERT: A 1142 TYR cc_start: 0.9007 (t80) cc_final: 0.8729 (t80) REVERT: B 157 MET cc_start: 0.7823 (ppp) cc_final: 0.7324 (ppp) REVERT: B 298 MET cc_start: 0.7172 (ppp) cc_final: 0.6836 (ppp) REVERT: B 387 PHE cc_start: 0.9078 (t80) cc_final: 0.8858 (t80) outliers start: 10 outliers final: 6 residues processed: 156 average time/residue: 0.2538 time to fit residues: 63.1120 Evaluate side-chains 140 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 472 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 184 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16567 Z= 0.270 Angle : 0.651 15.769 22514 Z= 0.326 Chirality : 0.046 0.498 2553 Planarity : 0.004 0.055 2889 Dihedral : 5.798 55.495 2402 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 0.89 % Allowed : 9.17 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.86 (0.18), residues: 2031 helix: -0.61 (0.33), residues: 214 sheet: -0.09 (0.17), residues: 908 loop : -0.95 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1173 HIS 0.004 0.001 HIS A 506 PHE 0.036 0.001 PHE A1286 TYR 0.016 0.001 TYR B 491 ARG 0.004 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6476 (m-10) cc_final: 0.6125 (m-90) REVERT: A 394 ASP cc_start: 0.7799 (p0) cc_final: 0.7526 (p0) REVERT: A 421 MET cc_start: 0.8083 (mmm) cc_final: 0.7771 (mmm) REVERT: A 578 GLU cc_start: 0.7900 (tt0) cc_final: 0.7281 (tt0) REVERT: A 985 LEU cc_start: 0.9070 (mm) cc_final: 0.8789 (mm) REVERT: A 1288 GLN cc_start: 0.7826 (mp-120) cc_final: 0.7583 (mm110) REVERT: B 157 MET cc_start: 0.7961 (ppp) cc_final: 0.7521 (ppp) REVERT: B 387 PHE cc_start: 0.9108 (t80) cc_final: 0.8835 (t80) REVERT: B 501 MET cc_start: 0.8120 (ttp) cc_final: 0.7591 (ttm) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.2369 time to fit residues: 55.9261 Evaluate side-chains 135 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 176 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16567 Z= 0.197 Angle : 0.606 11.533 22514 Z= 0.299 Chirality : 0.045 0.481 2553 Planarity : 0.004 0.058 2889 Dihedral : 5.583 55.353 2402 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 1.23 % Allowed : 10.68 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.67 (0.19), residues: 2031 helix: -0.16 (0.34), residues: 214 sheet: -0.05 (0.17), residues: 910 loop : -0.83 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 837 HIS 0.002 0.000 HIS A 506 PHE 0.041 0.001 PHE A1286 TYR 0.016 0.001 TYR B 491 ARG 0.003 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6449 (m-10) cc_final: 0.6131 (m-90) REVERT: A 394 ASP cc_start: 0.7790 (p0) cc_final: 0.7552 (p0) REVERT: A 421 MET cc_start: 0.8142 (mmm) cc_final: 0.7849 (mmm) REVERT: A 571 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: A 619 TRP cc_start: 0.6822 (p90) cc_final: 0.5961 (p-90) REVERT: A 953 MET cc_start: 0.5133 (ptt) cc_final: 0.4890 (ptt) REVERT: A 985 LEU cc_start: 0.9038 (mm) cc_final: 0.8740 (mm) REVERT: A 1065 TRP cc_start: 0.5886 (m100) cc_final: 0.5255 (m100) REVERT: A 1173 TRP cc_start: 0.6531 (m-90) cc_final: 0.6326 (m-90) REVERT: A 1288 GLN cc_start: 0.7825 (mp-120) cc_final: 0.7596 (mm110) REVERT: B 157 MET cc_start: 0.7945 (ppp) cc_final: 0.7552 (ppp) REVERT: B 387 PHE cc_start: 0.9122 (t80) cc_final: 0.8852 (t80) REVERT: B 501 MET cc_start: 0.8049 (ttp) cc_final: 0.7570 (ttm) REVERT: B 591 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8286 (tt) REVERT: B 608 SER cc_start: 0.9008 (t) cc_final: 0.8560 (p) outliers start: 22 outliers final: 15 residues processed: 153 average time/residue: 0.2434 time to fit residues: 60.5368 Evaluate side-chains 140 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 752 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 ASN A1163 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16567 Z= 0.272 Angle : 0.621 11.241 22514 Z= 0.310 Chirality : 0.045 0.470 2553 Planarity : 0.004 0.057 2889 Dihedral : 5.642 55.495 2402 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 2.40 % Allowed : 11.30 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.58 (0.19), residues: 2031 helix: 0.06 (0.35), residues: 220 sheet: -0.03 (0.17), residues: 906 loop : -0.76 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 837 HIS 0.003 0.001 HIS A 506 PHE 0.012 0.001 PHE B 209 TYR 0.016 0.001 TYR B 491 