Starting phenix.real_space_refine on Fri Mar 6 01:54:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uza_26884/03_2026/7uza_26884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uza_26884/03_2026/7uza_26884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uza_26884/03_2026/7uza_26884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uza_26884/03_2026/7uza_26884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uza_26884/03_2026/7uza_26884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uza_26884/03_2026/7uza_26884.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17180 2.51 5 N 4438 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26992 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "D" 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: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.20, per 1000 atoms: 0.23 Number of scatterers: 26992 At special positions: 0 Unit cell: (158.912, 164.736, 196.352, 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 120 16.00 O 5254 8.00 N 4438 7.00 C 17180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6372 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 56 sheets defined 22.9% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.676A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.615A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.501A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.691A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.204A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.020A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.782A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.923A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.586A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.630A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.658A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.216A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.140A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.913A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.153A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.810A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.866A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.363A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 86 removed outlier: 3.924A pdb=" N THR H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.030A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.256A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.738A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.128A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.998A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 14.677A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 14.644A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.224A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.548A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.122A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.693A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.703A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.496A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.331A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.354A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.562A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.001A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.479A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 90 through 94 removed outlier: 5.885A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AC5, first strand: chain 'B' and resid 116 through 121 removed outlier: 5.577A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TRP B 152 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 121 removed outlier: 7.251A pdb=" N LEU B 244 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N TYR B 145 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.341A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.709A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.717A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.571A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 727 removed outlier: 6.688A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 727 Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.928A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.309A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.019A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.736A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.119A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 144 through 146 removed outlier: 3.544A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.433A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.759A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.386A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.634A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 6.781A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.581A pdb=" N GLN H 5 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS H 24 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.050A pdb=" N MET H 39 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY H 54 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TRP H 41 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TRP H 52 " --> pdb=" O TRP H 41 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS H 43 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU H 50 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG H 