Starting phenix.real_space_refine on Tue Aug 26 17:12:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8si2_40496/08_2025/8si2_40496_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8si2_40496/08_2025/8si2_40496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8si2_40496/08_2025/8si2_40496_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8si2_40496/08_2025/8si2_40496_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8si2_40496/08_2025/8si2_40496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8si2_40496/08_2025/8si2_40496.map" } resolution = 2.19 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= 0.010 sd= 0.078 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: 6 Type Number sf(0) Gaussians P 56 5.49 5 S 240 5.16 5 Na 2 4.78 5 C 25768 2.51 5 N 6012 2.21 5 O 6944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39022 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8928 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "B" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8928 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "C" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8928 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "D" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8928 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "A" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 787 Unusual residues: {' NA': 2, 'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 3, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 785 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 2, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 785 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 2, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 785 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 2, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Time building chain proxies: 9.72, per 1000 atoms: 0.25 Number of scatterers: 39022 At special positions: 0 Unit cell: (180.11, 180.11, 156.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 240 16.00 P 56 15.00 Na 2 11.00 O 6944 8.00 N 6012 7.00 C 25768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.06 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.01 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 44 " distance=2.06 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 44 " distance=2.02 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 44 " distance=2.06 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 44 " distance=2.02 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 44 " distance=2.06 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 44 " distance=2.02 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " 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 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.2 microseconds 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8368 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 12 sheets defined 64.8% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.587A pdb=" N GLN A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.550A pdb=" N ALA A 52 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 3.898A pdb=" N TYR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.596A pdb=" N GLU A 76 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 removed outlier: 4.055A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 removed outlier: 3.841A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.540A pdb=" N HIS A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.504A pdb=" N LEU A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 259 through 270 removed outlier: 3.568A pdb=" N ARG A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.508A pdb=" N LEU A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.549A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.857A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.785A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.657A pdb=" N THR A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.816A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.603A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 removed outlier: 4.057A pdb=" N HIS A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.565A pdb=" N ASN A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.806A pdb=" N GLU A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 647 through 667 Processing helix chain 'A' and resid 675 through 701 removed outlier: 3.603A pdb=" N LEU A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 709 removed outlier: 3.621A pdb=" N LEU A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 736 through 749 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 768 through 774 removed outlier: 3.766A pdb=" N LEU A 774 " --> pdb=" O ILE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 794 removed outlier: 3.779A pdb=" N MET A 794 " --> pdb=" O ASP A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 850 removed outlier: 3.600A pdb=" N PHE A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 876 removed outlier: 3.642A pdb=" N ALA A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 905 Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 922 through 945 Processing helix chain 'A' and resid 955 through 975 removed outlier: 4.601A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 981 Processing helix chain 'A' and resid 985 through 1000 removed outlier: 3.970A pdb=" N TYR A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1023 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1030 through 1036 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.850A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 removed outlier: 3.722A pdb=" N ILE A1053 " --> pdb=" O ALA A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1066 Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1072 through 1086 Processing helix chain 'A' and resid 1087 through 1125 removed outlier: 5.101A pdb=" N LEU A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLN A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A1122 " --> pdb=" O PHE A1118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 4.289A pdb=" N SER A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1190 Processing helix chain 'A' and resid 1192 through 1229 removed outlier: 3.582A pdb=" N ILE A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A1212 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A1223 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.587A pdb=" N GLN B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.550A pdb=" N ALA B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.898A pdb=" N TYR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.594A pdb=" N GLU B 76 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 removed outlier: 4.055A pdb=" N ILE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 removed outlier: 3.840A pdb=" N GLN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.541A pdb=" N HIS B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.503A pdb=" N LEU B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 217' Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.568A pdb=" N ARG B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.508A pdb=" N LEU B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.549A pdb=" N THR B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 372 removed outlier: 3.856A pdb=" N LEU B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.786A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 418 removed outlier: 3.656A pdb=" N THR B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.815A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 449 Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.603A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 removed outlier: 4.057A pdb=" N HIS B 491 " --> pdb=" O PRO B 487 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 540 removed outlier: 3.565A pdb=" N ASN B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.806A pdb=" N GLU B 624 " --> pdb=" O TYR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 647 through 667 Processing helix chain 'B' and resid 675 through 701 removed outlier: 3.602A pdb=" N LEU B 679 " --> pdb=" O THR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 removed outlier: 3.621A pdb=" N LEU B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 736 through 749 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 768 through 774 removed outlier: 3.767A pdb=" N LEU B 774 " --> pdb=" O ILE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 794 removed outlier: 3.779A pdb=" N MET B 794 " --> pdb=" O ASP B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 850 removed outlier: 3.600A pdb=" N PHE B 845 " --> pdb=" O ILE B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 876 removed outlier: 3.643A pdb=" N ALA B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 905 Processing helix chain 'B' and resid 911 through 920 Processing helix chain 'B' and resid 922 through 945 Processing helix chain 'B' and resid 955 through 975 removed outlier: 4.602A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 981 Processing helix chain 'B' and resid 985 through 1000 removed outlier: 3.970A pdb=" N TYR B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1023 Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1030 through 1036 Processing helix chain 'B' and resid 1037 through 1044 removed outlier: 3.850A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1053 removed outlier: 3.723A pdb=" N ILE B1053 " --> pdb=" O ALA B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1069 through 1071 No H-bonds generated for 'chain 'B' and resid 1069 through 1071' Processing helix chain 'B' and resid 1072 through 1086 Processing helix chain 'B' and resid 1087 through 1125 removed outlier: 5.101A pdb=" N LEU B1101 " --> pdb=" O ASN B1097 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B1122 " --> pdb=" O PHE B1118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS B1123 " --> pdb=" O ILE B1119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B1124 " --> pdb=" O MET B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1146 removed outlier: 4.288A pdb=" N SER B1136 " --> pdb=" O LEU B1132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1190 Processing helix chain 'B' and resid 1192 through 1229 removed outlier: 3.582A pdb=" N ILE B1209 " --> pdb=" O GLU B1205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B1212 " --> pdb=" O SER B1208 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B1223 " --> pdb=" O