Starting phenix.real_space_refine on Tue Dec 31 17:53:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5v_21549/12_2024/6w5v_21549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5v_21549/12_2024/6w5v_21549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5v_21549/12_2024/6w5v_21549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5v_21549/12_2024/6w5v_21549.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5v_21549/12_2024/6w5v_21549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5v_21549/12_2024/6w5v_21549.cif" } resolution = 4.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6688 atoms to isotropic. 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 78 5.16 5 C 6855 2.51 5 N 1665 2.21 5 O 1988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10586 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9189 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1022 Classifications: {'peptide': 132} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 118} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {'CLR': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.43, per 1000 atoms: 0.61 Number of scatterers: 10586 At special positions: 0 Unit cell: (135.908, 95.804, 153.732, 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 78 16.00 O 1988 8.00 N 1665 7.00 C 6855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.06 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.06 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.04 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.02 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 99 " distance=2.02 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 BETA1-3 " NAG C 2 " - " BMA C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1413 " - " ASN A 961 " " NAG A1414 " - " ASN A 968 " " NAG A1415 " - " ASN A1064 " " NAG A1418 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG E 1 " - " ASN A 931 " " NAG F 1 " - " ASN A 222 " " NAG G 1 " - " ASN D 58 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.4 seconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2450 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 53.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.896A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 185 through 195 removed outlier: 4.246A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 268 through 295 removed outlier: 4.170A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 348 removed outlier: 4.159A pdb=" N GLU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.536A pdb=" N ASN A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.759A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.570A pdb=" N VAL A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 546' Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 574 through 594 Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.530A pdb=" N ASP A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 639 Processing helix chain 'A' and resid 653 through 679 Processing helix chain 'A' and resid 685 through 711 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 720 through 750 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 754 through 791 removed outlier: 4.104A pdb=" N SER A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 833 through 852 removed outlier: 3.743A pdb=" N ILE A 837 " --> pdb=" O TRP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 870 through 883 removed outlier: 3.976A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 941 through 951 removed outlier: 3.829A pdb=" N ASP A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.484A pdb=" N MET A 996 " --> pdb=" O GLY A 992 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1047 through 1069 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1093 through 1117 Processing helix chain 'A' and resid 1120 through 1146 Processing helix chain 'A' and