ARG 0.003 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.819 Fit side-chains revert: symmetry clash REVERT: A 985 LEU cc_start: 0.9077 (mm) cc_final: 0.8793 (mm) REVERT: A 1065 TRP cc_start: 0.5903 (m100) cc_final: 0.5266 (m100) REVERT: B 157 MET cc_start: 0.8037 (ppp) cc_final: 0.7597 (ppp) REVERT: B 387 PHE cc_start: 0.9102 (t80) cc_final: 0.8822 (t80) REVERT: B 501 MET cc_start: 0.8075 (ttp) cc_final: 0.7575 (ttm) REVERT: B 608 SER cc_start: 0.9075 (t) cc_final: 0.8642 (p) REVERT: B 619 TRP cc_start: 0.6284 (p90) cc_final: 0.6071 (p90) outliers start: 43 outliers final: 28 residues processed: 165 average time/residue: 0.2349 time to fit residues: 63.4710 Evaluate side-chains 148 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.0870 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 197 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN A1288 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16567 Z= 0.214 Angle : 0.616 11.090 22514 Z= 0.306 Chirality : 0.045 0.483 2553 Planarity : 0.004 0.058 2889 Dihedral : 5.551 55.268 2402 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 2.35 % Allowed : 12.14 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.50 (0.19), residues: 2031 helix: 0.16 (0.35), residues: 220 sheet: 0.02 (0.17), residues: 905 loop : -0.71 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 837 HIS 0.002 0.000 HIS B 506 PHE 0.040 0.001 PHE A1286 TYR 0.015 0.001 TYR B 491 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8784 (mm) REVERT: A 1065 TRP cc_start: 0.5900 (m100) cc_final: 0.5253 (m100) REVERT: A 1286 PHE cc_start: 0.8850 (t80) cc_final: 0.8606 (t80) REVERT: A 1288 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7488 (mm110) REVERT: B 157 MET cc_start: 0.7990 (ppp) cc_final: 0.7574 (ppp) REVERT: B 387 PHE cc_start: 0.9116 (t80) cc_final: 0.8867 (t80) REVERT: B 501 MET cc_start: 0.8029 (ttp) cc_final: 0.7577 (ttm) REVERT: B 608 SER cc_start: 0.9016 (t) cc_final: 0.8588 (p) outliers start: 42 outliers final: 33 residues processed: 158 average time/residue: 0.2419 time to fit residues: 63.8431 Evaluate side-chains 155 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16567 Z= 0.265 Angle : 0.635 11.004 22514 Z= 0.314 Chirality : 0.045 0.475 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.634 55.022 2402 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 2.24 % Allowed : 12.81 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.51 (0.19), residues: 2031 helix: 0.25 (0.35), residues: 220 sheet: 0.02 (0.17), residues: 900 loop : -0.75 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1173 HIS 0.003 0.001 HIS A 506 PHE 0.036 0.001 PHE A1286 TYR 0.024 0.001 TYR B 492 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 122 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8816 (mm) REVERT: A 1065 TRP cc_start: 0.5883 (m100) cc_final: 0.5232 (m100) REVERT: A 1173 TRP cc_start: 0.6913 (m-90) cc_final: 0.6346 (m-90) REVERT: A 1288 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7663 (mm110) REVERT: A 1298 TYR cc_start: 0.7707 (m-80) cc_final: 0.7340 (m-80) REVERT: B 157 MET cc_start: 0.8041 (ppp) cc_final: 0.7609 (ppp) REVERT: B 387 PHE cc_start: 0.9113 (t80) cc_final: 0.8883 (t80) REVERT: B 501 MET cc_start: 0.8070 (ttp) cc_final: 0.7608 (ttm) REVERT: B 608 SER cc_start: 0.9079 (t) cc_final: 0.8658 (p) outliers start: 40 outliers final: 32 residues processed: 156 average time/residue: 0.2388 time to fit residues: 61.1343 Evaluate side-chains 152 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16567 Z= 0.182 Angle : 0.620 10.888 22514 Z= 0.303 Chirality : 0.045 0.484 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.450 55.663 2402 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.32 % Rotamer: Outliers : 1.85 % Allowed : 13.53 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.40 (0.19), residues: 2031 helix: 0.30 (0.35), residues: 222 sheet: 0.08 (0.17), residues: 904 loop : -0.66 (0.22), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 837 HIS 0.002 0.000 HIS B 854 PHE 0.032 0.001 PHE A1286 TYR 0.023 0.001 TYR B 492 ARG 0.003 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.778 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6398 (m-90) cc_final: 0.5698 (m-10) REVERT: A 985 