45 " --> pdb=" O GLN H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.674A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE L 21 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS L 23 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 11 through 12 removed outlier: 7.116A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'L' and resid 51 through 54 removed outlier: 6.642A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR L 103 " --> pdb=" O TYR L 42 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2838 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: 6.74 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8509 1.34 - 1.46: 5878 1.46 - 1.58: 13083 1.58 - 1.70: 0 1.70 - 1.82: 155 Bond restraints: 27625 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.509 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" N VAL C 705 " pdb=" CA VAL C 705 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.27e-02 6.20e+03 7.74e+00 bond pdb=" N GLU C1072 " pdb=" CA GLU C1072 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.21e-02 6.83e+03 6.55e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 27620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 36770 1.82 - 3.63: 777 3.63 - 5.45: 66 5.45 - 7.26: 12 7.26 - 9.08: 6 Bond angle restraints: 37631 Sorted by residual: angle pdb=" C ASN C1074 " pdb=" CA ASN C1074 " pdb=" CB ASN C1074 " ideal model delta sigma weight residual 109.48 116.83 -7.35 1.68e+00 3.54e-01 1.91e+01 angle pdb=" C ALA L 9 " pdb=" CA ALA L 9 " pdb=" CB ALA L 9 " ideal model delta sigma weight residual 116.34 110.89 5.45 1.40e+00 5.10e-01 1.52e+01 angle pdb=" C SER A1030 " pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta sigma weight residual 122.67 116.61 6.06 1.59e+00 3.96e-01 1.45e+01 angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 111.36 115.10 -3.74 1.17e+00 7.31e-01 1.02e+01 angle pdb=" N ASP L 114 " pdb=" CA ASP L 114 " pdb=" C ASP L 114 " ideal model delta sigma weight residual 109.81 116.51 -6.70 2.21e+00 2.05e-01 9.18e+00 ... (remaining 37626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 16061 24.32 - 48.65: 717 48.65 - 72.97: 83 72.97 - 97.30: 18 97.30 - 121.62: 20 Dihedral angle restraints: 16899 sinusoidal: 6979 harmonic: 9920 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.21 64.21 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 141.58 -48.58 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.63 46.63 1 1.00e+01 1.00e-02 3.01e+01 ... (remaining 16896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4161 0.099 - 0.199: 190 0.199 - 0.298: 7 0.298 - 0.397: 2 0.397 - 0.496: 1 Chirality restraints: 4361 Sorted by residual: chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 4358 not shown) Planarity restraints: 4869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " 0.205 2.00e-02 2.50e+03 1.70e-01 3.61e+02 pdb=" C7 NAG C1308 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " -0.277 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " -0.006 2.00e-02 2.50e+03 3.30e-02 1.36e+01 pdb=" CG ASN C 801 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 41 " 0.016 2.00e-02 2.50e+03 1.63e-02 6.65e+00 pdb=" CG TRP L 41 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP L 41 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 41 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 41 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 41 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 41 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 41 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP L 41 " -0.005 2.00e-02 2.50e+03 ... (remaining 4866 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 650 2.69 - 3.24: 27182 3.24 - 3.80: 43547 3.80 - 4.35: 57861 4.35 - 4.90: 95394 Nonbonded interactions: 224634 Sorted by model distance: nonbonded pdb=" OD1 ASP A 568 " pdb=" N ILE A 569 " model vdw 2.139 3.120 nonbonded pdb=" OE1 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.170 3.040 nonbonded pdb=" O GLU C 780 " pdb=" NE2 GLN C 784 " model vdw 2.193 3.120 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN C 801 " pdb=" ND2 ASN C 928 " model vdw 2.201 3.120 ... (remaining 224629 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 'A' selection = chain 'B' selection = (chain 'C' and resid 26 through 1311) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 26.520 Find NCS groups from input model: 0.470 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 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 : 0.004 0.103 27701 Z= 0.199 Angle : 0.648 12.535 37821 Z= 0.341 Chirality : 0.046 0.496 4361 Planarity : 0.004 0.170 4833 Dihedral : 13.777 121.624 10413 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3369 helix: 1.38 (0.19), residues: 673 sheet: 0.00 (0.19), residues: 710 loop : -0.64 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 84 TYR 0.021 0.002 TYR C1138 PHE 0.029 0.002 PHE C 802 TRP 0.041 0.002 TRP L 41 HIS 0.006 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00409 (27625) covalent geometry : angle 0.62440 (37631) SS BOND : bond 0.00242 ( 38) SS BOND : angle 1.00754 ( 76) hydrogen bonds : bond 0.21396 ( 1004) hydrogen bonds : angle 9.16299 ( 2838) link_BETA1-4 : bond 0.00121 ( 2) link_BETA1-4 : angle 0.85690 ( 6) link_NAG-ASN : bond 0.00582 ( 36) link_NAG-ASN : angle 3.23368 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8408 (pp30) cc_final: 0.8022 (pp30) REVERT: A 351 TYR cc_start: 0.8347 (p90) cc_final: 0.7914 (p90) REVERT: A 584 ILE cc_start: 0.8987 (mm) cc_final: 0.8559 (tp) REVERT: A 663 ASP cc_start: 0.8009 (m-30) cc_final: 0.7411 (m-30) REVERT: B 106 PHE cc_start: 0.6849 (p90) cc_final: 0.6599 (p90) REVERT: B 229 LEU cc_start: 0.8528 (mt) cc_final: 0.8196 (tp) REVERT: B 313 TYR cc_start: 0.7685 (m-80) cc_final: 0.7316 (m-80) REVERT: B 420 ASP cc_start: 0.8199 (t70) cc_final: 0.7771 (t0) REVERT: B 501 ASN cc_start: 0.8262 (m110) cc_final: 0.7928 (m-40) REVERT: B 697 MET cc_start: 0.7325 (ptm) cc_final: 0.7066 (ptm) REVERT: B 900 MET cc_start: 0.6906 (mtm) cc_final: 0.6595 (mtp) REVERT: B 1141 LEU cc_start: 0.8652 (mm) cc_final: 0.8317 (tp) REVERT: H 40 HIS cc_start: 0.9306 (m170) cc_final: 0.8987 (m170) REVERT: H 51 GLU cc_start: 0.8448 (pp20) cc_final: 0.7894 (pp20) REVERT: H 88 TYR cc_start: 0.8881 (m-80) cc_final: 0.8140 (m-80) REVERT: H 89 MET cc_start: 0.7326 (ppp) cc_final: 0.7098 (ppp) REVERT: H 113 ASP cc_start: 0.7780 (m-30) cc_final: 0.7168 (m-30) REVERT: L 24 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.7908 (ttm110) REVERT: L 85 THR cc_start: 0.8694 (t) cc_final: 0.8124 (t) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.1579 time to fit residues: 82.9057 Evaluate side-chains 241 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 218 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 907 ASN B 913 GLN C 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 969 ASN H 59 ASN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.160619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100240 restraints weight = 47735.837| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.76 r_work: 0.3362 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27701 Z= 0.191 Angle : 0.653 11.869 37821 Z= 0.325 Chirality : 0.048 0.483 4361 Planarity : 0.004 0.042 4833 Dihedral : 9.193 113.343 4455 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.72 % Allowed : 6.39 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3369 helix: 1.25 (0.19), residues: 698 sheet: -0.02 (0.19), residues: 753 loop : -0.67 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.025 0.002 TYR C1067 PHE 0.027 0.002 PHE A 168 TRP 0.030 0.002 TRP L 41 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00436 (27625) covalent geometry : angle 0.62999 (37631) SS BOND : bond 0.00385 ( 38) SS BOND : angle 1.21263 ( 76) hydrogen bonds : bond 0.04974 ( 1004) hydrogen bonds : angle 6.97055 ( 2838) link_BETA1-4 : bond 0.00200 ( 2) link_BETA1-4 : angle 0.80336 ( 6) link_NAG-ASN : bond 0.00572 ( 36) link_NAG-ASN : angle 3.14426 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 266 time to evaluate : 0.993 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 52 GLN cc_start: 0.8532 (pp30) cc_final: 0.8032 (pp30) REVERT: A 86 PHE cc_start: 0.4430 (t80) cc_final: 0.4128 (t80) REVERT: A 160 TYR cc_start: 0.7649 (p90) cc_final: 0.7324 (p90) REVERT: A 351 TYR cc_start: 0.8307 (p90) cc_final: 0.7885 (p90) REVERT: A 400 PHE cc_start: 0.7558 (p90) cc_final: 0.7347 (p90) REVERT: B 55 PHE cc_start: 0.7254 (m-10) cc_final: 0.6496 (m-10) REVERT: B 313 TYR cc_start: 0.7848 (m-80) cc_final: 0.7418 (m-80) REVERT: B 501 ASN cc_start: 0.8295 (m110) cc_final: 0.7896 (m110) REVERT: B 571 ASP cc_start: 0.7330 (m-30) cc_final: 0.7006 (t0) REVERT: B 697 MET cc_start: 0.7612 (ptm) cc_final: 0.7235 (ptm) REVERT: B 740 MET cc_start: 0.8850 (tpp) cc_final: 0.8648 (tpt) REVERT: B 1141 LEU cc_start: 0.8624 (mm) cc_final: 0.8135 (tp) REVERT: B 1142 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8653 (mm110) REVERT: H 6 GLN cc_start: 0.3826 (mm-40) cc_final: 0.3556 (mm-40) REVERT: H 43 LYS cc_start: 0.4720 (pptt) cc_final: 0.4486 (ptmm) REVERT: H 113 ASP cc_start: 0.7598 (m-30) cc_final: 0.7296 (m-30) REVERT: L 24 ARG cc_start: 0.8486 (ptp-110) cc_final: 0.8279 (ttm110) REVERT: L 51 LYS cc_start: 0.8687 (tppt) cc_final: 0.8317 (tttm) REVERT: L 53 LEU cc_start: 0.7802 (mp) cc_final: 0.7460 (mp) REVERT: L 116 PHE cc_start: 0.8951 (m-80) cc_final: 0.8260 (m-80) outliers start: 21 outliers final: 8 residues processed: 279 average time/residue: 0.1457 time to fit residues: 68.8455 Evaluate side-chains 244 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 226 optimal weight: 2.9990 chunk 4 optimal weight: 0.0020 chunk 154 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 334 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 252 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 259 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 122 ASN B 774 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN H 59 ASN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.161966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102325 restraints weight = 47675.663| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.76 r_work: 0.3390 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27701 Z= 0.137 Angle : 0.597 12.085 37821 Z= 0.294 Chirality : 0.046 0.478 4361 Planarity : 0.004 0.049 4833 Dihedral : 7.939 108.436 4455 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.16 % Allowed : 8.31 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3369 helix: 1.46 (0.19), residues: 699 sheet: -0.15 (0.18), residues: 772 loop : -0.67 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 84 TYR 0.027 0.001 TYR A 91 PHE 0.031 0.002 PHE A 65 TRP 0.033 0.002 TRP L 41 HIS 0.005 0.001 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00305 (27625) covalent geometry : angle 0.57316 (37631) SS BOND : bond 0.00424 ( 38) SS BOND : angle 1.18935 ( 76) hydrogen bonds : bond 0.04372 ( 1004) hydrogen bonds : angle 6.45684 ( 2838) link_BETA1-4 : bond 0.00148 ( 2) link_BETA1-4 : angle 0.88970 ( 6) link_NAG-ASN : bond 0.00570 ( 36) link_NAG-ASN : angle 3.02907 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 1.027 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 52 GLN cc_start: 0.8469 (pp30) cc_final: 0.8002 (pp30) REVERT: A 160 TYR cc_start: 0.7737 (p90) cc_final: 0.7514 (p90) REVERT: A 400 PHE cc_start: 0.7679 (p90) cc_final: 0.7477 (p90) REVERT: A 740 MET cc_start: 0.8012 (tpt) cc_final: 0.7106 (mmt) REVERT: B 55 PHE cc_start: 0.7232 (m-10) cc_final: 0.6625 (m-10) REVERT: B 313 TYR cc_start: 0.7831 (m-80) cc_final: 0.7393 (m-80) REVERT: B 403 ARG cc_start: 0.7094 (ttp80) cc_final: 0.6670 (ttp80) REVERT: B 420 ASP cc_start: 0.8394 (t70) cc_final: 0.8159 (t0) REVERT: B 449 TYR cc_start: 0.7733 (m-80) cc_final: 0.7266 (m-80) REVERT: B 501 ASN cc_start: 0.8258 (m110) cc_final: 0.7848 (m110) REVERT: B 571 ASP cc_start: 0.7236 (m-30) cc_final: 0.6922 (t0) REVERT: B 578 ASP cc_start: 0.8539 (t70) cc_final: 0.8278 (t70) REVERT: B 697 MET cc_start: 0.7581 (ptm) cc_final: 0.7232 (ptm) REVERT: B 1141 LEU cc_start: 0.8605 (mm) cc_final: 0.8137 (tp) REVERT: B 1142 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8809 (mm110) REVERT: H 41 TRP cc_start: 0.6943 (m100) cc_final: 0.6626 (m100) REVERT: H 55 MET cc_start: 0.7299 (tmm) cc_final: 0.7088 (tmm) REVERT: H 67 TYR cc_start: 0.5507 (m-80) cc_final: 0.5211 (m-80) REVERT: H 113 ASP cc_start: 0.7615 (m-30) cc_final: 0.7274 (m-30) REVERT: L 24 ARG cc_start: 0.8631 (ptp-110) cc_final: 0.7654 (mtp-110) REVERT: L 51 LYS cc_start: 0.8784 (tppt) cc_final: 0.8348 (tttm) REVERT: L 53 LEU cc_start: 0.7676 (mp) cc_final: 0.7454 (mp) REVERT: L 118 PHE cc_start: 0.8439 (m-80) cc_final: 0.8091 (m-80) outliers start: 34 outliers final: 20 residues processed: 291 average time/residue: 0.1465 time to fit residues: 72.4312 Evaluate side-chains 253 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 6 optimal weight: 9.9990 chunk 326 optimal weight: 30.0000 chunk 21 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 12 optimal weight: 50.0000 chunk 196 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS B 493 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.162658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.103199 restraints weight = 47372.117| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.76 r_work: 0.3407 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27701 Z= 0.123 Angle : 0.575 11.947 37821 Z= 0.283 Chirality : 0.046 0.479 4361 Planarity : 0.004 0.049 4833 Dihedral : 7.195 107.192 4455 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.26 % Allowed : 10.15 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3369 helix: 1.67 (0.19), residues: 687 sheet: -0.15 (0.18), residues: 752 loop : -0.75 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 84 TYR 0.020 0.001 TYR C 248 PHE 0.038 0.001 PHE A 65 TRP 0.030 0.001 TRP A 353 HIS 0.018 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00277 (27625) covalent geometry : angle 0.55230 (37631) SS BOND : bond 0.00251 ( 38) SS BOND : angle 1.06936 ( 76) hydrogen bonds : bond 0.04025 ( 1004) hydrogen bonds : angle 6.15670 ( 2838) link_BETA1-4 : bond 0.00185 ( 2) link_BETA1-4 : angle 0.95164 ( 6) link_NAG-ASN : bond 0.00551 ( 36) link_NAG-ASN : angle 2.97029 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 1.029 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 52 GLN cc_start: 0.8457 (pp30) cc_final: 0.8095 (pp30) REVERT: A 160 TYR cc_start: 0.7755 (p90) cc_final: 0.7445 (p90) REVERT: A 368 LEU cc_start: 0.8158 (mm) cc_final: 0.7876 (tp) REVERT: A 386 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8451 (mmmt) REVERT: A 740 MET cc_start: 0.7990 (tpt) cc_final: 0.7102 (mmt) REVERT: B 170 TYR cc_start: 0.7967 (t80) cc_final: 0.7695 (t80) REVERT: B 273 ARG cc_start: 0.7286 (mmm-85) cc_final: 0.7014 (mmm-85) REVERT: B 313 TYR cc_start: 0.7882 (m-80) cc_final: 0.7425 (m-80) REVERT: B 420 ASP cc_start: 0.8371 (t70) cc_final: 0.8068 (t0) REVERT: B 449 TYR cc_start: 0.7764 (m-80) cc_final: 0.7298 (m-80) REVERT: B 501 ASN cc_start: 0.8262 (m110) cc_final: 0.7845 (m110) REVERT: B 571 ASP cc_start: 0.7155 (m-30) cc_final: 0.6880 (t0) REVERT: B 578 ASP cc_start: 0.8534 (t70) cc_final: 0.8243 (t70) REVERT: B 697 MET cc_start: 0.7574 (ptm) cc_final: 0.7244 (ptm) REVERT: B 1141 LEU cc_start: 0.8617 (mm) cc_final: 0.8114 (tp) REVERT: B 1142 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8797 (mm110) REVERT: C 318 PHE cc_start: 0.7937 (t80) cc_final: 0.7658 (t80) REVERT: C 987 PRO cc_start: 0.8313 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: H 5 GLN cc_start: 0.7987 (mp10) cc_final: 0.7604 (mp10) REVERT: H 6 GLN cc_start: 0.4369 (mm110) cc_final: 0.3761 (tp40) REVERT: H 41 TRP cc_start: 0.6907 (m100) cc_final: 0.6547 (m100) REVERT: H 113 ASP cc_start: 0.7671 (m-30) cc_final: 0.7287 (m-30) REVERT: L 24 ARG cc_start: 0.8615 (ptp-110) cc_final: 0.7546 (mtp-110) REVERT: L 51 LYS cc_start: 0.8803 (tppt) cc_final: 0.8313 (tttm) REVERT: L 53 LEU cc_start: 0.7662 (mp) cc_final: 0.7440 (mp) REVERT: L 118 PHE cc_start: 0.8425 (m-80) cc_final: 0.7857 (m-10) outliers start: 37 outliers final: 20 residues processed: 289 average time/residue: 0.1521 time to fit residues: 74.2525 Evaluate side-chains 252 