resid 1150 through 1177 removed outlier: 3.889A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 removed outlier: 4.153A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1219 through 1242 removed outlier: 4.645A pdb=" N PHE A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1252 Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.747A pdb=" N LYS D 94 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY D 96 " --> pdb=" O CYS D 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 129 removed outlier: 6.145A pdb=" N GLU A 143 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR A 126 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 141 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N THR A 139 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 206 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 405 Processing sheet with id=AA3, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA6, first strand: chain 'A' and resid 1036 through 1043 removed outlier: 3.661A pdb=" N THR A1036 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1038 " --> pdb=" O PHE A 891 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 959 Processing sheet with id=AA8, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.185A pdb=" N LEU D 49 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.565A pdb=" N LEU D 130 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS D 140 " --> pdb=" O TRP D 128 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP D 128 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 142 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL D 126 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU D 124 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 125 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 32 through 40 removed outlier: 6.593A pdb=" N THR D 60 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL D 37 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN D 58 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL D 39 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER D 56 " --> pdb=" O VAL D 39 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1506 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: 3.46 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3278 1.35 - 1.48: 2881 1.48 - 1.61: 4596 1.61 - 1.74: 0 1.74 - 1.87: 108 Bond restraints: 10863 Sorted by residual: bond pdb=" CA LEU A 748 " pdb=" C LEU A 748 " ideal model delta sigma weight residual 1.522 1.448 0.075 1.36e-02 5.41e+03 3.02e+01 bond pdb=" CA THR A 777 " pdb=" C THR A 777 " ideal model delta sigma weight residual 1.524 1.574 -0.051 1.26e-02 6.30e+03 1.61e+01 bond pdb=" CA ALA A1017 " pdb=" C ALA A1017 " ideal model delta sigma weight residual 1.522 1.474 0.049 1.37e-02 5.33e+03 1.26e+01 bond pdb=" C PHE A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.334 1.297 0.037 1.11e-02 8.12e+03 1.09e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 10858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 14632 4.69 - 9.38: 158 9.38 - 14.08: 21 14.08 - 18.77: 2 18.77 - 23.46: 1 Bond angle restraints: 14814 Sorted by residual: angle pdb=" N ASP A 551 " pdb=" CA ASP A 551 " pdb=" C ASP A 551 " ideal model delta sigma weight residual 112.72 126.58 -13.86 1.14e+00 7.69e-01 1.48e+02 angle pdb=" N THR A 777 " pdb=" CA THR A 777 " pdb=" C THR A 777 " ideal model delta sigma weight residual 111.14 123.53 -12.39 1.08e+00 8.57e-01 1.32e+02 angle pdb=" N ARG A 789 " pdb=" CA ARG A 789 " pdb=" C ARG A 789 " ideal model delta sigma weight residual 111.28 123.10 -11.82 1.09e+00 8.42e-01 1.18e+02 angle pdb=" C ARG A 372 " pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " ideal model delta sigma weight residual 111.78 135.24 -23.46 2.20e+00 2.07e-01 1.14e+02 angle pdb=" N ILE A1202 " pdb=" CA ILE A1202 " pdb=" C ILE A1202 " ideal model delta sigma weight residual 110.72 121.40 -10.68 1.01e+00 