ASN B1219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.587A pdb=" N GLN C 37 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.549A pdb=" N ALA C 52 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.898A pdb=" N TYR C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.594A pdb=" N GLU C 76 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.055A pdb=" N ILE C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 166 removed outlier: 3.841A pdb=" N GLN C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 157 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.541A pdb=" N HIS C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.503A pdb=" N LEU C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 259 through 270 removed outlier: 3.568A pdb=" N ARG C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.509A pdb=" N LEU C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.548A pdb=" N THR C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 372 removed outlier: 3.857A pdb=" N LEU C 364 " --> pdb=" O GLU C 360 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.785A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.656A pdb=" N THR C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.815A pdb=" N ALA C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 449 Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 464 through 469 Processing helix chain 'C' and resid 470 through 480 removed outlier: 3.603A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 498 removed outlier: 4.056A pdb=" N HIS C 491 " --> pdb=" O PRO C 487 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 540 removed outlier: 3.565A pdb=" N ASN C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.806A pdb=" N GLU C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 647 through 667 Processing helix chain 'C' and resid 675 through 701 removed outlier: 3.603A pdb=" N LEU C 679 " --> pdb=" O THR C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 709 removed outlier: 3.620A pdb=" N LEU C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 736 through 749 Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 768 through 774 removed outlier: 3.768A pdb=" N LEU C 774 " --> pdb=" O ILE C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 794 removed outlier: 3.779A pdb=" N MET C 794 " --> pdb=" O ASP C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 850 removed outlier: 3.600A pdb=" N PHE C 845 " --> pdb=" O ILE C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 876 removed outlier: 3.643A pdb=" N ALA C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 905 Processing helix chain 'C' and resid 911 through 920 Processing helix chain 'C' and resid 922 through 945 Processing helix chain 'C' and resid 955 through 975 removed outlier: 4.602A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 981 Processing helix chain 'C' and resid 985 through 1000 removed outlier: 3.971A pdb=" N TYR C 989 " --> pdb=" O GLN C 985 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 994 " --> pdb=" O VAL C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1023 Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1030 through 1036 Processing helix chain 'C' and resid 1037 through 1044 removed outlier: 3.850A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1053 removed outlier: 3.722A pdb=" N ILE C1053 " --> pdb=" O ALA C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1062 through 1066 Processing helix chain 'C' and resid 1069 through 1071 No H-bonds generated for 'chain 'C' and resid 1069 through 1071' Processing helix chain 'C' and resid 1072 through 1086 Processing helix chain 'C' and resid 1087 through 1125 removed outlier: 5.102A pdb=" N LEU C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN C1102 " --> pdb=" O ASN C1098 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C1122 " --> pdb=" O PHE C1118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C1123 " --> pdb=" O ILE C1119 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C1124 " --> pdb=" O MET C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1146 removed outlier: 4.289A pdb=" N SER C1136 " --> pdb=" O LEU C1132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1190 Processing helix chain 'C' and resid 1192 through 1229 removed outlier: 3.583A pdb=" N ILE C1209 " --> pdb=" O GLU C1205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C1212 " --> pdb=" O SER C1208 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C1223 " --> pdb=" O ASN C1219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 11 Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.587A pdb=" N GLN D 37 " --> pdb=" O CYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.550A pdb=" N ALA D 52 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.898A pdb=" N TYR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.595A pdb=" N GLU D 76 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 126 removed outlier: 4.055A pdb=" N ILE D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 166 removed outlier: 3.841A pdb=" N GLN D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 190 removed outlier: 3.541A pdb=" N HIS D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.503A pdb=" N LEU D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 217' Processing helix chain 'D' and resid 259 through 270 removed outlier: 3.568A pdb=" N ARG D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.509A pdb=" N LEU D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 329 Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.548A pdb=" N THR D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 removed outlier: 3.856A pdb=" N LEU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 370 " --> pdb=" O GLN D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.785A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 418 removed outlier: 3.657A pdb=" N THR D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.815A pdb=" N ALA D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 449 Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 470 through 480 removed outlier: 3.603A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 498 removed outlier: 4.056A pdb=" N HIS D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN D 498 " --> pdb=" O ARG D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 526 through 529 Processing helix chain 'D' and resid 530 through 540 removed outlier: 3.565A pdb=" N ASN D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 632 removed outlier: 3.806A pdb=" N GLU D 624 " --> pdb=" O TYR D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 647 through 667 Processing helix chain 'D' and resid 675 through 701 removed outlier: 3.603A pdb=" N LEU D 679 " --> pdb=" O THR D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 709 removed outlier: 3.621A pdb=" N LEU D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 730 through 735 Processing helix chain 'D' and resid 736 through 749 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 768 through 774 removed outlier: 3.767A pdb=" N LEU D 774 " --> pdb=" O ILE D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 794 removed outlier: 3.780A pdb=" N MET D 794 " --> pdb=" O ASP D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 850 removed outlier: 3.600A pdb=" N PHE D 845 " --> pdb=" O ILE D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 876 removed outlier: 3.642A pdb=" N ALA D 862 " --> pdb=" O PHE D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 905 Processing helix chain 'D' and resid 911 through 920 Processing helix chain 'D' and resid 922 through 945 Processing helix chain 'D' and resid 955 through 975 removed outlier: 4.602A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 981 Processing helix chain 'D' and resid 985 through 1000 removed outlier: 3.970A pdb=" N TYR D 989 " --> pdb=" O GLN D 985 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY D 994 " --> pdb=" O VAL D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1023 Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1030 through 1036 Processing helix chain 'D' and resid 1037 through 1044 removed outlier: 3.849A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1053 removed outlier: 3.722A pdb=" N ILE D1053 " --> pdb=" O ALA D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1066 Processing helix chain 'D' and resid 1069 through 1071 No H-bonds generated for 'chain 'D' and resid 1069 through 1071' Processing helix chain 'D' and resid 1072 through 1086 Processing helix chain 'D' and resid 1087 through 1125 removed outlier: 5.102A pdb=" N LEU D1101 " --> pdb=" O ASN D1097 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLN D1102 " --> pdb=" O ASN D1098 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D1122 " --> pdb=" O PHE D1118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS D1123 " --> pdb=" O ILE D1119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D1124 " --> pdb=" O MET D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1146 removed outlier: 4.289A pdb=" N SER D1136 " --> pdb=" O LEU D1132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1190 Processing helix chain 'D' and resid 1192 through 1229 removed outlier: 3.581A pdb=" N ILE D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D1212 " --> pdb=" O SER D1208 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG D1223 " --> pdb=" O ASN D1219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.538A pdb=" N SER A 87 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 15 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 85 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.860A pdb=" N TYR A 92 " --> pdb=" O GLY A 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 245 removed outlier: 6.199A pdb=" N VAL A 136 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 288 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 138 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL A 313 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 287 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N CYS A 315 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE A 289 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 312 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 16 removed outlier: 3.538A pdb=" N SER B 87 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 15 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 85 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.860A pdb=" N TYR B 92 " --> pdb=" O GLY B 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 245 removed outlier: 