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 222 optimal weight: 40.0000 chunk 172 optimal weight: 2.9990 chunk 144 optimal weight: 0.0970 chunk 128 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 285 optimal weight: 0.0870 chunk 227 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 127 optimal weight: 40.0000 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B1011 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 804 GLN L 44 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.161263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101376 restraints weight = 47335.019| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.74 r_work: 0.3379 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27701 Z= 0.152 Angle : 0.583 11.812 37821 Z= 0.287 Chirality : 0.046 0.464 4361 Planarity : 0.004 0.073 4833 Dihedral : 6.957 105.889 4455 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.16 % Allowed : 11.21 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3369 helix: 1.66 (0.19), residues: 684 sheet: -0.26 (0.18), residues: 753 loop : -0.75 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 509 TYR 0.020 0.001 TYR C 248 PHE 0.027 0.001 PHE A 65 TRP 0.022 0.001 TRP A 353 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00349 (27625) covalent geometry : angle 0.56127 (37631) SS BOND : bond 0.00298 ( 38) SS BOND : angle 1.04765 ( 76) hydrogen bonds : bond 0.04072 ( 1004) hydrogen bonds : angle 6.10702 ( 2838) link_BETA1-4 : bond 0.00139 ( 2) link_BETA1-4 : angle 0.97350 ( 6) link_NAG-ASN : bond 0.00531 ( 36) link_NAG-ASN : angle 2.93102 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.877 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 52 GLN cc_start: 0.8495 (pp30) cc_final: 0.8014 (pp30) REVERT: A 160 TYR cc_start: 0.7824 (p90) cc_final: 0.7492 (p90) REVERT: A 368 LEU cc_start: 0.8171 (mm) cc_final: 0.7917 (tp) REVERT: A 740 MET cc_start: 0.7987 (tpt) cc_final: 0.7062 (mmt) REVERT: B 101 ILE cc_start: 0.8124 (mp) cc_final: 0.7812 (mm) REVERT: B 313 TYR cc_start: 0.7946 (m-80) cc_final: 0.7436 (m-80) REVERT: B 403 ARG cc_start: 0.6948 (ttp80) cc_final: 0.6614 (ttp80) REVERT: B 420 ASP cc_start: 0.8315 (t70) cc_final: 0.8017 (t0) REVERT: B 501 ASN cc_start: 0.8268 (m110) cc_final: 0.7847 (m110) REVERT: B 571 ASP cc_start: 0.7191 (m-30) cc_final: 0.6926 (t0) REVERT: B 697 MET cc_start: 0.7601 (ptm) cc_final: 0.7194 (ptm) REVERT: B 1141 LEU cc_start: 0.8617 (mm) cc_final: 0.8117 (tp) REVERT: B 1142 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8814 (mm110) REVERT: C 318 PHE cc_start: 0.7954 (t80) cc_final: 0.7683 (t80) REVERT: C 987 PRO cc_start: 0.8261 (Cg_exo) cc_final: 0.7644 (Cg_endo) REVERT: C 1127 ASP cc_start: 0.8357 (t0) cc_final: 0.7411 (m-30) REVERT: H 5 GLN cc_start: 0.7972 (mp10) cc_final: 0.7455 (mp10) REVERT: H 6 GLN cc_start: 0.4301 (mm110) cc_final: 0.3680 (tp40) REVERT: H 41 TRP cc_start: 0.6991 (m100) cc_final: 0.6598 (m100) REVERT: H 89 MET cc_start: 0.6532 (ppp) cc_final: 0.6292 (ppp) REVERT: H 113 ASP cc_start: 0.7678 (m-30) cc_final: 0.7338 (m-30) REVERT: L 24 ARG cc_start: 0.8604 (ptp-110) cc_final: 0.8039 (ttm110) REVERT: L 51 LYS cc_start: 0.8850 (tppt) cc_final: 0.8395 (tttm) REVERT: L 53 LEU cc_start: 0.7677 (mp) cc_final: 0.7451 (mp) outliers start: 34 outliers final: 28 residues processed: 270 average time/residue: 0.1491 time to fit residues: 68.2487 Evaluate side-chains 252 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 141 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 218 optimal weight: 30.0000 chunk 23 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 chunk 246 optimal weight: 40.0000 chunk 118 optimal weight: 20.0000 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 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 901 GLN L 44 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.161791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101949 restraints weight = 47404.703| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.74 r_work: 0.3386 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27701 Z= 0.132 Angle : 0.572 11.554 37821 Z= 0.281 Chirality : 0.045 0.461 4361 Planarity : 0.004 0.054 4833 Dihedral : 6.735 103.845 4455 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.68 % Allowed : 11.73 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3369 helix: 1.64 (0.19), residues: 701 sheet: -0.18 (0.19), residues: 714 loop : -0.80 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 45 TYR 0.021 0.001 TYR C 248 PHE 0.032 0.001 PHE L 118 TRP 0.034 0.001 TRP A 353 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (27625) covalent geometry : angle 0.55018 (37631) SS BOND : bond 0.00259 ( 38) SS BOND : angle 1.08863 ( 76) hydrogen bonds : bond 0.03961 ( 1004) hydrogen bonds : angle 5.97320 ( 2838) link_BETA1-4 : bond 0.00124 ( 2) link_BETA1-4 : angle 0.94890 ( 6) link_NAG-ASN : bond 0.00522 ( 36) link_NAG-ASN : angle 2.86667 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 1.022 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 52 GLN cc_start: 0.8475 (pp30) cc_final: 0.8000 (pp30) REVERT: A 104 TRP cc_start: 0.6158 (m-90) cc_final: 0.5860 (m-10) REVERT: A 160 TYR cc_start: 0.7848 (p90) cc_final: 0.7503 (p90) REVERT: A 314 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 368 LEU cc_start: 0.8179 (mm) cc_final: 0.7915 (tp) REVERT: A 386 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8474 (mmmt) REVERT: A 1031 GLU cc_start: 0.7586 (pm20) cc_final: 