9.80e-01 1.12e+02 ... (remaining 14809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.61: 6304 26.61 - 53.23: 418 53.23 - 79.84: 96 79.84 - 106.46: 27 106.46 - 133.07: 18 Dihedral angle restraints: 6863 sinusoidal: 3056 harmonic: 3807 Sorted by residual: dihedral pdb=" C ARG A 372 " pdb=" N ARG A 372 " pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " ideal model delta harmonic sigma weight residual -122.60 -147.37 24.77 0 2.50e+00 1.60e-01 9.82e+01 dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 4.05 88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS D 42 " pdb=" SG CYS D 42 " pdb=" SG CYS D 47 " pdb=" CB CYS D 47 " ideal model delta sinusoidal sigma weight residual 93.00 6.57 86.43 1 1.00e+01 1.00e-02 9.00e+01 ... (remaining 6860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.912: 1732 0.912 - 1.824: 1 1.824 - 2.736: 1 2.736 - 3.648: 0 3.648 - 4.560: 2 Chirality restraints: 1736 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.16 -4.56 2.00e-02 2.50e+03 5.20e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 1.94 -4.34 2.00e-02 2.50e+03 4.72e+04 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-02 2.50e+03 1.59e+03 ... (remaining 1733 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.340 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG F 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.283 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG E 2 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.016 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.411 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 58 " 0.226 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" CG ASN D 58 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN D 58 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN D 58 " -0.368 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.269 2.00e-02 2.50e+03 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 118 2.56 - 3.15: 9925 3.15 - 3.73: 16431 3.73 - 4.32: 22610 4.32 - 4.90: 36246 Nonbonded interactions: 85330 Sorted by model distance: nonbonded pdb=" OG SER A 741 " pdb=" CD1 ILE A1109 " model vdw 1.979 3.460 nonbonded pdb=" O3 NAG B 2 " pdb=" O7 NAG B 2 " model vdw 2.053 3.040 nonbonded pdb=" N TYR A 129 " pdb=" O LYS A 138 " model vdw 2.056 3.120 nonbonded pdb=" O ASP A 501 " pdb=" O PHE A 504 " model vdw 2.074 3.040 nonbonded pdb=" OG SER A 849 " pdb=" O VAL A1136 " model vdw 2.101 3.040 ... (remaining 85325 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 26.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.008 0.075 10863 Z= 0.508 Angle : 1.372 23.460 14814 Z= 0.844 Chirality : 0.184 4.560 1736 Planarity : 0.012 0.287 1851 Dihedral : 19.775 133.072 4359 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 62.54 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.02 % Favored : 92.29 % Rotamer: Outliers : 9.99 % Allowed : 11.66 % Favored : 78.35 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.21 (0.22), residues: 1297 helix: -0.45 (0.21), residues: 594 sheet: -1.27 (0.43), residues: 133 loop : -2.65 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP D 128 HIS 0.008 0.002 HIS A 497 PHE 0.036 0.003 PHE A 503 TYR 0.025 0.002 TYR A 35 ARG 0.011 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 335 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7664 (tpt-90) cc_final: 0.7410 (mmm160) REVERT: A 110 GLU cc_start: 0.7651 (pt0) cc_final: 0.7172 (pt0) REVERT: A 218 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8448 (tp30) REVERT: A 232 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7293 (t70) REVERT: A 233 GLU cc_start: 0.7731 (pt0) cc_final: 0.7238 (mp0) REVERT: A 235 THR cc_start: 0.8580 (m) cc_final: 0.8257 (p) REVERT: A 617 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.7875 (t) REVERT: A 738 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 747 PHE cc_start: 0.8733 (m-10) cc_final: 0.7108 (t80) REVERT: A 754 MET cc_start: 0.7482 (tmm) cc_final: 0.7247 (tmm) REVERT: A 866 MET cc_start: 0.8210 (mmt) cc_final: 0.7541 (ptt) REVERT: A 899 TYR cc_start: 0.7565 (m-80) cc_final: 0.7278 (m-80) REVERT: A 928 GLN cc_start: 0.7856 (tp40) cc_final: 0.7609 (tp-100) REVERT: A 1025 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 1101 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8198 (t0) REVERT: A 1133 MET cc_start: 0.8014 (ttt) cc_final: 0.7617 (ttt) REVERT: A 1137 ASN cc_start: 0.9000 (m-40) cc_final: 0.8776 (m110) REVERT: A 1138 MET cc_start: 0.8978 (tpt) cc_final: 0.8770 (tpp) REVERT: A 1173 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8171 (tpp80) REVERT: A 1194 MET cc_start: 0.8637 (tpp) cc_final: 0.8411 (mmt) REVERT: A 1218 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7603 (t) REVERT: A 1251 ILE cc_start: 0.8565 (mm) cc_final: 0.8339 (tt) REVERT: D 36 GLU cc_start: 0.6167 (tt0) cc_final: 0.5267 (tm-30) REVERT: D 56 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8851 (p) REVERT: D 64 ASN cc_start: 0.9133 (t0) cc_final: 0.8808 (m-40) REVERT: D 116 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7443 (ttpt) REVERT: D 129 GLN cc_start: 0.8006 (mt0) cc_final: 0.6890 (mt0) REVERT: D 131 GLN cc_start: 0.4672 (OUTLIER) cc_final: 0.4067 (mt0) REVERT: D 146 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7488 (pm20) outliers start: 114 outliers final: 28 residues processed: 398 average time/residue: 0.2246 time to fit residues: 125.8195 Evaluate side-chains 248 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1101 ASN Chi-restraints excluded: chain A residue 1173 ARG Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 41 ASN A 86 ASN A 92 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A 614 ASN A 641 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS A 988 GLN A1046 GLN A1170 HIS D 53 GLN D 66 GLN D 150 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10863 Z= 0.277 Angle : 0.945 11.858 14814 Z= 0.454 Chirality : 0.054 0.463 1736 Planarity : 0.006 0.047 1851 Dihedral : 14.919 103.565 2109 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.61 % Allowed : 19.19 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.29 (0.22), residues: 1297 helix: 0.21 (0.20), residues: 608 sheet: -1.17 (0.42), residues: 138 loop : -1.98 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 141 HIS 0.008 0.002 HIS D 75 PHE 0.020 0.002 PHE A1243 TYR 0.021 0.002 TYR A1225 ARG 0.007 0.001 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7704 (tpt-90) cc_final: 0.7400 (mmm160) REVERT: A 147 TYR cc_start: 0.6733 (m-80) cc_final: 0.6161 (m-80) REVERT: A 217 MET cc_start: 0.5654 (mtm) cc_final: 0.4399 (mtm) REVERT: A 232 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7218 (t70) REVERT: A 233 GLU cc_start: 0.7794 (pt0) cc_final: 0.7160 (mp0) REVERT: A 235 THR cc_start: 0.8649 (m) cc_final: 0.8423 (p) REVERT: A 754 MET cc_start: 0.7925 (tmm) cc_final: 0.7423 (tmm) REVERT: A 789 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.6066 (ptp-170) REVERT: A 899 TYR cc_start: 0.7421 (m-80) cc_final: 0.6995 (m-80) REVERT: A 921 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8414 (tp-100) REVERT: A 1133 MET cc_start: 0.7632 (ttt) cc_final: 0.7407 (ttt) REVERT: A 1161 CYS cc_start: 0.8357 (p) cc_final: 0.8047 (p) REVERT: A 1173 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8235 (tpp80) REVERT: A 1251 ILE cc_start: 0.8682 (mm) cc_final: 0.8260 (tt) REVERT: D 36 GLU cc_start: 0.6896 (tt0) cc_final: 0.6102 (tp30) REVERT: D 64 ASN cc_start: 0.9186 (t0) cc_final: 0.8797 (m110) REVERT: D 75 HIS cc_start: 0.7839 (m-70) cc_final: 0.7243 (m-70) REVERT: D 146 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7348 (tm-30) outliers start: 64 outliers final: 28 residues processed: 310 average time/residue: 0.1937 time to fit residues: 88.6462 Evaluate side-chains 237 