6.199A pdb=" N VAL B 136 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 288 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 138 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL B 313 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 287 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N CYS B 315 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE B 289 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL B 312 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 381 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 314 " --> pdb=" O PHE B 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 16 removed outlier: 3.537A pdb=" N SER C 87 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU C 15 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 85 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.860A pdb=" N TYR C 92 " --> pdb=" O GLY C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 244 through 245 removed outlier: 6.199A pdb=" N VAL C 136 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 288 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER C 138 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL C 313 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 287 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N CYS C 315 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE C 289 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL C 312 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE C 381 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL C 314 " --> pdb=" O PHE C 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 13 through 16 removed outlier: 3.537A pdb=" N SER D 87 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU D 15 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 85 " --> pdb=" O GLU D 15 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.860A pdb=" N TYR D 92 " --> pdb=" O GLY D 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 244 through 245 removed outlier: 6.198A pdb=" N VAL D 136 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU D 288 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER D 138 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL D 313 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA D 287 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N CYS D 315 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE D 289 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL D 312 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE D 381 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL D 314 " --> pdb=" O PHE D 381 " (cutoff:3.500A) 1796 hydrogen bonds defined for protein. 5232 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: 8.56 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6397 1.32 - 1.45: 10316 1.45 - 1.58: 22467 1.58 - 1.71: 112 1.71 - 1.84: 392 Bond restraints: 39684 Sorted by residual: bond pdb=" C29 POV C1308 " pdb="C210 POV C1308 " ideal model delta sigma weight residual 1.333 1.508 -0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" C29 POV A1305 " pdb="C210 POV A1305 " ideal model delta sigma weight residual 1.333 1.507 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C29 POV D1309 " pdb="C210 POV D1309 " ideal model delta sigma weight residual 1.333 1.507 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C29 POV B1308 " pdb="C210 POV B1308 " ideal model delta sigma weight residual 1.333 1.507 -0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" CG LEU A 722 " pdb=" CD2 LEU A 722 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.24e+01 ... (remaining 39679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 51699 2.96 - 5.91: 1425 5.91 - 8.87: 108 8.87 - 11.83: 12 11.83 - 14.78: 8 Bond angle restraints: 53252 Sorted by residual: angle pdb=" N PRO C1130 " pdb=" CA PRO C1130 " pdb=" C PRO C1130 " ideal model delta sigma weight residual 110.70 116.77 -6.07 1.22e+00 6.72e-01 2.48e+01 angle pdb=" N PRO A1130 " pdb=" CA PRO A1130 " pdb=" C PRO A1130 " ideal model delta sigma weight residual 110.70 116.76 -6.06 1.22e+00 6.72e-01 2.47e+01 angle pdb=" N PRO D1130 " pdb=" CA PRO D1130 " pdb=" C PRO D1130 " ideal model delta sigma weight residual 110.70 116.74 -6.04 1.22e+00 6.72e-01 2.45e+01 angle pdb=" N PRO B1130 " pdb=" CA PRO B1130 " pdb=" C PRO B1130 " ideal model delta sigma weight residual 110.70 116.72 -6.02 1.22e+00 6.72e-01 2.43e+01 angle pdb=" C28 POV A1305 " pdb=" C29 POV A1305 " pdb="C210 POV A1305 " ideal model delta sigma weight residual 127.79 113.01 14.78 3.00e+00 1.11e-01 2.43e+01 ... (remaining 53247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 23804 35.81 - 71.62: 791 71.62 - 107.43: 161 107.43 - 143.24: 43 143.24 - 179.05: 45 Dihedral angle restraints: 24844 sinusoidal: 11876 harmonic: 12968 Sorted by residual: dihedral pdb=" CA SER C 22 " pdb=" C SER C 22 " pdb=" N SER C 23 " pdb=" CA SER C 23 " ideal model delta harmonic sigma weight residual -180.00 -145.38 -34.62 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA SER B 22 " pdb=" C SER B 22 " pdb=" N SER B 23 " pdb=" CA SER B 23 " ideal model delta harmonic sigma weight residual -180.00 -145.41 -34.59 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA SER D 22 " pdb=" C SER D 22 " pdb=" N SER D 23 " pdb=" CA SER D 23 " ideal model delta harmonic sigma weight residual -180.00 -145.42 -34.58 0 5.00e+00 4.00e-02 4.78e+01 ... (remaining 24841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3822 0.055 - 0.110: 1507 0.110 - 0.164: 275 0.164 - 0.219: 48 0.219 - 0.274: 24 Chirality restraints: 5676 Sorted by residual: chirality pdb=" CB VAL C1037 " pdb=" CA VAL C1037 " pdb=" CG1 VAL C1037 " pdb=" CG2 VAL C1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL B1037 " pdb=" CA VAL B1037 " pdb=" CG1 VAL B1037 " pdb=" CG2 VAL B1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL A1037 " pdb=" CA VAL A1037 " pdb=" CG1 VAL A1037 " pdb=" CG2 VAL A1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5673 not shown) Planarity restraints: 6364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D1310 " -0.069 2.00e-02 2.50e+03 1.48e-01 2.19e+02 pdb=" C29 POV D1310 " 0.196 2.00e-02 2.50e+03 pdb="C210 POV D1310 " -0.198 2.00e-02 2.50e+03 pdb="C211 POV D1310 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1309 " 0.069 2.00e-02 2.50e+03 1.47e-01 2.16e+02 pdb=" C29 POV B1309 " -0.195 2.00e-02 2.50e+03 pdb="C210 POV B1309 " 0.197 2.00e-02 2.50e+03 pdb="C211 POV B1309 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1309 " 0.064 2.00e-02 2.50e+03 1.32e-01 1.74e+02 pdb=" C29 POV C1309 " -0.175 2.00e-02 2.50e+03 pdb="C210 POV C1309 " 0.175 2.00e-02 2.50e+03 pdb="C211 POV C1309 " -0.064 2.00e-02 2.50e+03 ... (remaining 6361 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 435 2.60 - 3.18: 34098 3.18 - 3.75: 58957 3.75 - 4.33: 88226 4.33 - 4.90: 140809 Nonbonded interactions: 322525 Sorted by model distance: nonbonded pdb=" OE1 GLU B 692 " pdb=" OH TYR B1181 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLU C 692 " pdb=" OH TYR C1181 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLU D 692 " pdb=" OH TYR D1181 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLU A 692 " pdb=" OH TYR A1181 " model vdw 2.027 3.040 nonbonded pdb=" O ILE A1221 " pdb=" OG SER A1224 " model vdw 2.033 3.040 ... (remaining 322520 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' and (resid 3 through 1301 or (resid 1303 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313)) or (resid 1305 and (name \ C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or \ name C29)) or (resid 1306 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P or name C210 or name C211 or name C212)) or (resid 1309 and (name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216)) or resid 1310 through 1313 or (resid 1315 and (name N or name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name P or name C210 or name C211 or name C212 or name C213 or name C2 \ 14 or name C215 or name C216 or name C217 or name C218)) or resid 1316)) selection = (chain 'B' and (resid 3 through 1301 or (resid 1303 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313)) or (resid 1305 and (name \ C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or \ name C29)) or (resid 1306 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P or name C210 or name C211 or name C212)) or (resid 1309 and (name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216)) or resid 1310 or (resid 1311 and (name N or name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me P or name C210 or name C211 or name C212 or name C213 or name C214 or name C2 \ 15 or name C216 or name C217 or name C218)) or resid 1312 through 1313 or (resid \ 1315 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name P or name C210 or name C211 or n \ ame C212 or name C213 or name C214 or name C215 or name C216 or name C217 or nam \ e C218)) or resid 1316)) selection = (chain 'C' and (resid 3 through 1301 or (resid 1303 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313)) or (resid 1305 and (name \ C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or \ name C29)) or (resid 1306 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P or name C210 or name C211 or name C212)) or (resid 1309 and (name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216)) or resid 1310 or (resid 1311 and (name N or name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me P or name C210 or name C211 or name C212 or name C213 or name C214 or name C2 \ 15 or name C216 or name C217 or name C218)) or resid 1312 through 1313 or (resid \ 1315 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name P or name C210 or name C211 or n \ ame C212 or name C213 or name C214 or name C215 or name C216 or name C217 or nam \ e C218)) or resid 1316)) selection = (chain 'D' and (resid 3 through 1301 or resid 1303 or (resid 1305 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name \ C29)) or resid 1306 or resid 1309 through 1310 or (resid 1311 and (name N or nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or n \ ame C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name P or name C210 or name C211 or name C212 or name C213 or \ name C214 or name C215 or name C216 or name C217 or name C218)) or resid 1312 t \ hrough 1313 or resid 1315 through 1316)) } 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: 1.930 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: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 37.700 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 0.012 0.175 39696 Z= 0.496 Angle : 1.127 14.784 53276 