0.7342 (pt0) REVERT: B 101 ILE cc_start: 0.8193 (mp) cc_final: 0.7903 (mm) REVERT: B 313 TYR cc_start: 0.7952 (m-80) cc_final: 0.7429 (m-80) REVERT: B 355 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7295 (ttp80) REVERT: B 403 ARG cc_start: 0.6943 (ttp80) cc_final: 0.6561 (ttp80) REVERT: B 449 TYR cc_start: 0.7979 (m-80) cc_final: 0.7565 (m-80) REVERT: B 501 ASN cc_start: 0.8274 (m110) cc_final: 0.7862 (m110) REVERT: B 571 ASP cc_start: 0.7070 (m-30) cc_final: 0.6867 (t0) REVERT: B 697 MET cc_start: 0.7587 (ptm) cc_final: 0.7164 (ptm) REVERT: B 1138 TYR cc_start: 0.6803 (t80) cc_final: 0.6593 (t80) REVERT: C 318 PHE cc_start: 0.7974 (t80) cc_final: 0.7674 (t80) REVERT: H 41 TRP cc_start: 0.7006 (m100) cc_final: 0.6108 (m100) REVERT: H 113 ASP cc_start: 0.7706 (m-30) cc_final: 0.7307 (m-30) REVERT: L 24 ARG cc_start: 0.8579 (ptp-110) cc_final: 0.7674 (mtp-110) REVERT: L 51 LYS cc_start: 0.8885 (tppt) cc_final: 0.8387 (tttm) outliers start: 49 outliers final: 34 residues processed: 281 average time/residue: 0.1487 time to fit residues: 70.3605 Evaluate side-chains 260 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 57 HIS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 118 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 259 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 262 optimal weight: 0.5980 chunk 287 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 289 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C1088 HIS L 44 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.158244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097108 restraints weight = 47329.998| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.72 r_work: 0.3305 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 27701 Z= 0.237 Angle : 0.650 11.890 37821 Z= 0.320 Chirality : 0.047 0.450 4361 Planarity : 0.004 0.048 4833 Dihedral : 6.865 104.403 4455 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.88 % Allowed : 12.65 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3369 helix: 1.26 (0.19), residues: 695 sheet: -0.28 (0.19), residues: 722 loop : -0.86 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 45 TYR 0.024 0.002 TYR C1067 PHE 0.031 0.002 PHE L 118 TRP 0.037 0.002 TRP A 353 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00551 (27625) covalent geometry : angle 0.62925 (37631) SS BOND : bond 0.00470 ( 38) SS BOND : angle 1.29521 ( 76) hydrogen bonds : bond 0.04455 ( 1004) hydrogen bonds : angle 6.21458 ( 2838) link_BETA1-4 : bond 0.00067 ( 2) link_BETA1-4 : angle 1.00305 ( 6) link_NAG-ASN : bond 0.00517 ( 36) link_NAG-ASN : angle 2.94121 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8597 (pp30) cc_final: 0.8060 (pp30) REVERT: A 104 TRP cc_start: 0.6233 (m-90) cc_final: 0.5962 (m-10) REVERT: A 160 TYR cc_start: 0.7877 (p90) cc_final: 0.7521 (p90) REVERT: A 368 LEU cc_start: 0.8162 (mm) cc_final: 0.7895 (tp) REVERT: A 428 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7205 (p0) REVERT: A 740 MET cc_start: 0.7925 (tpt) cc_final: 0.7001 (mmt) REVERT: B 101 ILE cc_start: 0.8224 (mp) cc_final: 0.7914 (tp) REVERT: B 237 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6897 (mmm-85) REVERT: B 313 TYR cc_start: 0.8074 (m-80) cc_final: 0.7473 (m-80) REVERT: B 355 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7369 (ttp80) REVERT: B 403 ARG cc_start: 0.6989 (ttp80) cc_final: 0.6590 (ttp80) REVERT: B 420 ASP cc_start: 0.8252 (t70) cc_final: 0.7856 (t0) REVERT: B 501 ASN cc_start: 0.8248 (m110) cc_final: 0.7827 (m110) REVERT: B 571 ASP cc_start: 0.7214 (m-30) cc_final: 0.6968 (t0) REVERT: B 697 MET cc_start: 0.7662 (ptm) cc_final: 0.7227 (ptm) REVERT: B 823 PHE cc_start: 0.7683 (m-80) cc_final: 0.7177 (m-80) REVERT: B 916 LEU cc_start: 0.7688 (tp) cc_final: 0.7439 (tt) REVERT: B 1138 TYR cc_start: 0.6838 (t80) cc_final: 0.6629 (t80) REVERT: B 1141 LEU cc_start: 0.8639 (mm) cc_final: 0.8153 (tp) REVERT: C 318 PHE cc_start: 0.8007 (t80) cc_final: 0.7758 (t80) REVERT: C 987 PRO cc_start: 0.7661 (Cg_exo) cc_final: 0.7443 (Cg_endo) REVERT: C 1082 CYS cc_start: 0.7628 (t) cc_final: 0.7381 (t) REVERT: C 1089 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: C 1127 ASP cc_start: 0.8395 (t0) cc_final: 0.7518 (m-30) REVERT: H 5 GLN cc_start: 0.7752 (mp10) cc_final: 0.7411 (mp10) REVERT: H 6 GLN cc_start: 0.4092 (mm-40) cc_final: 0.3445 (tp40) REVERT: H 71 PHE cc_start: 0.2780 (t80) cc_final: 0.2537 (t80) REVERT: H 113 ASP cc_start: 0.7745 (m-30) cc_final: 0.7384 (m-30) REVERT: L 24 ARG cc_start: 0.8491 (ptp-110) cc_final: 0.8053 (ttm110) REVERT: L 29 VAL cc_start: 0.5592 (OUTLIER) cc_final: 0.5371 (m) REVERT: L 51 LYS cc_start: 0.9004 (tppt) cc_final: 0.8478 (tttm) outliers start: 55 outliers final: 37 residues processed: 273 average time/residue: 0.1480 time to fit residues: 68.3291 Evaluate side-chains 262 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 118 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 94 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 307 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 223 optimal weight: 0.0170 chunk 142 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 115 optimal weight: 30.0000 chunk 234 optimal weight: 8.9990 chunk 325 optimal weight: 20.0000 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** 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 = 0.4401 r_free = 0.4401 target = 0.161107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101171 