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 118 optimal weight: 0.0970 chunk 127 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 94 optimal weight: 0.0370 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10863 Z= 0.211 Angle : 0.832 11.694 14814 Z= 0.392 Chirality : 0.049 0.308 1736 Planarity : 0.005 0.044 1851 Dihedral : 12.100 99.547 2057 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.38 % Allowed : 23.31 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.82 (0.23), residues: 1297 helix: 0.54 (0.20), residues: 613 sheet: -0.85 (0.40), residues: 149 loop : -1.72 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 141 HIS 0.004 0.001 HIS A 398 PHE 0.023 0.002 PHE A 503 TYR 0.027 0.002 TYR A1225 ARG 0.005 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.7398 (mmm160) REVERT: A 217 MET cc_start: 0.5719 (mtm) cc_final: 0.5517 (mtm) REVERT: A 232 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7245 (t70) REVERT: A 233 GLU cc_start: 0.7832 (pt0) cc_final: 0.7122 (mp0) REVERT: A 235 THR cc_start: 0.8570 (m) cc_final: 0.8237 (p) REVERT: A 754 MET cc_start: 0.7758 (tmm) cc_final: 0.7103 (tmm) REVERT: A 789 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.5872 (tmt-80) REVERT: A 899 TYR cc_start: 0.7339 (m-80) cc_final: 0.6718 (m-80) REVERT: A 921 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8247 (tp-100) REVERT: A 1122 TRP cc_start: 0.6208 (m-10) cc_final: 0.5850 (m100) REVERT: A 1173 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8181 (tpp80) REVERT: D 36 GLU cc_start: 0.7090 (tt0) cc_final: 0.6818 (tp30) REVERT: D 64 ASN cc_start: 0.9335 (t0) cc_final: 0.8840 (m110) REVERT: D 75 HIS cc_start: 0.8095 (m-70) cc_final: 0.7883 (m90) REVERT: D 104 ASP cc_start: 0.9025 (m-30) cc_final: 0.8424 (p0) REVERT: D 146 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: D 147 ILE cc_start: 0.8325 (mt) cc_final: 0.7746 (mt) outliers start: 50 outliers final: 27 residues processed: 266 average time/residue: 0.1963 time to fit residues: 77.6270 Evaluate side-chains 228 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10863 Z= 0.238 Angle : 0.812 12.055 14814 Z= 0.383 Chirality : 0.048 0.289 1736 Planarity : 0.005 0.042 1851 Dihedral : 10.810 96.128 2048 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.08 % Allowed : 24.10 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -0.55 (0.23), residues: 1297 helix: 0.75 (0.21), residues: 619 sheet: -0.69 (0.40), residues: 149 loop : -1.61 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 141 HIS 0.006 0.001 HIS A1042 PHE 0.019 0.002 PHE A 769 TYR 0.024 0.002 TYR D 109 ARG 0.004 0.001 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7708 (tpt-90) cc_final: 0.7365 (mmm160) REVERT: A 233 GLU cc_start: 0.7853 (pt0) cc_final: 0.7051 (mp0) REVERT: A 235 THR cc_start: 0.8569 (m) cc_final: 0.8321 (p) REVERT: A 754 MET cc_start: 0.7897 (tmm) cc_final: 0.7158 (tmm) REVERT: A 789 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5885 (tmt170) REVERT: A 899 TYR cc_start: 0.7314 (m-80) cc_final: 0.6724 (m-80) REVERT: A 921 GLN cc_start: 0.8744 (tp-100) cc_final: 0.8375 (tp-100) REVERT: A 1102 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 1122 TRP cc_start: 0.6227 (m-10) cc_final: 0.5761 (m100) REVERT: A 1173 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8149 (tpp80) REVERT: D 36 GLU cc_start: 0.7076 (tt0) cc_final: 0.6741 (tp30) REVERT: D 64 ASN cc_start: 0.9270 (t0) cc_final: 0.8861 (m110) REVERT: D 75 HIS cc_start: 0.8012 (m-70) cc_final: 0.7748 (m90) REVERT: D 104 ASP cc_start: 0.9036 (m-30) cc_final: 0.8442 (p0) REVERT: D 111 ASN cc_start: 0.4738 (OUTLIER) cc_final: 0.4426 (t0) REVERT: D 146 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7334 (tm-30) outliers start: 58 outliers final: 38 residues processed: 246 average time/residue: 0.1836 time to fit residues: 68.6736 Evaluate side-chains 232 