Z= 0.576 Chirality : 0.059 0.274 5676 Planarity : 0.007 0.148 6364 Dihedral : 20.098 179.053 16440 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.75 % Favored : 90.98 % Rotamer: Outliers : 0.20 % Allowed : 3.58 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 aren not related in a simple way. whole: -3.93 (0.10), residues: 4388 helix: -2.11 (0.08), residues: 2492 sheet: -3.83 (0.25), residues: 172 loop : -3.10 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B1115 TYR 0.071 0.004 TYR C 870 PHE 0.082 0.004 PHE B 858 TRP 0.032 0.004 TRP C1042 HIS 0.011 0.003 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.01206 (39684) covalent geometry : angle 1.12670 (53252) SS BOND : bond 0.01804 ( 12) SS BOND : angle 1.79535 ( 24) hydrogen bonds : bond 0.24056 ( 1796) hydrogen bonds : angle 8.29621 ( 5232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 629 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.0322 (mpp) cc_final: -0.0673 (ppp) REVERT: A 906 MET cc_start: 0.6556 (mtt) cc_final: 0.6289 (mtp) REVERT: A 1161 PHE cc_start: 0.7621 (t80) cc_final: 0.7167 (m-80) REVERT: B 60 MET cc_start: -0.0410 (mpp) cc_final: -0.0733 (ppp) REVERT: B 906 MET cc_start: 0.6576 (mtt) cc_final: 0.6320 (mtp) REVERT: B 1161 PHE cc_start: 0.7597 (t80) cc_final: 0.7187 (m-80) REVERT: C 60 MET cc_start: -0.0628 (mpp) cc_final: -0.1093 (ppp) REVERT: C 906 MET cc_start: 0.6676 (mtt) cc_final: 0.6346 (mtp) REVERT: C 1161 PHE cc_start: 0.7631 (t80) cc_final: 0.7081 (m-80) REVERT: D 60 MET cc_start: -0.0355 (mpp) cc_final: -0.0680 (ppp) REVERT: D 422 ILE cc_start: 0.8177 (mm) cc_final: 0.7972 (mm) REVERT: D 906 MET cc_start: 0.6581 (mtt) cc_final: 0.6316 (mtp) REVERT: D 1161 PHE cc_start: 0.7615 (t80) cc_final: 0.7178 (m-80) outliers start: 8 outliers final: 5 residues processed: 633 average time/residue: 0.9166 time to fit residues: 683.6451 Evaluate side-chains 366 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 361 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain D residue 951 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 177 ASN A 239 ASN A 242 HIS A 272 GLN A 276 HIS A 388 HIS A 538 ASN A 948 ASN A 968 ASN A 983 ASN A1098 ASN A1137 HIS A1210 GLN B 149 HIS B 177 ASN B 239 ASN B 242 HIS B 272 GLN B 276 HIS B 388 HIS B 538 ASN B 948 ASN B 968 ASN B 983 ASN B1098 ASN B1137 HIS B1210 GLN C 149 HIS C 177 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS C 272 GLN C 276 HIS C 388 HIS C 948 ASN C 968 ASN C 983 ASN C1025 HIS C1098 ASN C1137 HIS C1210 GLN D 149 HIS D 177 ASN D 239 ASN D 242 HIS D 272 GLN D 276 HIS D 388 HIS D 948 ASN D 983 ASN D1025 HIS D1098 ASN D1137 HIS D1210 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.225072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149056 restraints weight = 40317.059| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.90 r_work: 0.3393 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39696 Z= 0.166 Angle : 0.734 9.967 53276 Z= 0.369 Chirality : 0.044 0.188 5676 Planarity : 0.005 0.044 6364 Dihedral : 24.730 179.988 7774 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.68 % Favored : 93.05 % Rotamer: Outliers : 1.17 % Allowed : 8.86 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 aren not related in a simple way. whole: -1.81 (0.12), residues: 4388 helix: -0.11 (0.09), residues: 2612 sheet: -3.62 (0.28), residues: 180 loop : -2.71 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 530 TYR 0.025 0.002 TYR A 18 PHE 0.033 0.002 PHE B 858 TRP 0.013 0.002 TRP B 947 HIS 0.005 0.001 HIS C1137 Details of bonding type rmsd covalent geometry : bond 0.00372 (39684) covalent geometry : angle 0.73382 (53252) SS BOND : bond 0.00413 ( 12) SS BOND : angle 1.05491 ( 24) hydrogen bonds : bond 0.05161 ( 1796) hydrogen bonds : angle 4.68951 ( 5232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.0849 (mpp) cc_final: -0.1327 (ppp) REVERT: A 90 ASP cc_start: 0.4926 (OUTLIER) cc_final: 0.4531 (t0) REVERT: A 467 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7933 (mmmt) REVERT: A 843 ARG cc_start: 0.7090 (mpt-90) cc_final: 0.6875 (mtt-85) REVERT: A 881 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 906 MET cc_start: 0.7223 (mtt) cc_final: 0.6869 (mtp) REVERT: A 1161 PHE cc_start: 0.7874 (t80) cc_final: 0.6838 (m-80) REVERT: B 60 MET cc_start: -0.0797 (mpp) cc_final: -0.1276 (ppp) REVERT: B 90 ASP cc_start: 0.4934 (OUTLIER) cc_final: 0.4519 (t0) REVERT: B 665 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7396 (mm-30) REVERT: B 843 ARG cc_start: 0.7077 (mpt-90) cc_final: 0.6866 (mtt-85) REVERT: B 881 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8481 (mt) REVERT: B 906 MET cc_start: 0.7251 (mtt) cc_final: 0.6893 (mtp) REVERT: B 1161 PHE cc_start: 0.7892 (t80) cc_final: 0.6884 (m-80) REVERT: C 60 MET cc_start: -0.0800 (mpp) cc_final: -0.1286 (ppp) REVERT: C 90 ASP cc_start: 0.4886 (OUTLIER) cc_final: 0.4555 (t0) REVERT: C 467 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7909 (mmmt) REVERT: C 665 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7425 (mm-30) REVERT: C 843 ARG cc_start: 0.6724 (mpp-170) cc_final: 0.6324 (mpp80) REVERT: C 881 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8470 (mt) REVERT: C 906 MET cc_start: 0.7257 (mtt) cc_final: 0.6897 (mtp) REVERT: C 1161 PHE cc_start: 0.7907 (t80) cc_final: 0.6867 (m-80) REVERT: D 60 MET cc_start: -0.0807 (mpp) cc_final: -0.1280 (ppp) REVERT: D 90 ASP cc_start: 0.4951 (OUTLIER) cc_final: 0.4520 (t0) REVERT: D 467 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7903 (mmmt) REVERT: D 665 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7250 (mm-30) REVERT: D 843 ARG cc_start: 0.6728 (mpp-170) cc_final: 0.6331 (mpp80) REVERT: D 881 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8469 (mt) REVERT: D 906 MET cc_start: 0.7252 (mtt) cc_final: 0.6891 (mtp) REVERT: D 1161 PHE cc_start: 0.7887 (t80) cc_final: 0.6875 (m-80) outliers start: 46 outliers final: 13 residues processed: 463 average time/residue: 0.8257 time to fit residues: 456.6281 Evaluate side-chains 370 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 349 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 951 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 123 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 437 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 360 optimal weight: 0.0870 chunk 121 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 GLN A 718 ASN A 787 GLN A 789 GLN A 951 ASN A 955 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN B 718 ASN B 787 GLN B 789 GLN B 951 ASN B 955 ASN C 239 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN C 635 GLN C 718 ASN C 787 GLN C 789 GLN C 951 ASN C 955 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 GLN D 718 ASN D 787 GLN D 789 GLN D 951 ASN D 955 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.220068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142228 restraints weight = 38714.094| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.50 r_work: 0.3223 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 39696 Z= 0.248 Angle : 0.782 9.204 53276 Z= 0.392 Chirality : 0.049 0.208 5676 Planarity : 0.006 0.055 6364 Dihedral : 24.333 179.859 7774 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.91 % Favored : 91.91 % Rotamer: Outliers : 1.76 % Allowed : 10.39 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.27 (0.12), residues: 4388 helix: 0.34 (0.10), residues: 2600 sheet: -3.16 (0.30), residues: 188 loop : -2.54 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 274 TYR 0.023 0.003 TYR D 776 PHE 0.033 0.003 PHE C 858 TRP 0.019 0.003 TRP C 78 HIS 0.010 0.002 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00588 (39684) covalent geometry : angle 0.78124 (53252) SS BOND : bond 0.00453 ( 12) SS BOND : angle 1.43823 ( 24) hydrogen bonds : bond 0.06068 ( 1796) hydrogen bonds : angle 4.66271 ( 5232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 383 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.0921 (mpp) cc_final: -0.1424 (ppp) REVERT: A 130 MET cc_start: 0.6391 (mtm) cc_final: 0.6184 (mtm) REVERT: A 143 MET cc_start: 0.4798 (mpt) cc_final: 0.4298 (mmp) REVERT: A 467 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7917 (mmmt) REVERT: A 473 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7687 (mtt-85) REVERT: A 481 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6795 (mptt) REVERT: A 665 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 843 ARG cc_start: 0.7002 (mpt-90) cc_final: 0.6765 (mtt-85) REVERT: A 881 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 906 MET cc_start: 0.7250 (mtt) cc_final: 0.6824 (mtp) REVERT: A 956 HIS cc_start: 0.8014 (m-70) cc_final: 0.7478 (m-70) REVERT: A 1161 PHE cc_start: 0.7946 (t80) cc_final: 0.6759 (m-80) REVERT: A 1202 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: B 60 MET cc_start: -0.0988 (mpp) cc_final: -0.1456 (ppp) REVERT: B 143 MET cc_start: 0.4801 (mpt) cc_final: 0.4317 (mmp) REVERT: B 473 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7673 (mtt-85) REVERT: B 481 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6907 (mptt) REVERT: B 665 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 843 ARG cc_start: 0.7005 (mpt-90) cc_final: 0.6772 (mtt-85) REVERT: B 881 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8369 (mp) REVERT: B 906 MET cc_start: 0.7215 (mtt) cc_final: 0.6794 (mtp) REVERT: B 956 HIS cc_start: 0.8018 (m-70) cc_final: 0.7473 (m-70) REVERT: B 1027 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: B 1161 PHE cc_start: 0.7916 (t80) cc_final: 0.6760 (m-80) REVERT: C 60 MET cc_start: -0.0956 (mpp) cc_final: -0.1442 (ppp) REVERT: C 143 MET cc_start: 0.4771 (mpt) cc_final: 0.4266 (mmp) REVERT: C 467 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7934 (mmmt) REVERT: C 473 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7669 (mtt-85) REVERT: C 481 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6804 (mptt) REVERT: C 665 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7426 (mm-30) REVERT: C 843 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6224 (mpp80) REVERT: C 881 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 906 MET cc_start: 0.7243 (mtt) cc_final: 0.6814 (mtp) REVERT: C 956 HIS cc_start: 0.7969 (m-70) cc_final: 0.7494 (m-70) REVERT: C 1027 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: C 1161 PHE cc_start: 0.7936 (t80) cc_final: 0.6754 (m-80) REVERT: D 60 MET cc_start: -0.0930 (mpp) cc_final: -0.1414 (ppp) REVERT: D 143 MET cc_start: 0.4796 (mpt) cc_final: 0.4294 (mmp) REVERT: D 467 