restraints weight = 47297.755| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.71 r_work: 0.3377 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27701 Z= 0.127 Angle : 0.592 11.505 37821 Z= 0.289 Chirality : 0.046 0.454 4361 Planarity : 0.004 0.049 4833 Dihedral : 6.519 100.641 4455 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.47 % Allowed : 13.33 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3369 helix: 1.54 (0.19), residues: 696 sheet: -0.25 (0.19), residues: 731 loop : -0.86 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 84 TYR 0.024 0.001 TYR C 248 PHE 0.029 0.001 PHE L 118 TRP 0.037 0.001 TRP A 353 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00287 (27625) covalent geometry : angle 0.57256 (37631) SS BOND : bond 0.00281 ( 38) SS BOND : angle 1.02424 ( 76) hydrogen bonds : bond 0.03973 ( 1004) hydrogen bonds : angle 5.94907 ( 2838) link_BETA1-4 : bond 0.00154 ( 2) link_BETA1-4 : angle 0.92593 ( 6) link_NAG-ASN : bond 0.00517 ( 36) link_NAG-ASN : angle 2.79208 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8527 (pp30) cc_final: 0.7978 (pp30) REVERT: A 104 TRP cc_start: 0.6259 (m-90) cc_final: 0.5851 (m-10) REVERT: A 160 TYR cc_start: 0.7864 (p90) cc_final: 0.7499 (p90) REVERT: A 321 GLN cc_start: 0.8218 (mp10) cc_final: 0.7821 (pm20) REVERT: A 368 LEU cc_start: 0.8143 (mm) cc_final: 0.7918 (tp) REVERT: A 428 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 740 MET cc_start: 0.7883 (tpt) cc_final: 0.6951 (mmt) REVERT: B 101 ILE cc_start: 0.8274 (mp) cc_final: 0.8031 (mm) REVERT: B 313 TYR cc_start: 0.7985 (m-80) cc_final: 0.7441 (m-80) REVERT: B 355 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7252 (ttp80) REVERT: B 403 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6568 (ttp80) REVERT: B 501 ASN cc_start: 0.8263 (m110) cc_final: 0.7846 (m110) REVERT: B 571 ASP cc_start: 0.7068 (m-30) cc_final: 0.6853 (t0) REVERT: B 697 MET cc_start: 0.7645 (ptm) cc_final: 0.7225 (ptm) REVERT: B 858 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8581 (pp) REVERT: B 1138 TYR cc_start: 0.6849 (t80) cc_final: 0.6614 (t80) REVERT: C 318 PHE cc_start: 0.7998 (t80) cc_final: 0.7709 (t80) REVERT: C 987 PRO cc_start: 0.7681 (Cg_exo) cc_final: 0.7458 (Cg_endo) REVERT: C 1082 CYS cc_start: 0.7494 (t) cc_final: 0.7260 (t) REVERT: C 1127 ASP cc_start: 0.8355 (t0) cc_final: 0.7495 (m-30) REVERT: H 5 GLN cc_start: 0.7698 (mp10) cc_final: 0.7337 (mp10) REVERT: H 6 GLN cc_start: 0.3949 (mm-40) cc_final: 0.3190 (tp40) REVERT: H 43 LYS cc_start: 0.4335 (pttm) cc_final: 0.3577 (pttp) REVERT: H 113 ASP cc_start: 0.7801 (m-30) cc_final: 0.7345 (m-30) REVERT: L 24 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.8131 (ttm110) REVERT: L 29 VAL cc_start: 0.5617 (OUTLIER) cc_final: 0.5387 (m) outliers start: 43 outliers final: 33 residues processed: 273 average time/residue: 0.1536 time to fit residues: 71.0981 Evaluate side-chains 257 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 41 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 312 optimal weight: 0.1980 chunk 172 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.160920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100984 restraints weight = 47269.722| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.73 r_work: 0.3376 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27701 Z= 0.134 Angle : 0.595 11.659 37821 Z= 0.290 Chirality : 0.046 0.453 4361 Planarity : 0.004 0.050 4833 Dihedral : 6.383 98.923 4455 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.44 % Allowed : 13.68 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3369 helix: 1.60 (0.19), residues: 692 sheet: -0.24 (0.19), residues: 746 loop : -0.87 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 84 TYR 0.021 0.001 TYR C 248 PHE 0.022 0.001 PHE L 118 TRP 0.041 0.002 TRP A 353 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00307 (27625) covalent geometry : angle 0.57549 (37631) SS BOND : bond 0.00267 ( 38) SS BOND : angle 1.14244 ( 76) hydrogen bonds : bond 0.03929 ( 1004) hydrogen bonds : angle 5.88591 ( 2838) link_BETA1-4 : bond 0.00164 ( 2) link_BETA1-4 : angle 0.93074 ( 6) link_NAG-ASN : bond 0.00498 ( 36) link_NAG-ASN : angle 2.76270 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8527 (pp30) cc_final: 0.7939 (pp30) REVERT: A 160 TYR cc_start: 0.7836 (p90) cc_final: 0.7480 (p90) REVERT: A 321 GLN cc_start: 0.8128 (mp10) cc_final: 0.7778 (pm20) REVERT: A 368 LEU cc_start: 0.8169 (mm) cc_final: 0.7923 (tp) REVERT: A 428 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7280 (p0) REVERT: A 508 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8604 (t80) REVERT: A 740 MET cc_start: 0.7910 (tpt) cc_final: 0.6982 (mmt) REVERT: B 101 ILE cc_start: 0.8288 (mp) cc_final: 0.7992 (tp) REVERT: B 313 TYR cc_start: 0.8003 (m-80) cc_final: 0.7464 (m-80) REVERT: B 355 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7302 (ttp80) REVERT: B 403 ARG cc_start: 0.6987 (ttp80) cc_final: 0.6545 (ttp80) REVERT: B 501 ASN cc_start: 0.8273 (m110) cc_final: 0.7848 (m110) REVERT: B 697 MET cc_start: 0.7632 (ptm) cc_final: 0.7210 (ptm) REVERT: B 858 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8616 (pp) REVERT: B 1138 TYR cc_start: 0.6837 (t80) cc_final: 0.6606 (t80) REVERT: C 318 PHE cc_start: 0.8003 (t80) cc_final: 0.7747 (t80) REVERT: C 987 PRO cc_start: 0.7710 (Cg_exo) cc_final: 0.7480 (Cg_endo) REVERT: C 1082 CYS cc_start: 0.7482 (t) cc_final: 0.7265 (t) REVERT: C 1127 ASP cc_start: 0.8335 (t0) cc_final: 0.7477 (m-30) REVERT: H 6 GLN cc_start: 0.3908 (mm-40) cc_final: 0.3167 (tp40) REVERT: H 43 LYS cc_start: 0.4334 (pttm) cc_final: 0.3958 (pttp) REVERT: H 67 TYR cc_start: 0.5829 (m-80) cc_final: 0.5397 (m-80) REVERT: H 113 ASP cc_start: 0.7754 (m-30) cc_final: 0.7364 (m-30) REVERT: L 24 ARG cc_start: 0.8469 (ptp-110) cc_final: 0.8054 (ttm110) REVERT: L 116 PHE cc_start: 0.8581 (m-80) cc_final: 0.8264 (m-80) outliers start: 42 outliers final: 36 residues processed: 265 average time/residue: 0.1459 time to fit residues: 65.7569 Evaluate side-chains 266 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 41 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 127 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 246 optimal weight: 30.0000 chunk 308 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 263 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1010 GLN C1088 HIS ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.155749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094371 restraints weight = 47155.115| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.67 r_work: 0.3239 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 27701 Z= 0.370 Angle : 0.764 13.479 37821 Z= 0.380 Chirality : 0.051 0.458 4361 Planarity : 0.005 0.062 4833 Dihedral : 6.974 105.213 4455 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.40 % Allowed : 14.05 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 3369 helix: 0.79 (0.18), residues: 690 sheet: -0.57 (0.19), residues: 737 loop : -1.06 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 84 TYR 0.032 0.002 TYR B1067 PHE 0.040 0.003 PHE A1121 TRP 0.046 0.003 TRP A 353 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00868 (27625) covalent geometry : angle 0.74344 (37631) SS BOND : bond 0.00740 ( 38) SS BOND : angle 1.72006 ( 76) hydrogen bonds : bond 0.05039 ( 1004) hydrogen bonds : angle 6.53551 ( 2838) link_BETA1-4 : bond 0.00297 ( 2) link_BETA1-4 : angle 1.07365 ( 6) link_NAG-ASN : bond 0.00530 ( 36) link_NAG-ASN : angle 3.07135 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8750 (pp30) cc_final: 0.8000 (pp30) REVERT: A 160 TYR cc_start: 0.7918 (p90) cc_final: 0.7556 (p90) REVERT: A 201 PHE cc_start: 0.8018 (t80) cc_final: 0.7573 (t80) REVERT: A 321 GLN cc_start: 0.8202 (mp10) cc_final: 0.7935 (pm20) REVERT: A 368 LEU cc_start: 0.8190 (mm) cc_final: 0.7946 (tp) REVERT: A 386 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8617 (mmmm) REVERT: A 428 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7439 (p0) REVERT: A 508 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8682 (t80) REVERT: A 740 MET cc_start: 0.8047 (tpt) cc_final: 0.7126 (mmt) REVERT: B 101 ILE cc_start: 0.8375 (mp) cc_final: 0.8162 (tp) REVERT: B 104 TRP cc_start: 0.6386 (m-90) cc_final: 0.5749 (m-90) REVERT: B 313 TYR cc_start: 0.8339 (m-80) cc_final: 0.7699 (m-80) REVERT: B 355 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7407 (ttp80) REVERT: B 501 ASN cc_start: 0.8270 (m110) cc_final: 0.7863 (m110) REVERT: B 546 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7739 (tt) REVERT: B 823 PHE cc_start: 0.7709 (m-80) cc_final: 0.7257 (m-80) REVERT: B 957 GLN cc_start: 0.9149 (tt0) cc_final: 0.8933 (tp40) REVERT: B 1141 LEU cc_start: 0.8605 (mm) cc_final: 0.8080 (tp) REVERT: C 318 PHE cc_start: 0.8083 (t80) cc_final: 0.7848 (t80) REVERT: C 987 PRO cc_start: 0.8114 (Cg_exo) cc_final: 0.7883 (Cg_endo) REVERT: H 5 GLN cc_start: 0.7766 (mp10) cc_final: 0.7395 (mp10) REVERT: H 6 GLN cc_start: 0.3660 (mm-40) cc_final: 0.3052 (tp40) REVERT: H 43 LYS cc_start: 0.4718 (pttm) cc_final: 0.3895 (pttp) REVERT: H 113 ASP cc_start: 0.7619 (m-30) cc_final: 0.7296 (m-30) REVERT: H 115 PHE cc_start: 0.7234 (m-80) cc_final: 0.7020 (m-10) REVERT: L 24 ARG cc_start: 0.8539 (ptp-110) cc_final: 0.7968 (ttp-110) outliers start: 41 outliers final: 32 residues processed: 262 average time/residue: 0.1553 time to fit residues: 68.2442 Evaluate side-chains 259 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 41 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 184 optimal weight: 0.7980 chunk 283 optimal weight: 0.0040 chunk 249 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.158118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097401 restraints weight = 47151.153| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.69 r_work: 0.3309 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27701 Z= 0.180 Angle : 0.638 13.878 37821 Z= 0.313 Chirality : 0.047 0.481 4361 Planarity : 0.004 0.044 4833 Dihedral : 6.622 101.723 4455 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.30 % Allowed : 14.67 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3369 helix: 1.13 (0.19), residues: 688 sheet: -0.51 (0.19), residues: 717 loop : -0.99 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.028 0.001 TYR C 248 PHE 0.021 0.002 PHE C 562 TRP 0.044 0.002 TRP A 353 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00414 (27625) covalent geometry : angle 0.61866 (37631) SS BOND : bond 0.00394 ( 38) SS BOND : angle 1.37059 ( 76) hydrogen bonds : bond 0.04297 ( 1004) hydrogen bonds : angle 6.18900 ( 2838) link_BETA1-4 : bond 0.00038 ( 2) link_BETA1-4 : angle 0.94255 ( 6) link_NAG-ASN : bond 0.00640 ( 36) link_NAG-ASN : angle 2.83051 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10626.56 seconds wall clock time: 181 minutes 6.82 seconds (10866.82 seconds total)