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 0.1980 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10863 Z= 0.203 Angle : 0.788 11.404 14814 Z= 0.368 Chirality : 0.047 0.287 1736 Planarity : 0.004 0.043 1851 Dihedral : 9.962 92.081 2046 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.56 % Allowed : 25.42 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 (0.23), residues: 1297 helix: 0.81 (0.21), residues: 622 sheet: -0.69 (0.40), residues: 150 loop : -1.51 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 141 HIS 0.006 0.001 HIS A1042 PHE 0.018 0.001 PHE A 632 TYR 0.020 0.001 TYR A1225 ARG 0.003 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7677 (tpt-90) cc_final: 0.7348 (mmm160) REVERT: A 233 GLU cc_start: 0.7820 (pt0) cc_final: 0.7061 (mp0) REVERT: A 604 THR cc_start: 0.8424 (t) cc_final: 0.8195 (m) REVERT: A 754 MET cc_start: 0.7816 (tmm) cc_final: 0.7057 (tmm) REVERT: A 789 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.5518 (ptt180) REVERT: A 1001 MET cc_start: 0.8744 (mtm) cc_final: 0.7586 (mtm) REVERT: A 1102 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8528 (mm) REVERT: A 1122 TRP cc_start: 0.6213 (m-10) cc_final: 0.5812 (m100) REVERT: A 1173 ARG cc_start: 0.8483 (tpp80) cc_final: 0.8180 (tpp80) REVERT: A 1229 TYR cc_start: 0.7902 (m-10) cc_final: 0.7309 (m-10) REVERT: A 1232 MET cc_start: 0.8071 (ptt) cc_final: 0.7702 (tmm) REVERT: D 36 GLU cc_start: 0.7172 (tt0) cc_final: 0.6747 (tp30) REVERT: D 55 TYR cc_start: 0.6728 (m-80) cc_final: 0.6183 (m-80) REVERT: D 64 ASN cc_start: 0.9199 (t0) cc_final: 0.8842 (m110) REVERT: D 75 HIS cc_start: 0.7974 (m-70) cc_final: 0.7721 (m90) REVERT: D 104 ASP cc_start: 0.9005 (m-30) cc_final: 0.8435 (p0) REVERT: D 112 LYS cc_start: 0.8294 (tptt) cc_final: 0.7860 (mmtm) REVERT: D 146 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7616 (tm-30) outliers start: 52 outliers final: 39 residues processed: 256 average time/residue: 0.1858 time to fit residues: 72.4134 Evaluate side-chains 241 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10863 Z= 0.330 Angle : 0.816 11.374 14814 Z= 0.394 Chirality : 0.048 0.300 1736 Planarity : 0.005 0.042 1851 Dihedral : 9.833 89.084 2046 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.70 % Allowed : 26.99 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -0.44 (0.23), residues: 1297 helix: 0.74 (0.21), residues: 620 sheet: -0.64 (0.42), residues: 150 loop : -1.39 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 141 HIS 0.006 0.001 HIS A1042 PHE 0.024 0.002 PHE A 632 TYR 0.024 0.002 TYR A1225 ARG 0.005 0.001 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7885 (tpt-90) cc_final: 0.7496 (mmm160) REVERT: A 233 GLU cc_start: 0.7963 (pt0) cc_final: 0.7008 (mp0) REVERT: A 754 MET cc_start: 0.7983 (tmm) cc_final: 0.7121 (tmm) REVERT: A 789 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.5356 (ptm160) REVERT: A 1102 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 1122 TRP cc_start: 0.6210 (OUTLIER) cc_final: 0.5649 (m100) REVERT: A 1173 ARG cc_start: 0.8475 (tpp80) cc_final: 0.8239 (tpp80) REVERT: D 36 GLU cc_start: 0.7106 (tt0) cc_final: 0.6063 (tp30) REVERT: D 55 TYR cc_start: 0.6826 (m-80) cc_final: 0.6569 (m-80) REVERT: D 64 ASN cc_start: 0.9259 (t0) cc_final: 0.8927 (m110) REVERT: D 146 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7776 (tm-30) outliers start: 65 outliers final: 53 residues processed: 238 average time/residue: 0.1992 time to fit residues: 71.6491 Evaluate side-chains 245 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10863 Z= 0.207 Angle : 0.789 13.985 14814 Z= 0.372 Chirality : 0.047 0.294 1736 Planarity : 0.004 0.041 1851 Dihedral : 9.435 84.218 2046 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.91 % Allowed : 28.75 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 (0.24), residues: 1297 helix: 0.81 (0.21), residues: 622 sheet: -0.31 (0.43), residues: 146 loop : -1.39 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1143 HIS 0.005 0.001 HIS A1042 PHE 0.018 0.001 PHE A 632 TYR 0.019 0.002 TYR A 146 ARG 0.003 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7695 (mmm-85) REVERT: A 193 MET cc_start: 0.9193 (tpp) cc_final: 0.8959 (tpp) REVERT: A 233 GLU cc_start: 0.7976 (pt0) cc_final: 0.6947 (mp0) REVERT: A 268 MET cc_start: 0.8779 (tpp) cc_final: 0.8475 (tpp) REVERT: A 604 THR cc_start: 0.8437 (t) cc_final: 0.8180 (m) REVERT: A 631 MET cc_start: 0.8319 (mmm) cc_final: 0.8043 (mmt) REVERT: A 754 MET cc_start: 0.7887 (tmm) cc_final: 0.7005 (tmm) REVERT: A 789 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.5215 (ptp-170) REVERT: A 1102 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 1122 TRP cc_start: 0.6157 (m-10) cc_final: 0.5917 (m100) REVERT: A 1173 ARG cc_start: 0.8356 (tpp80) cc_final: 0.8114 (tpp80) REVERT: D 36 GLU cc_start: 0.7301 (tt0) cc_final: 0.6724 (tp30) REVERT: D 55 TYR cc_start: 0.6782 (m-80) cc_final: 0.6479 (m-80) REVERT: D 64 ASN cc_start: 0.9261 (t0) cc_final: 0.8925 (m110) REVERT: D 75 HIS cc_start: 0.7855 (m90) cc_final: 0.7545 (m90) outliers start: 56 outliers final: 46 residues processed: 250 average time/residue: 0.1854 time to fit residues: 71.0762 Evaluate side-chains 238 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 136 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.0670 chunk 98 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10863 Z= 0.350 Angle : 0.825 12.428 14814 Z= 0.402 Chirality : 0.048 0.319 1736 Planarity : 0.005 0.039 1851 Dihedral : 9.440 82.532 2043 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.26 % Allowed : 28.31 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.56 (0.23), residues: 1297 helix: 0.61 (0.21), residues: 623 sheet: -0.53 (0.43), residues: 146 loop : -1.49 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1143 HIS 0.004 0.001 HIS A 497 PHE 0.025 0.002 PHE A 587 TYR 0.023 0.002 TYR A1225 ARG 0.006 0.001 ARG A1227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8094 (tpt-90) cc_final: 0.7789 (mmm-85) REVERT: A 268 MET cc_start: 0.8793 (tpp) cc_final: 0.8557 (tpp) REVERT: A 604 THR cc_start: 0.8488 (t) cc_final: 0.8254 (m) REVERT: A 631 MET cc_start: 0.8270 (mmm) cc_final: 0.8035 (mmt) REVERT: A 754 MET cc_start: 0.8063 (tmm) cc_final: 0.7139 (tmm) REVERT: A 789 ARG cc_start: 0.5784 (OUTLIER) cc_final: 0.5215 (ptm160) REVERT: A 1102 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8575 (mm) REVERT: A 1173 ARG cc_start: 0.8395 (tpp80) cc_final: 0.8177 (tpp80) REVERT: D 36 GLU cc_start: 0.7223 (tt0) cc_final: 0.7003 (tp30) REVERT: D 55 TYR cc_start: 0.6881 (m-80) cc_final: 0.6637 (m-80) REVERT: D 64 ASN cc_start: 0.9200 (t0) cc_final: 0.8882 (m110) REVERT: D 75 HIS cc_start: 0.7864 (m90) cc_final: 0.7562 (m90) outliers start: 60 outliers final: 51 residues processed: 230 average time/residue: 0.1875 time to fit residues: 65.2558 Evaluate side-chains 228 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 136 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 120 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 123 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 HIS ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10863 Z= 0.191 Angle : 0.800 13.685 14814 Z= 0.378 Chirality : 0.047 0.301 1736 Planarity : 0.004 0.050 1851 Dihedral : 9.015 75.570 2043 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.03 % Allowed : 29.36 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.43 (0.24), residues: 1297 helix: 0.69 (0.21), residues: 624 sheet: -0.33 (0.43), residues: 143 loop : -1.41 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1143 HIS 0.005 0.001 HIS A 497 PHE 0.022 0.001 PHE A 632 TYR 0.029 0.002 TYR A 628 ARG 0.003 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 THR cc_start: 0.8439 (t) cc_final: 0.8152 (m) REVERT: A 754 MET