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7926 (mmmt) REVERT: D 473 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7670 (mtt-85) REVERT: D 665 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7570 (tp30) REVERT: D 843 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6216 (mpp80) REVERT: D 881 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8373 (mp) REVERT: D 906 MET cc_start: 0.7231 (mtt) cc_final: 0.6807 (mtp) REVERT: D 956 HIS cc_start: 0.8024 (m-70) cc_final: 0.7482 (m-70) REVERT: D 1027 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: D 1161 PHE cc_start: 0.7903 (t80) cc_final: 0.6756 (m-80) outliers start: 69 outliers final: 11 residues processed: 431 average time/residue: 0.8463 time to fit residues: 435.7354 Evaluate side-chains 375 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 347 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 843 ARG Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 843 ARG Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 1027 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 342 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 381 optimal weight: 0.9990 chunk 430 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.220926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136468 restraints weight = 38893.079| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.95 r_work: 0.3275 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39696 Z= 0.164 Angle : 0.656 8.879 53276 Z= 0.331 Chirality : 0.043 0.219 5676 Planarity : 0.005 0.050 6364 Dihedral : 23.455 175.927 7766 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 1.99 % Allowed : 11.95 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.76 (0.12), residues: 4388 helix: 0.79 (0.10), residues: 2620 sheet: -2.86 (0.32), residues: 188 loop : -2.48 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 530 TYR 0.016 0.002 TYR C1122 PHE 0.017 0.002 PHE A 936 TRP 0.015 0.002 TRP D 78 HIS 0.004 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00379 (39684) covalent geometry : angle 0.65565 (53252) SS BOND : bond 0.00471 ( 12) SS BOND : angle 1.19536 ( 24) hydrogen bonds : bond 0.04866 ( 1796) hydrogen bonds : angle 4.28231 ( 5232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 356 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.1117 (mpp) cc_final: -0.1548 (ppp) REVERT: A 90 ASP cc_start: 0.4913 (OUTLIER) cc_final: 0.4685 (t0) REVERT: A 143 MET cc_start: 0.4813 (mpt) cc_final: 0.4316 (mmp) REVERT: A 449 MET cc_start: 0.8394 (mtp) cc_final: 0.8164 (mtp) REVERT: A 467 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7871 (mmmt) REVERT: A 473 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7623 (mtt-85) REVERT: A 481 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6802 (mptt) REVERT: A 665 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 671 LEU cc_start: 0.3988 (OUTLIER) cc_final: 0.3753 (tp) REVERT: A 750 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8206 (mtp85) REVERT: A 843 ARG cc_start: 0.6961 (mpt-90) cc_final: 0.6691 (mtt-85) REVERT: A 906 MET cc_start: 0.7190 (mtt) cc_final: 0.6792 (mtp) REVERT: A 956 HIS cc_start: 0.7789 (m-70) cc_final: 0.7213 (m-70) REVERT: A 1161 PHE cc_start: 0.7868 (t80) cc_final: 0.6673 (m-80) REVERT: A 1188 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7649 (tmmm) REVERT: B 60 MET cc_start: -0.1158 (mpp) cc_final: -0.1594 (ppp) REVERT: B 90 ASP cc_start: 0.4773 (OUTLIER) cc_final: 0.4535 (t0) REVERT: B 143 MET cc_start: 0.4818 (mpt) cc_final: 0.4311 (mmp) REVERT: B 473 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7618 (mtt-85) REVERT: B 481 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6835 (mptt) REVERT: B 665 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7264 (mm-30) REVERT: B 671 LEU cc_start: 0.3981 (OUTLIER) cc_final: 0.3743 (tp) REVERT: B 750 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8205 (mtp85) REVERT: B 843 ARG cc_start: 0.6922 (mpt-90) cc_final: 0.6646 (mtt-85) REVERT: B 906 MET cc_start: 0.7119 (mtt) cc_final: 0.6713 (mtp) REVERT: B 956 HIS cc_start: 0.7783 (m-70) cc_final: 0.7219 (m-70) REVERT: B 1161 PHE cc_start: 0.7879 (t80) cc_final: 0.6685 (m-80) REVERT: B 1188 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7651 (tmmm) REVERT: C 60 MET cc_start: -0.1079 (mpp) cc_final: -0.1521 (ppp) REVERT: C 90 ASP cc_start: 0.4943 (OUTLIER) cc_final: 0.4655 (t0) REVERT: C 143 MET cc_start: 0.4817 (mpt) cc_final: 0.4312 (mmp) REVERT: C 467 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7866 (mmmt) REVERT: C 473 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7619 (mtt-85) REVERT: C 481 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6833 (mptt) REVERT: C 665 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7229 (mm-30) REVERT: C 671 LEU cc_start: 0.3991 (OUTLIER) cc_final: 0.3749 (tp) REVERT: C 750 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8204 (mtp85) REVERT: C 843 ARG cc_start: 0.6580 (mpp-170) cc_final: 0.6122 (mpp80) REVERT: C 906 MET cc_start: 0.7121 (mtt) cc_final: 0.6714 (mtp) REVERT: C 956 HIS cc_start: 0.7791 (m-70) cc_final: 0.7273 (m-70) REVERT: C 1161 PHE cc_start: 0.7882 (t80) cc_final: 0.6702 (m-80) REVERT: C 1188 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7657 (tmmm) REVERT: D 60 MET cc_start: -0.1134 (mpp) cc_final: -0.1582 (ppp) REVERT: D 90 ASP cc_start: 0.4904 (OUTLIER) cc_final: 0.4609 (t0) REVERT: D 143 MET cc_start: 0.4818 (mpt) cc_final: 0.4315 (mmp) REVERT: D 467 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7884 (mmmt) REVERT: D 473 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7612 (mtt-85) REVERT: D 671 LEU cc_start: 0.3911 (OUTLIER) cc_final: 0.3702 (tp) REVERT: D 750 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8201 (mtp85) REVERT: D 843 ARG cc_start: 0.6585 (mpp-170) cc_final: 0.6126 (mpp80) REVERT: D 906 MET cc_start: 0.7125 (mtt) cc_final: 0.6732 (mtp) REVERT: D 956 HIS cc_start: 0.7777 (m-70) cc_final: 0.7195 (m-70) REVERT: D 1161 PHE cc_start: 0.7872 (t80) cc_final: 0.6693 (m-80) REVERT: D 1188 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7654 (tmmm) outliers start: 78 outliers final: 15 residues processed: 417 average time/residue: 0.8751 time to fit residues: 433.6903 Evaluate side-chains 365 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 327 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 49 optimal weight: 0.9980 chunk 264 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 276 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 425 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 50 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 50 GLN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.220146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140407 restraints weight = 38840.859| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.60 r_work: 0.3215 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 39696 Z= 0.188 Angle : 0.683 8.617 53276 Z= 0.342 Chirality : 0.045 0.236 5676 Planarity : 0.005 0.053 6364 Dihedral : 23.011 172.390 7766 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.00 % Favored : 92.82 % Rotamer: Outliers : 2.60 % Allowed : 12.05 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.63 (0.12), residues: 4388 helix: 0.89 (0.10), residues: 2628 sheet: -2.94 (0.31), residues: 228 loop : -2.36 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 530 TYR 0.015 0.002 TYR A1122 PHE 0.018 0.002 PHE D 936 TRP 0.016 0.002 TRP A 78 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00442 (39684) covalent geometry : angle 0.68217 (53252) SS BOND : bond 0.00456 ( 12) SS BOND : angle 1.32182 ( 24) hydrogen bonds : bond 0.05194 ( 1796) hydrogen bonds : angle 4.28911 ( 5232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 349 time to evaluate : 1.516 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 60 MET cc_start: -0.1147 (mpp) cc_final: -0.1593 (ppp) REVERT: A 90 ASP cc_start: 0.4865 (OUTLIER) cc_final: 0.4577 (t0) REVERT: A 143 MET cc_start: 0.4824 (mpt) cc_final: 0.4296 (mmp) REVERT: A 265 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6703 (tp30) REVERT: A 449 MET cc_start: 0.8478 (mtp) cc_final: 0.8265 (mtp) REVERT: A 467 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7898 (mmmt) REVERT: A 473 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7662 (mtt-85) REVERT: A 481 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6738 (mptt) REVERT: A 665 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7406 (tp30) REVERT: A 671 LEU cc_start: 0.3892 (OUTLIER) cc_final: 0.3663 (tp) REVERT: A 750 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8235 (mtp85) REVERT: A 843 ARG cc_start: 0.7024 (mpt-90) cc_final: 0.6764 (mtt-85) REVERT: A 906 MET cc_start: 0.7213 (mtt) cc_final: 0.6823 (mtp) REVERT: A 956 HIS cc_start: 0.7963 (m-70) cc_final: 0.7384 (m-70) REVERT: A 1161 PHE cc_start: 0.7886 (t80) cc_final: 0.6728 (m-80) REVERT: A 1168 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6571 (tmmm) REVERT: A 1188 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7691 (tmmm) REVERT: B 60 MET cc_start: -0.1106 (mpp) cc_final: -0.1560 (ppp) REVERT: B 90 ASP cc_start: 0.4859 (OUTLIER) cc_final: 0.4596 (t0) REVERT: B 143 MET cc_start: 0.4881 (mpt) cc_final: 0.4342 (mmp) REVERT: B 473 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7665 (mtt-85) REVERT: B 481 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6758 (mptt) REVERT: B 665 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 671 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3670 (tp) REVERT: B 750 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8248 (mtp85) REVERT: B 843 ARG cc_start: 0.7007 (mpt-90) cc_final: 0.6740 (mtt-85) REVERT: B 906 MET cc_start: 0.7167 (mtt) cc_final: 0.6781 (mtp) REVERT: B 956 HIS cc_start: 0.7865 (m-70) cc_final: 0.7279 (m-70) REVERT: B 1027 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: B 1161 PHE cc_start: 0.7880 (t80) cc_final: 0.6724 (m-80) REVERT: B 1188 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7695 (tmmm) REVERT: C 60 MET cc_start: -0.1091 (mpp) cc_final: -0.1548 (ppp) REVERT: C 90 ASP cc_start: 0.4935 (OUTLIER) cc_final: 0.4630 (t0) REVERT: C 143 MET cc_start: 0.4971 (mpt) cc_final: 0.4415 (mmp) REVERT: C 467 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7853 (mmmt) REVERT: C 473 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7662 (mtt-85) REVERT: C 481 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6757 (mptt) REVERT: C 665 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 750 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8240 (mtp85) REVERT: C 843 ARG cc_start: 0.6664 (mpp-170) cc_final: 0.6163 (mpp80) REVERT: C 906 MET cc_start: 0.7165 (mtt) cc_final: 0.6783 (mtp) REVERT: C 956 HIS cc_start: 0.7943 (m-70) cc_final: 0.7403 (m-70) REVERT: C 1027 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: C 1161 PHE cc_start: 0.7883 (t80) cc_final: 0.6722 (m-80) REVERT: C 1168 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6586 (tmmm) REVERT: C 1188 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7694 (tmmm) REVERT: D 60 MET cc_start: -0.1092 (mpp) cc_final: -0.1550 (ppp) REVERT: D 90 ASP cc_start: 0.4930 (OUTLIER) cc_final: 0.4629 (t0) REVERT: D 143 MET cc_start: 0.4883 (mpt) cc_final: 0.4340 (mmp) REVERT: D 467 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7855 (mmmt) REVERT: D 473 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7649 (mtt-85) REVERT: D 671 LEU cc_start: 0.3913 (OUTLIER) cc_final: 0.3680 (tp) REVERT: D 750 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8234 (mtp85) REVERT: D 843 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6168 (mpp80) REVERT: D 906 MET cc_start: 0.7168 (mtt) cc_final: 0.6786 (mtp) REVERT: D 956 HIS cc_start: 0.7858 (m-70) cc_final: 0.7318 (m-70) REVERT: D 1027 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: D 1161 PHE cc_start: 0.7881 (t80) cc_final: 0.6719 (m-80) REVERT: D 1188 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7688 (tmmm) outliers start: 102 outliers final: 26 residues processed: 430 average time/residue: 0.7463 time to fit residues: 385.3313 Evaluate side-chains 382 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain B residue 1218 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1168 LYS Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 843 ARG Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 312 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 379 optimal weight: 0.9990 chunk 318 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 391 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 435 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.221938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145742 restraints weight = 39224.116| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.67 r_work: 0.3247 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39696 Z= 0.126 Angle : 0.602 8.360 53276 Z= 0.304 Chirality : 0.041 0.217 5676 Planarity : 0.004 0.052 6364 Dihedral : 22.245 172.648 7766 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 2.12 % Allowed : 13.00 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.25 (0.13), residues: 4388 helix: 1.22 (0.10), residues: 2632 sheet: -2.80 (0.32), residues: 228 loop : -2.28 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 530 TYR 0.012 0.002 TYR C 759 PHE 0.013 0.001 PHE C 936 TRP 0.013 0.001 TRP D 747 HIS 0.005 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00283 (39684) covalent geometry : angle 0.60152 (53252) SS BOND : bond 0.00426 ( 12) SS BOND : angle 1.11486 ( 24) hydrogen bonds : bond 0.04227 ( 1796) hydrogen bonds : angle 4.04994 ( 5232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 363 time to evaluate : 1.177 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 60 MET cc_start: -0.1201 (mpp) cc_final: -0.1663 (ppp) REVERT: A 90 ASP cc_start: 0.4861 (OUTLIER) cc_final: 0.4573 (t0) REVERT: A 111 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7418 (mt) REVERT: A 143 MET cc_start: 0.4863 (mpt) cc_final: 0.4304 (mmp) REVERT: A 162 LYS cc_start: 0.7320 (tttp) cc_final: 0.6876 (tttp) REVERT: A 449 MET cc_start: 0.8440 (mtp) cc_final: 0.8200 (mtp) REVERT: A 467 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7939 (mmmt) REVERT: A 473 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7709 (mtt-85) REVERT: A 624 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: A 671 LEU cc_start: 0.3966 (OUTLIER) cc_final: 0.3610 (tp) REVERT: A 906 MET cc_start: 0.7133 (mtt) cc_final: 0.6798 (mtp) REVERT: A 956 HIS cc_start: 0.7989 (m-70) cc_final: 0.7399 (m-70) REVERT: A 1161 PHE cc_start: 0.7910 (t80) cc_final: 0.6756 (m-80) REVERT: A 1188 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7696 (tmmm) REVERT: A 1202 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7934 (mm-30) REVERT: B 60 MET cc_start: -0.1275 (mpp) cc_final: -0.1737 (ppp) REVERT: B 90 ASP cc_start: 0.4863 (OUTLIER) cc_final: 0.4580 (t0) REVERT: B 111 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7414 (mt) REVERT: B 143 MET cc_start: 0.4874 (mpt) cc_final: 0.4316 (mmp) REVERT: B 162 LYS cc_start: 0.7324 (tttp) cc_final: 0.6877 (tttp) REVERT: B 473 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7706 (mtt-85) REVERT: B 624 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: B 906 MET cc_start: 0.7133 (mtt) cc_final: 0.6800 (mtp) REVERT: B 956 HIS cc_start: 0.7998 (m-70) cc_final: 0.7405 (m-70) REVERT: B 1161 PHE cc_start: 0.7935 (t80) cc_final: 0.6790 (m-80) REVERT: B 1188 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7711 (tmmm) REVERT: C 60 MET cc_start: -0.1360 (mpp) cc_final: -0.1786 (ppp) REVERT: C 90 ASP cc_start: 0.4960 (OUTLIER) cc_final: 0.4658 (t0) REVERT: C 111 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7410 (mt) REVERT: C 143 MET cc_start: 0.4857 (mpt) cc_final: 0.4303 (mmp) REVERT: C 162 LYS cc_start: 0.7314 (tttp) cc_final: 0.6853 (tttp) REVERT: C 467 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7928 (mmmt) REVERT: C 473 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7720 (mtt-85) REVERT: C 624 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8091 (mm-30) REVERT: C 843 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6161 (mpp80) REVERT: C 906 MET cc_start: 0.7129 (mtt) cc_final: 0.6797 (mtp) REVERT: C 956 HIS cc_start: 0.7969 (m-70) cc_final: 0.7390 (m-70) REVERT: C 1161 PHE cc_start: 0.7910 (t80) cc_final: 0.6774 (m-80) REVERT: C 1188 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7691 (tmmm) REVERT: D 60 MET cc_start: -0.1441 (mpp) cc_final: -0.1843 (ppp) REVERT: D 90 ASP cc_start: 0.4959 (OUTLIER) cc_final: 0.4686 (t0) REVERT: D 111 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7405 (mt) REVERT: D 143 MET cc_start: 0.4864 (mpt) cc_final: 0.4307 (mmp) REVERT: D 162 LYS cc_start: 0.7356 (tttp) cc_final: 0.6884 (tttp) REVERT: D 467 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7898 (mmmt) REVERT: D 473 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7694 (mtt-85) REVERT: D 624 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: D 843 ARG cc_start: 0.6657 (mpp-170) cc_final: 0.6137 (mpp80) REVERT: D 906 MET cc_start: 0.7111 (mtt) cc_final: 0.6778 (mtp) REVERT: D 956 HIS cc_start: 0.7995 (m-70) cc_final: 0.7404 (m-70) REVERT: D 1161 PHE cc_start: 0.7895 (t80) cc_final: 0.6731 (m-80) REVERT: D 1188 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7679 (tmmm) outliers start: 83 outliers final: 26 residues processed: 433 average time/residue: 0.7425 time to fit residues: 386.2279 Evaluate side-chains 385 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 337 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 624 GLU Chi-restraints excluded: chain C residue 843 ARG Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 624 GLU Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 7 optimal weight: 50.0000 chunk 88 optimal weight: 2.9990 chunk 262 optimal weight: 0.0030 chunk 301 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 225 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 chunk 313 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.219828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142510 restraints weight = 38678.179| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.80 r_work: 0.3202 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 39696 Z= 0.213 Angle : 0.699 8.436 53276 Z= 0.350 Chirality : 0.046 0.238 5676 Planarity : 0.005 0.055 6364 Dihedral : 22.389 170.468 7766 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.20 % Favored : 92.62 % Rotamer: Outliers : 2.37 % Allowed : 13.20 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.45 (0.13), residues: 4388 helix: 1.03 (0.10), residues: 2640 sheet: -2.73 (0.32), residues: 228 loop : -2.33 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 843 TYR 0.019 0.002 TYR A1122 PHE 0.020 0.002 PHE A 936 TRP 0.015 0.002 TRP A 78 HIS 0.006 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00505 (39684) covalent geometry : angle 0.69876 (53252) SS BOND : bond 0.00452 ( 12) SS BOND : angle 1.42072 ( 24) hydrogen bonds : bond 0.05360 ( 1796) hydrogen bonds : angle 4.25668 ( 5232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 347 time to evaluate : 1.261 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 60 MET cc_start: -0.1060 (mpp) cc_final: -0.1542 (ppp) REVERT: A 90 ASP cc_start: 0.4860 (OUTLIER) cc_final: 0.4364 (t0) REVERT: A 110 ARG cc_start: 0.6190 (tpt-90) cc_final: 0.5531 (tpt-90) REVERT: A 111 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7431 (mt) REVERT: A 143 MET cc_start: 0.4820 (mpt) cc_final: 0.4291 (mmp) REVERT: A 368 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.5247 (mpp) REVERT: A 369 MET cc_start: 0.5822 (tpt) cc_final: 0.5493 (mtt) REVERT: A 467 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7931 (mmmt) REVERT: A 473 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7729 (mtt-85) REVERT: A 530 ARG cc_start: 0.7152 (mmm160) cc_final: 0.6921 (mmm-85) REVERT: A 671 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3616 (tp) REVERT: A 906 MET cc_start: 0.7230 (mtt) cc_final: 0.6844 (mtp) REVERT: A 956 HIS cc_start: 0.8029 (m-70) cc_final: 0.7478 (m-70) REVERT: A 1161 PHE cc_start: 0.7910 (t80) cc_final: 0.6755 (m-80) REVERT: A 1168 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6607 (tmmm) REVERT: A 1188 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7725 (tmmm) REVERT: B 60 MET cc_start: -0.1010 (mpp) cc_final: -0.1672 (ppp) REVERT: B 90 ASP cc_start: 0.4929 (OUTLIER) cc_final: 0.4632 (t0) REVERT: B 111 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7415 (mt) REVERT: B 143 MET cc_start: 0.4822 (mpt) cc_final: 0.4293 (mmp) REVERT: B 473 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7729 (mtt-85) REVERT: B 530 ARG cc_start: 0.7170 (mmm160) cc_final: 0.6938 (mmm-85) REVERT: B 906 MET cc_start: 0.7229 (mtt) cc_final: 0.6856 (mtp) REVERT: B 956 HIS cc_start: 0.8007 (m-70) cc_final: 0.7529 (m-70) REVERT: B 1161 PHE cc_start: 0.7910 (t80) cc_final: 0.6752 (m-80) REVERT: B 1188 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7703 (tmmm) REVERT: C 60 MET cc_start: -0.1232 (mpp) cc_final: -0.1650 (ppp) REVERT: C 90 