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8784 (mm) REVERT: A 1065 TRP cc_start: 0.5870 (m100) cc_final: 0.5233 (m100) REVERT: A 1173 TRP cc_start: 0.6820 (m-90) cc_final: 0.6254 (m-90) REVERT: A 1288 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7658 (mm110) REVERT: B 157 MET cc_start: 0.7930 (ppp) cc_final: 0.7522 (ppp) REVERT: B 387 PHE cc_start: 0.9118 (t80) cc_final: 0.8908 (t80) REVERT: B 501 MET cc_start: 0.7953 (ttp) cc_final: 0.7481 (ttm) REVERT: B 608 SER cc_start: 0.8979 (t) cc_final: 0.8557 (p) outliers start: 33 outliers final: 30 residues processed: 154 average time/residue: 0.2357 time to fit residues: 59.9769 Evaluate side-chains 148 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN B 331 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16567 Z= 0.359 Angle : 0.695 10.922 22514 Z= 0.344 Chirality : 0.046 0.464 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.875 55.001 2402 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 2.29 % Allowed : 13.70 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.52 (0.19), residues: 2031 helix: 0.32 (0.35), residues: 218 sheet: -0.03 (0.17), residues: 908 loop : -0.73 (0.22), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1036 HIS 0.006 0.001 HIS B 506 PHE 0.030 0.002 PHE A1286 TYR 0.015 0.001 TYR A1309 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8864 (mm) REVERT: A 1065 TRP cc_start: 0.5847 (m100) cc_final: 0.5205 (m100) REVERT: A 1173 TRP cc_start: 0.6970 (m-90) cc_final: 0.6338 (m-90) REVERT: A 1288 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7666 (mm110) REVERT: B 173 GLU cc_start: 0.7664 (tp30) cc_final: 0.7463 (tp30) REVERT: B 387 PHE cc_start: 0.9103 (t80) cc_final: 0.8892 (t80) REVERT: B 501 MET cc_start: 0.8102 (ttp) cc_final: 0.7640 (ttm) REVERT: B 608 SER cc_start: 0.9135 (t) cc_final: 0.8728 (p) outliers start: 41 outliers final: 33 residues processed: 155 average time/residue: 0.2382 time to fit residues: 60.5110 Evaluate side-chains 152 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 0.4980 chunk 161 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16567 Z= 0.208 Angle : 0.658 12.464 22514 Z= 0.321 Chirality : 0.046 0.485 2553 Planarity : 0.004 0.056 2889 Dihedral : 5.656 55.552 2402 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 1.79 % Allowed : 14.32 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.45 (0.19), residues: 2031 helix: 0.25 (0.35), residues: 220 sheet: 0.05 (0.17), residues: 904 loop : -0.69 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 837 HIS 0.002 0.000 HIS B 506 PHE 0.031 0.001 PHE A1286 TYR 0.016 0.001 TYR B 334 ARG 0.004 0.000 ARG A 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8756 (mm) REVERT: A 1065 TRP cc_start: 0.5863 (m100) cc_final: 0.5241 (m100) REVERT: A 1173 TRP cc_start: 0.6779 (m-90) cc_final: 0.6193 (m-90) REVERT: A 1288 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7658 (mm110) REVERT: B 608 SER cc_start: 0.9011 (t) cc_final: 0.8599 (p) outliers start: 32 outliers final: 31 residues processed: 149 average time/residue: 0.2505 time to fit residues: 61.7335 Evaluate side-chains 149 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.6980 chunk 49 optimal weight: 0.0040 chunk 149 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 162 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 166 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.115215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081862 restraints weight = 42517.355| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.89 r_work: 0.3286 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16567 Z= 0.181 Angle : 0.636 11.632 22514 Z= 0.312 Chirality : 0.045 0.476 2553 Planarity : 0.004 0.054 2889 Dihedral : 5.458 55.518 2402 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 1.85 % Allowed : 14.71 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.32 (0.19), residues: 2031 helix: 0.27 (0.35), residues: 220 sheet: 0.16 (0.17), residues: 898 loop : -0.60 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 837 HIS 0.002 0.000 HIS B 854 PHE 0.029 0.001 PHE A1286 TYR 0.016 0.001 TYR B 491 ARG 0.002 0.000 ARG B 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.16 seconds wall clock time: 66 minutes 7.14 seconds (3967.14 seconds total)