cc_start: 0.7930 (tmm) cc_final: 0.6979 (tmm) REVERT: A 789 ARG cc_start: 0.5494 (OUTLIER) cc_final: 0.5027 (ptp-170) REVERT: A 921 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8381 (tp-100) REVERT: A 1102 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 1142 MET cc_start: 0.7538 (mtm) cc_final: 0.7225 (mtp) REVERT: A 1160 SER cc_start: 0.9249 (m) cc_final: 0.8932 (m) REVERT: A 1194 MET cc_start: 0.8773 (mmm) cc_final: 0.8074 (tpt) REVERT: A 1223 ILE cc_start: 0.8605 (mt) cc_final: 0.8302 (mt) REVERT: D 36 GLU cc_start: 0.7319 (tt0) cc_final: 0.6385 (tp30) REVERT: D 55 TYR cc_start: 0.6681 (m-80) cc_final: 0.6399 (m-80) REVERT: D 64 ASN cc_start: 0.9178 (t0) cc_final: 0.8872 (m-40) REVERT: D 75 HIS cc_start: 0.7813 (m90) cc_final: 0.7538 (m90) REVERT: D 141 TRP cc_start: 0.6430 (p-90) cc_final: 0.5142 (p-90) REVERT: D 143 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7883 (mt) outliers start: 46 outliers final: 37 residues processed: 244 average time/residue: 0.2002 time to fit residues: 72.7813 Evaluate side-chains 240 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 143 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10863 Z= 0.204 Angle : 0.802 13.336 14814 Z= 0.382 Chirality : 0.047 0.305 1736 Planarity : 0.004 0.054 1851 Dihedral : 8.823 73.142 2043 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.86 % Allowed : 29.89 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.39 (0.24), residues: 1297 helix: 0.63 (0.21), residues: 625 sheet: -0.15 (0.44), residues: 146 loop : -1.34 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1143 HIS 0.005 0.001 HIS A 497 PHE 0.021 0.001 PHE A 632 TYR 0.024 0.002 TYR D 109 ARG 0.003 0.000 ARG A 978 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8227 (pt0) cc_final: 0.7975 (pt0) REVERT: A 268 MET cc_start: 0.8576 (tpp) cc_final: 0.8346 (tpp) REVERT: A 604 THR cc_start: 0.8439 (t) cc_final: 0.8213 (m) REVERT: A 754 MET cc_start: 0.7900 (tmm) cc_final: 0.6926 (tmm) REVERT: A 1102 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8472 (mm) REVERT: A 1194 MET cc_start: 0.8764 (mmm) cc_final: 0.8144 (tpt) REVERT: A 1219 GLN cc_start: 0.8149 (mt0) cc_final: 0.7875 (mt0) REVERT: A 1223 ILE cc_start: 0.8550 (mt) cc_final: 0.8281 (mt) REVERT: D 36 GLU cc_start: 0.7313 (tt0) cc_final: 0.6576 (tm-30) REVERT: D 55 TYR cc_start: 0.6696 (m-80) cc_final: 0.6422 (m-80) REVERT: D 64 ASN cc_start: 0.9187 (t0) cc_final: 0.8912 (m-40) REVERT: D 75 HIS cc_start: 0.7727 (m90) cc_final: 0.7432 (m90) REVERT: D 141 TRP cc_start: 0.6522 (p-90) cc_final: 0.5288 (p-90) REVERT: D 143 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7910 (mt) outliers start: 44 outliers final: 37 residues processed: 237 average time/residue: 0.1793 time to fit residues: 65.3136 Evaluate side-chains 237 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 899 TYR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 143 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.077206 restraints weight = 32622.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.079425 restraints weight = 17676.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.080846 restraints weight = 11838.567| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10863 Z= 0.229 Angle : 0.795 12.981 14814 Z= 0.384 Chirality : 0.046 0.306 1736 Planarity : 0.004 0.039 1851 Dihedral : 8.589 69.806 2039 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.77 % Allowed : 30.15 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.36 (0.24), residues: 1297 helix: 0.66 (0.21), residues: 625 sheet: -0.24 (0.43), residues: 144 loop : -1.30 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1143 HIS 0.005 0.001 HIS A 497 PHE 0.022 0.001 PHE A 632 TYR 0.022 0.002 TYR A1225 ARG 0.004 0.000 ARG A1173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.52 seconds wall clock time: 42 minutes 39.80 seconds (2559.80 seconds total)