ASP cc_start: 0.4937 (OUTLIER) cc_final: 0.4411 (t0) REVERT: C 110 ARG cc_start: 0.6176 (tpt-90) cc_final: 0.5512 (tpt-90) REVERT: C 111 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7428 (mt) REVERT: C 143 MET cc_start: 0.4826 (mpt) cc_final: 0.4297 (mmp) REVERT: C 467 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7910 (mmmt) REVERT: C 473 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7735 (mtt-85) REVERT: C 843 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6180 (mpp80) REVERT: C 906 MET cc_start: 0.7228 (mtt) cc_final: 0.6843 (mtp) REVERT: C 956 HIS cc_start: 0.8106 (m-70) cc_final: 0.7611 (m-70) REVERT: C 1161 PHE cc_start: 0.7903 (t80) cc_final: 0.6742 (m-80) REVERT: C 1168 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6594 (tmmm) REVERT: C 1188 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7709 (tmmm) REVERT: D 60 MET cc_start: -0.1039 (mpp) cc_final: -0.1684 (ppp) REVERT: D 90 ASP cc_start: 0.4991 (OUTLIER) cc_final: 0.4659 (t0) REVERT: D 111 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7437 (mt) REVERT: D 143 MET cc_start: 0.4821 (mpt) cc_final: 0.4286 (mmp) REVERT: D 467 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7941 (mmmt) REVERT: D 473 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7718 (mtt-85) REVERT: D 530 ARG cc_start: 0.7163 (mmm160) cc_final: 0.6932 (mmm-85) REVERT: D 843 ARG cc_start: 0.6702 (mpp-170) cc_final: 0.6186 (mpp80) REVERT: D 906 MET cc_start: 0.7231 (mtt) cc_final: 0.6887 (mtp) REVERT: D 956 HIS cc_start: 0.8006 (m-70) cc_final: 0.7563 (m-70) REVERT: D 1161 PHE cc_start: 0.7910 (t80) cc_final: 0.6750 (m-80) REVERT: D 1188 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7708 (tmmm) outliers start: 93 outliers final: 50 residues processed: 417 average time/residue: 0.6637 time to fit residues: 335.1748 Evaluate side-chains 405 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 334 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 794 MET Chi-restraints excluded: chain C residue 843 ARG Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1168 LYS Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 737 THR Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 198 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 337 optimal weight: 7.9990 chunk 365 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 364 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 305 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.219921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137250 restraints weight = 38665.231| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.21 r_work: 0.3206 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 39696 Z= 0.204 Angle : 0.688 8.552 53276 Z= 0.345 Chirality : 0.046 0.243 5676 Planarity : 0.005 0.055 6364 Dihedral : 22.307 171.630 7766 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.34 % Favored : 92.48 % Rotamer: Outliers : 1.97 % Allowed : 13.92 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.52 (0.12), residues: 4388 helix: 0.93 (0.10), residues: 2672 sheet: -2.74 (0.32), residues: 228 loop : -2.33 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 843 TYR 0.017 0.002 TYR A1122 PHE 0.019 0.002 PHE A 936 TRP 0.015 0.002 TRP D 78 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00486 (39684) covalent geometry : angle 0.68723 (53252) SS BOND : bond 0.00442 ( 12) SS BOND : angle 1.34065 ( 24) hydrogen bonds : bond 0.05200 ( 1796) hydrogen bonds : angle 4.24495 ( 5232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 332 time to evaluate : 1.133 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 60 MET cc_start: -0.1014 (mpp) cc_final: -0.1686 (ppp) REVERT: A 90 ASP cc_start: 0.4858 (OUTLIER) cc_final: 0.4378 (t0) REVERT: A 110 ARG cc_start: 0.6161 (tpt-90) cc_final: 0.5491 (tpt-90) REVERT: A 111 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7433 (mt) REVERT: A 143 MET cc_start: 0.4823 (mpt) cc_final: 0.4295 (mmp) REVERT: A 368 MET cc_start: 0.5492 (OUTLIER) cc_final: 0.5290 (mpp) REVERT: A 369 MET cc_start: 0.5835 (tpt) cc_final: 0.5537 (mtt) REVERT: A 401 LYS cc_start: 0.6850 (mmmm) cc_final: 0.6612 (mmmm) REVERT: A 467 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7877 (mmmt) REVERT: A 473 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7640 (mtt-85) REVERT: A 843 ARG cc_start: 0.6970 (mtt-85) cc_final: 0.6756 (mtt-85) REVERT: A 906 MET cc_start: 0.7186 (mtt) cc_final: 0.6776 (mtp) REVERT: A 956 HIS cc_start: 0.7967 (m-70) cc_final: 0.7471 (m-70) REVERT: A 1161 PHE cc_start: 0.7885 (t80) cc_final: 0.6637 (m-80) REVERT: A 1168 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6542 (tmmm) REVERT: A 1188 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7634 (tmmm) REVERT: B 60 MET cc_start: -0.0986 (mpp) cc_final: -0.1629 (ppp) REVERT: B 90 ASP cc_start: 0.4985 (OUTLIER) cc_final: 0.4444 (t0) REVERT: B 110 ARG cc_start: 0.6169 (tpt-90) cc_final: 0.5504 (tpt-90) REVERT: B 111 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 143 MET cc_start: 0.4826 (mpt) cc_final: 0.4283 (mmp) REVERT: B 368 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.5219 (mpp) REVERT: B 473 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7639 (mtt-85) REVERT: B 843 ARG cc_start: 0.6959 (mtt-85) cc_final: 0.6755 (mtt-85) REVERT: B 906 MET cc_start: 0.7174 (mtt) cc_final: 0.6762 (mtp) REVERT: B 956 HIS cc_start: 0.7939 (m-70) cc_final: 0.7469 (m-70) REVERT: B 1161 PHE cc_start: 0.7878 (t80) cc_final: 0.6630 (m-80) REVERT: B 1188 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7623 (tmmm) REVERT: C 60 MET cc_start: -0.1227 (mpp) cc_final: -0.1877 (ppp) REVERT: C 90 ASP cc_start: 0.4932 (OUTLIER) cc_final: 0.4429 (t0) REVERT: C 110 ARG cc_start: 0.6148 (tpt-90) cc_final: 0.5416 (tpt-90) REVERT: C 111 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7441 (mt) REVERT: C 143 MET cc_start: 0.4827 (mpt) cc_final: 0.4281 (mmp) REVERT: C 467 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7875 (mmmt) REVERT: C 473 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7646 (mtt-85) REVERT: C 843 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.6081 (mpp80) REVERT: C 906 MET cc_start: 0.7170 (mtt) cc_final: 0.6761 (mtp) REVERT: C 956 HIS cc_start: 0.8028 (m-70) cc_final: 0.7578 (m-70) REVERT: C 1161 PHE cc_start: 0.7879 (t80) cc_final: 0.6627 (m-80) REVERT: C 1168 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6555 (tmmm) REVERT: C 1188 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7629 (tmmm) REVERT: D 60 MET cc_start: -0.1078 (mpp) cc_final: -0.1719 (ppp) REVERT: D 90 ASP cc_start: 0.4986 (OUTLIER) cc_final: 0.4451 (t0) REVERT: D 110 ARG cc_start: 0.6169 (tpt-90) cc_final: 0.5456 (tpt-90) REVERT: D 111 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7440 (mt) REVERT: D 143 MET cc_start: 0.4824 (mpt) cc_final: 0.4280 (mmp) REVERT: D 401 LYS cc_start: 0.6806 (mmmm) cc_final: 0.6330 (mtpm) REVERT: D 467 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7865 (mmmt) REVERT: D 473 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7638 (mtt-85) REVERT: D 843 ARG cc_start: 0.6599 (mpp-170) cc_final: 0.6064 (mpp80) REVERT: D 906 MET cc_start: 0.7182 (mtt) cc_final: 0.6770 (mtp) REVERT: D 956 HIS cc_start: 0.7944 (m-70) cc_final: 0.7468 (m-70) REVERT: D 1161 PHE cc_start: 0.7886 (t80) cc_final: 0.6633 (m-80) REVERT: D 1188 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7619 (tmmm) outliers start: 77 outliers final: 46 residues processed: 389 average time/residue: 0.7219 time to fit residues: 338.7589 Evaluate side-chains 391 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 324 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain C residue 794 MET Chi-restraints excluded: chain C residue 843 ARG Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1168 LYS Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 192 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 428 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 318 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN ** D 281 GLN ** 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 = 0.4521 r_free = 0.4521 target = 0.221148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135528 restraints weight = 38861.007| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.89 r_work: 0.3282 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39696 Z= 0.142 Angle : 0.626 8.319 53276 Z= 0.315 Chirality : 0.042 0.232 5676 Planarity : 0.004 0.054 6364 Dihedral : 21.788 172.087 7764 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.00 % Favored : 92.82 % Rotamer: Outliers : 1.74 % Allowed : 14.45 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.24 (0.13), residues: 4388 helix: 1.13 (0.10), residues: 2692 sheet: -2.60 (0.33), residues: 228 loop : -2.23 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 843 TYR 0.012 0.002 TYR A1122 PHE 0.015 0.002 PHE B 936 TRP 0.014 0.002 TRP D 747 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00326 (39684) covalent geometry : angle 0.62563 (53252) SS BOND : bond 0.00458 ( 12) SS BOND : angle 1.25516 ( 24) hydrogen bonds : bond 0.04490 ( 1796) hydrogen bonds : angle 4.09043 ( 5232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 333 time to evaluate : 1.490 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 60 MET cc_start: -0.0963 (mpp) cc_final: -0.1668 (ppp) REVERT: A 90 ASP cc_start: 0.4900 (OUTLIER) cc_final: 0.4431 (t0) REVERT: A 110 ARG cc_start: 0.6114 (tpt-90) cc_final: 0.5277 (tpt-90) REVERT: A 111 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7473 (mt) REVERT: A 143 MET cc_start: 0.4785 (mpt) cc_final: 0.4258 (mmp) REVERT: A 369 MET cc_start: 0.5808 (tpt) cc_final: 0.5508 (mtt) REVERT: A 401 LYS cc_start: 0.6766 (mmmm) cc_final: 0.6510 (mmmm) REVERT: A 449 MET cc_start: 0.8491 (mtp) cc_final: 0.8256 (mtp) REVERT: A 467 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7851 (mmmt) REVERT: A 473 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7632 (mtt-85) REVERT: A 906 MET cc_start: 0.7140 (mtt) cc_final: 0.6782 (mtp) REVERT: A 956 HIS cc_start: 0.7951 (m-70) cc_final: 0.7436 (m-70) REVERT: A 1161 PHE cc_start: 0.7851 (t80) cc_final: 0.6653 (m-80) REVERT: A 1188 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7645 (tmmm) REVERT: A 1202 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7766 (mm-30) REVERT: B 60 MET cc_start: -0.0951 (mpp) cc_final: -0.1616 (ppp) REVERT: B 90 ASP cc_start: 0.4913 (OUTLIER) cc_final: 0.4436 (t0) REVERT: B 110 ARG cc_start: 0.6111 (tpt-90) cc_final: 0.5276 (tpt-90) REVERT: B 111 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7472 (mt) REVERT: B 143 MET cc_start: 0.4792 (mpt) cc_final: 0.4269 (mmp) REVERT: B 265 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6726 (tp30) REVERT: B 401 LYS cc_start: 0.6799 (mmmm) cc_final: 0.6512 (mmmm) REVERT: B 473 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7627 (mtt-85) REVERT: B 906 MET cc_start: 0.7133 (mtt) cc_final: 0.6777 (mtp) REVERT: B 956 HIS cc_start: 0.7864 (m-70) cc_final: 0.7373 (m-70) REVERT: B 1161 PHE cc_start: 0.7837 (t80) cc_final: 0.6608 (m-80) REVERT: B 1188 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7634 (tmmm) REVERT: C 60 MET cc_start: -0.1035 (mpp) cc_final: -0.1754 (ppp) REVERT: C 90 ASP cc_start: 0.4906 (OUTLIER) cc_final: 0.4399 (t0) REVERT: C 110 ARG cc_start: 0.6110 (tpt-90) cc_final: 0.5464 (tpt-90) REVERT: C 111 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7445 (mt) REVERT: C 143 MET cc_start: 0.4793 (mpt) cc_final: 0.4268 (mmp) REVERT: C 265 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: C 401 LYS cc_start: 0.6802 (mmmm) cc_final: 0.6510 (mmmm) REVERT: C 467 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7854 (mmmt) REVERT: C 473 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7637 (mtt-85) REVERT: C 843 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6088 (mpp80) REVERT: C 906 MET cc_start: 0.7133 (mtt) cc_final: 0.6777 (mtp) REVERT: C 956 HIS cc_start: 0.7945 (m-70) cc_final: 0.7418 (m-70) REVERT: C 1161 PHE cc_start: 0.7838 (t80) cc_final: 0.6610 (m-80) REVERT: C 1188 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7628 (tmmm) REVERT: D 60 MET cc_start: -0.0969 (mpp) cc_final: -0.1628 (ppp) REVERT: D 90 ASP cc_start: 0.4904 (OUTLIER) cc_final: 0.4411 (t0) REVERT: D 110 ARG cc_start: 0.6107 (tpt-90) cc_final: 0.5478 (tpt-90) REVERT: D 111 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7442 (mt) REVERT: D 143 MET cc_start: 0.4789 (mpt) cc_final: 0.4269 (mmp) REVERT: D 162 LYS cc_start: 0.7281 (tttp) cc_final: 0.6816 (tttp) REVERT: D 265 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6716 (tp30) REVERT: D 401 LYS cc_start: 0.6822 (mmmm) cc_final: 0.6359 (mmmm) REVERT: D 467 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7854 (mmmt) REVERT: D 473 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7635 (mtt-85) REVERT: D 843 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6088 (mpp80) REVERT: D 906 MET cc_start: 0.7138 (mtt) cc_final: 0.6781 (mtp) REVERT: D 956 HIS cc_start: 0.7955 (m-70) cc_final: 0.7467 (m-70) REVERT: D 1161 PHE cc_start: 0.7843 (t80) cc_final: 0.6615 (m-80) REVERT: D 1188 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7626 (tmmm) outliers start: 68 outliers final: 37 residues processed: 387 average time/residue: 0.8354 time to fit residues: 388.5037 Evaluate side-chains 390 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 332 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 843 ARG Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 737 THR Chi-restraints excluded: chain D residue 843 ARG Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 70 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 340 optimal weight: 20.0000 chunk 312 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 278 optimal weight: 9.9990 chunk 250 optimal weight: 0.0050 chunk 166 optimal weight: 8.9990 overall best weight: 3.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** 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 = 0.4512 r_free = 0.4512 target = 0.220255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137240 restraints weight = 38623.145| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.05 r_work: 0.3220 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 39696 Z= 0.182 Angle : 0.669 8.418 53276 Z= 0.335 Chirality : 0.044 0.237 5676 Planarity : 0.005 0.055 6364 Dihedral : 21.797 171.446 7764 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.27 % Favored : 92.55 % Rotamer: Outliers : 1.63 % Allowed : 14.76 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.31 (0.13), residues: 4388 helix: 1.07 (0.10), residues: 2676 sheet: -2.54 (0.33), residues: 228 loop : -2.23 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 525 TYR 0.017 0.002 TYR A1122 PHE 0.021 0.002 PHE A 428 TRP 0.013 0.002 TRP A 747 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00431 (39684) covalent geometry : angle 0.66837 (53252) SS BOND : bond 0.00439 ( 12) SS BOND : angle 1.35803 ( 24) hydrogen bonds : bond 0.05001 ( 1796) hydrogen bonds : angle 4.17486 ( 5232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 334 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.0971 (mpp) cc_final: -0.1640 (ppp) REVERT: A 90 ASP cc_start: 0.4940 (OUTLIER) cc_final: 0.4478 (t0) REVERT: A 110 ARG cc_start: 0.6149 (tpt-90) cc_final: 0.5498 (tpt-90) REVERT: A 111 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7451 (mt) REVERT: A 143 MET cc_start: 0.4784 (mpt) cc_final: 0.4264 (mmp) REVERT: A 369 MET cc_start: 0.5876 (tpt) cc_final: 0.5567 (mtt) REVERT: A 401 LYS cc_start: 0.6757 (mmmm) cc_final: 0.6510 (mmmm) REVERT: A 467 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7863 (mmmt) REVERT: A 473 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7654 (mtt-85) REVERT: A 843 ARG cc_start: 0.6942 (mtt-85) cc_final: 0.6201 (mpp-170) REVERT: A 906 MET cc_start: 0.7155 (mtt) cc_final: 0.6809 (mtp) REVERT: A 956 HIS cc_start: 0.8033 (m-70) cc_final: 0.7543 (m-70) REVERT: A 1161 PHE cc_start: 0.7902 (t80) cc_final: 0.6680 (m-80) REVERT: A 1188 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7648 (tmmm) REVERT: B 60 MET cc_start: -0.0965 (mpp) cc_final: -0.1727 (pp-130) REVERT: B 90 ASP cc_start: 0.4963 (OUTLIER) cc_final: 0.4505 (t0) REVERT: B 110 ARG cc_start: 0.6153 (tpt-90) cc_final: 0.5453 (tpt-90) REVERT: B 111 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7448 (mt) REVERT: B 143 MET cc_start: 0.4785 (mpt) cc_final: 0.4257 (mmp) REVERT: B 265 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: B 368 MET cc_start: 0.5454 (OUTLIER) cc_final: 0.5233 (mpp) REVERT: B 401 LYS cc_start: 0.6816 (mmmm) cc_final: 0.6566 (mmmm) REVERT: B 473 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7655 (mtt-85) REVERT: B 843 ARG cc_start: 0.6944 (mtt-85) cc_final: 0.6184 (mpp-170) REVERT: B 906 MET cc_start: 0.7147 (mtt) cc_final: 0.6801 (mtp) REVERT: B 956 HIS cc_start: 0.7996 (m-70) cc_final: 0.7532 (m-70) REVERT: B 1161 PHE cc_start: 0.7886 (t80) cc_final: 0.6656 (m-80) REVERT: B 1188 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7653 (tmmm) REVERT: C 60 MET cc_start: -0.1158 (mpp) cc_final: -0.1880 (pp-130) REVERT: C 90 ASP cc_start: 0.4966 (OUTLIER) cc_final: 0.4445 (t0) REVERT: C 110 ARG cc_start: 0.6132 (tpt-90) cc_final: 0.5425 (tpt-90) REVERT: C 111 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7415 (mp) REVERT: C 143 MET cc_start: 0.4791 (mpt) cc_final: 0.4257 (mmp) REVERT: C 265 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: C 369 MET cc_start: 0.5850 (tpt) cc_final: 0.5533 (mtt) REVERT: C 401 LYS cc_start: 0.6813 (mmmm) cc_final: 0.6526 (mmmm) REVERT: C 467 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7868 (mmmt) REVERT: C 473 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7665 (mtt-85) REVERT: C 843 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6093 (mpp80) REVERT: C 906 MET cc_start: 0.7154 (mtt) cc_final: 0.6810 (mtp) REVERT: C 956 HIS cc_start: 0.8024 (m-70) cc_final: 0.7536 (m-70) REVERT: C 1161 PHE cc_start: 0.7886 (t80) cc_final: 0.6655 (m-80) REVERT: C 1168 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6517 (tmmm) REVERT: C 1188 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7644 (tmmm) REVERT: D 60 MET cc_start: -0.0982 (mpp) cc_final: -0.1737 (pp-130) REVERT: D 90 ASP cc_start: 0.5023 (OUTLIER) cc_final: 0.4542 (t0) REVERT: D 110 ARG cc_start: 0.6156 (tpt-90) cc_final: 0.5458 (tpt-90) REVERT: D 111 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7458 (mt) REVERT: D 143 MET cc_start: 0.4783 (mpt) cc_final: 0.4254 (mmp) REVERT: D 265 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: D 401 LYS cc_start: 0.6843 (mmmm) cc_final: 0.6470 (mmmm) REVERT: D 467 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7864 (mmmt) REVERT: D 473 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7661 (mtt-85) REVERT: D 843 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6083 (mpp80) REVERT: D 906 MET cc_start: 0.7151 (mtt) cc_final: 0.6803 (mtp) REVERT: D 956 HIS cc_start: 0.8023 (m-70) cc_final: 0.7557 (m-70) REVERT: D 1161 PHE cc_start: 0.7900 (t80) cc_final: 0.6675 (m-80) REVERT: D 1188 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7631 (tmmm) outliers start: 64 outliers final: 39 residues processed: 381 average time/residue: 0.7070 time to fit residues: 323.7588 Evaluate side-chains 388 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 326 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 843 ARG Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1168 LYS Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 737 THR Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 843 ARG Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 214 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 412 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 417 optimal weight: 0.8980 chunk 303 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** 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 = 0.4512 r_free = 0.4512 target = 0.220258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136519 restraints weight = 38683.899| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.02 r_work: 0.3245 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 39696 Z= 0.181 Angle : 0.669 12.460 53276 Z= 0.335 Chirality : 0.044 0.241 5676 Planarity : 0.005 0.055 6364 Dihedral : 21.715 172.169 7764 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.34 % Favored : 92.48 % Rotamer: Outliers : 1.94 % Allowed : 14.50 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.35 (0.13), residues: 4388 helix: 1.01 (0.10), residues: 2704 sheet: -2.51 (0.33), residues: 228 loop : -2.24 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 843 TYR 0.016 0.002 TYR A1122 PHE 0.018 0.002 PHE D 936 TRP 0.014 0.002 TRP C1111 HIS 0.006 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00429 (39684) covalent geometry : angle 0.66847 (53252) SS BOND : bond 0.00443 ( 12) SS BOND : angle 1.34844 ( 24) hydrogen bonds : bond 0.04966 ( 1796) hydrogen bonds : angle 4.18285 ( 5232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26672.32 seconds wall clock time: 451 minutes 57.86 seconds (27117.86 seconds total)