Starting phenix.real_space_refine on Mon Jul 6 20:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8si2_40496/07_2026/8si2_40496_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8si2_40496/07_2026/8si2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8si2_40496/07_2026/8si2_40496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8si2_40496/07_2026/8si2_40496.map" model { file = "/net/cci-nas-00/data/ceres_data/8si2_40496/07_2026/8si2_40496_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8si2_40496/07_2026/8si2_40496_neut.cif" } 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-dev-6108/lib/python3.11/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, 785 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain breaks: 2 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: 8.32, per 1000 atoms: 0.21 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: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.12 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: 8.28 Time building geometry restraints manager: 4.67 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.820 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 are 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/Z covalent geometry : bond 0.01206 / 0.50 (39684) covalent geometry : angle 1.12670 / 0.58 (53252) SS BOND : bond 0.01804 / 1.00 ( 12) SS BOND : angle 1.79535 / 1.01 ( 24) hydrogen bonds : bond 0.24056 / 16.13 ( 1796) hydrogen bonds : angle 8.29621 / 5.75 ( 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 : 1.505 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: 0.8193 time to fit residues: 614.7974 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 : 1.393 ------------------------------------------------------------------------------- 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... A 149 HIS A 177 ASN A 239 ASN A 242 HIS A 272 GLN A 276 HIS A 388 HIS 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 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 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 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.225087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150772 restraints weight = 40308.476| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.36 r_work: 0.3357 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39696 Z= 0.169 Angle : 0.730 9.933 53276 Z= 0.370 Chirality : 0.044 0.189 5676 Planarity : 0.005 0.044 6364 Dihedral : 24.778 179.736 7774 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.75 % Favored : 92.98 % Rotamer: Outliers : 1.10 % Allowed : 9.07 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 4388 helix: -0.12 (0.09), residues: 2608 sheet: -3.63 (0.28), residues: 180 loop : -2.73 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 530 TYR 0.026 0.002 TYR D 518 PHE 0.032 0.002 PHE B 858 TRP 0.014 0.002 TRP B 947 HIS 0.005 0.001 HIS C1137 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (39684) covalent geometry : angle 0.73010 / 0.37 (53252) SS BOND : bond 0.00414 / 0.25 ( 12) SS BOND : angle 1.06765 / 0.61 ( 24) hydrogen bonds : bond 0.05317 / 3.59 ( 1796) hydrogen bonds : angle 4.70586 / 3.25 ( 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 474 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 431 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.0845 (mpp) cc_final: -0.1327 (ppp) REVERT: A 90 ASP cc_start: 0.4884 (OUTLIER) cc_final: 0.4597 (t0) REVERT: A 110 ARG cc_start: 0.6210 (tpt-90) cc_final: 0.5110 (mtp85) REVERT: A 467 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7973 (mmmt) REVERT: A 843 ARG cc_start: 0.7126 (mpt-90) cc_final: 0.6912 (mtt-85) REVERT: A 881 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 906 MET cc_start: 0.7261 (mtt) cc_final: 0.6915 (mtp) REVERT: A 1161 PHE cc_start: 0.7910 (t80) cc_final: 0.6876 (m-80) REVERT: B 60 MET cc_start: -0.0793 (mpp) cc_final: -0.1276 (ppp) REVERT: B 90 ASP cc_start: 0.4935 (OUTLIER) cc_final: 0.4529 (t0) REVERT: B 665 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7452 (mm-30) REVERT: B 843 ARG cc_start: 0.7110 (mpt-90) cc_final: 0.6900 (mtt-85) REVERT: B 881 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8514 (mt) REVERT: B 906 MET cc_start: 0.7300 (mtt) cc_final: 0.6938 (mtp) REVERT: B 1161 PHE cc_start: 0.7925 (t80) cc_final: 0.6921 (m-80) REVERT: C 60 MET cc_start: -0.0799 (mpp) cc_final: -0.1289 (ppp) REVERT: C 90 ASP cc_start: 0.4885 (OUTLIER) cc_final: 0.4555 (t0) REVERT: C 467 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7926 (mmmt) REVERT: C 665 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7505 (mm-30) REVERT: C 843 ARG cc_start: 0.6772 (mpp-170) cc_final: 0.6368 (mpp80) REVERT: C 881 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8503 (mt) REVERT: C 906 MET cc_start: 0.7311 (mtt) cc_final: 0.6946 (mtp) REVERT: C 1161 PHE cc_start: 0.7933 (t80) cc_final: 0.6913 (m-80) REVERT: D 60 MET cc_start: -0.0802 (mpp) cc_final: -0.1303 (ppp) REVERT: D 90 ASP cc_start: 0.4953 (OUTLIER) cc_final: 0.4532 (t0) REVERT: D 467 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7934 (mmmt) REVERT: D 665 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7352 (mm-30) REVERT: D 843 ARG cc_start: 0.6765 (mpp-170) cc_final: 0.6359 (mpp80) REVERT: D 881 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8500 (mt) REVERT: D 906 MET cc_start: 0.7302 (mtt) cc_final: 0.6933 (mtp) REVERT: D 1161 PHE cc_start: 0.7921 (t80) cc_final: 0.6913 (m-80) outliers start: 43 outliers final: 13 residues processed: 464 average time/residue: 0.7985 time to fit residues: 445.2433 Evaluate side-chains 373 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 352 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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: 2.9990 chunk 360 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN 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 50 GLN 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.219282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139908 restraints weight = 38744.268| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.49 r_work: 0.3209 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 39696 Z= 0.307 Angle : 0.836 9.329 53276 Z= 0.418 Chirality : 0.053 0.264 5676 Planarity : 0.006 0.055 6364 Dihedral : 24.755 179.523 7774 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.25 % Favored : 91.57 % Rotamer: Outliers : 2.20 % Allowed : 10.29 % Favored : 87.51 % 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 are not related in a simple way. whole: -1.48 (0.12), residues: 4388 helix: 0.13 (0.09), residues: 2648 sheet: -3.26 (0.31), residues: 180 loop : -2.64 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 274 TYR 0.025 0.003 TYR D 776 PHE 0.032 0.003 PHE C 858 TRP 0.021 0.003 TRP C1111 HIS 0.010 0.002 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.31 (39684) covalent geometry : angle 0.83539 / 0.42 (53252) SS BOND : bond 0.00455 / 0.28 ( 12) SS BOND : angle 1.54235 / 0.86 ( 24) hydrogen bonds : bond 0.06370 / 4.31 ( 1796) hydrogen bonds : angle 4.76185 / 3.28 ( 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 461 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 375 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.0750 (mpp) cc_final: -0.1312 (ppp) REVERT: A 90 ASP cc_start: 0.4818 (OUTLIER) cc_final: 0.4515 (t0) REVERT: A 143 MET cc_start: 0.4789 (mpt) cc_final: 0.4315 (mmp) REVERT: A 467 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7914 (mmmt) REVERT: A 473 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7696 (mtt-85) REVERT: A 481 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6846 (mptt) REVERT: A 665 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 750 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7781 (mtm180) REVERT: A 843 ARG cc_start: 0.7037 (mpt-90) cc_final: 0.6796 (mtt-85) REVERT: A 881 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 906 MET cc_start: 0.7222 (mtt) cc_final: 0.6799 (mtp) REVERT: A 956 HIS cc_start: 0.7981 (m-70) cc_final: 0.7452 (m-70) REVERT: A 1161 PHE cc_start: 0.7919 (t80) cc_final: 0.6738 (m-80) REVERT: B 60 MET cc_start: -0.0828 (mpp) cc_final: -0.1362 (ppp) REVERT: B 473 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7673 (mtt-85) REVERT: B 481 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6884 (mptt) REVERT: B 665 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 750 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7800 (mtm180) REVERT: B 843 ARG cc_start: 0.7029 (mpt-90) cc_final: 0.6791 (mtt-85) REVERT: B 881 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 906 MET cc_start: 0.7204 (mtt) cc_final: 0.6776 (mtp) REVERT: B 956 HIS cc_start: 0.7977 (m-70) cc_final: 0.7440 (m-70) REVERT: B 1027 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: B 1161 PHE cc_start: 0.7910 (t80) cc_final: 0.6737 (m-80) REVERT: C 60 MET cc_start: -0.0949 (mpp) cc_final: -0.1449 (ppp) REVERT: C 143 MET cc_start: 0.4813 (mpt) cc_final: 0.4361 (mmp) REVERT: C 467 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7935 (mmmt) REVERT: C 473 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7675 (mtt-85) REVERT: C 481 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6886 (mptt) REVERT: C 665 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7481 (mm-30) REVERT: C 750 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7784 (mtm180) REVERT: C 843 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6241 (mpp80) REVERT: C 881 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8394 (mp) REVERT: C 906 MET cc_start: 0.7221 (mtt) cc_final: 0.6802 (mtp) REVERT: C 956 HIS cc_start: 0.7962 (m-70) cc_final: 0.7484 (m-70) REVERT: C 1027 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: C 1161 PHE cc_start: 0.7916 (t80) cc_final: 0.6749 (m-80) REVERT: D 60 MET cc_start: -0.0958 (mpp) cc_final: -0.1442 (ppp) REVERT: D 143 MET cc_start: 0.4798 (mpt) cc_final: 0.4316 (mmp) REVERT: D 401 LYS cc_start: 0.6949 (mmmm) cc_final: 0.6728 (mmtp) REVERT: D 467 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7931 (mmmt) REVERT: D 473 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7667 (mtt-85) REVERT: D 481 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6865 (mptt) REVERT: D 665 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7383 (mm-30) REVERT: D 750 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7770 (mtm180) REVERT: D 843 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6235 (mpp80) REVERT: D 881 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8391 (mp) REVERT: D 906 MET cc_start: 0.7220 (mtt) cc_final: 0.6794 (mtp) REVERT: D 956 HIS cc_start: 0.7970 (m-70) cc_final: 0.7425 (m-70) REVERT: D 1027 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: D 1161 PHE cc_start: 0.7909 (t80) cc_final: 0.6732 (m-80) outliers start: 86 outliers final: 15 residues processed: 444 average time/residue: 0.8232 time to fit residues: 435.8340 Evaluate side-chains 372 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 335 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 750 ARG Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 158 LYS 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 750 ARG Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1037 VAL 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 527 THR Chi-restraints excluded: chain C residue 750 ARG 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 481 LYS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 750 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: 4.9990 chunk 381 optimal weight: 3.9990 chunk 430 optimal weight: 0.9980 chunk 278 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 31 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.221233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136850 restraints weight = 38951.510| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.05 r_work: 0.3276 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39696 Z= 0.151 Angle : 0.652 8.959 53276 Z= 0.329 Chirality : 0.043 0.213 5676 Planarity : 0.005 0.052 6364 Dihedral : 23.674 177.375 7766 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 1.56 % Allowed : 12.00 % Favored : 86.44 % 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 are not related in a simple way. whole: -0.86 (0.12), residues: 4388 helix: 0.71 (0.10), residues: 2640 sheet: -2.96 (0.32), residues: 188 loop : -2.52 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 530 TYR 0.013 0.002 TYR B 18 PHE 0.016 0.002 PHE A 936 TRP 0.014 0.002 TRP D 78 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (39684) covalent geometry : angle 0.65157 / 0.33 (53252) SS BOND : bond 0.00474 / 0.29 ( 12) SS BOND : angle 1.12468 / 0.63 ( 24) hydrogen bonds : bond 0.04781 / 3.22 ( 1796) hydrogen bonds : angle 4.33705 / 2.99 ( 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 414 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 353 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.1094 (mpp) cc_final: -0.1531 (ppp) REVERT: A 143 MET cc_start: 0.4769 (mpt) cc_final: 0.4306 (mmp) REVERT: A 213 ARG cc_start: 0.5448 (mtp85) cc_final: 0.5192 (mtp85) REVERT: A 449 MET cc_start: 0.8359 (mtp) cc_final: 0.8125 (mtp) REVERT: A 467 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7833 (mmmt) REVERT: A 473 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7603 (mtt-85) REVERT: A 481 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6797 (mptt) REVERT: A 665 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 671 LEU cc_start: 0.4002 (OUTLIER) cc_final: 0.3781 (tp) REVERT: A 843 ARG cc_start: 0.6917 (mpt-90) cc_final: 0.6235 (mtt90) REVERT: A 906 MET cc_start: 0.7187 (mtt) cc_final: 0.6772 (mtp) REVERT: A 956 HIS cc_start: 0.7798 (m-70) cc_final: 0.7226 (m-70) REVERT: A 1161 PHE cc_start: 0.7869 (t80) cc_final: 0.6663 (m-80) REVERT: A 1202 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7811 (mm-30) REVERT: B 60 MET cc_start: -0.1092 (mpp) cc_final: -0.1532 (ppp) REVERT: B 90 ASP cc_start: 0.4969 (OUTLIER) cc_final: 0.4656 (t0) REVERT: B 143 MET cc_start: 0.4783 (mpt) cc_final: 0.4301 (mmp) REVERT: B 473 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7585 (mtt-85) REVERT: B 481 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6795 (mptt) REVERT: B 525 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7492 (mmm-85) REVERT: B 665 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7156 (mm-30) REVERT: B 843 ARG cc_start: 0.6916 (mpt-90) cc_final: 0.6630 (mtt-85) REVERT: B 906 MET cc_start: 0.7179 (mtt) cc_final: 0.6764 (mtp) REVERT: B 956 HIS cc_start: 0.7786 (m-70) cc_final: 0.7211 (m-70) REVERT: B 1161 PHE cc_start: 0.7867 (t80) cc_final: 0.6679 (m-80) REVERT: C 60 MET cc_start: -0.1119 (mpp) cc_final: -0.1550 (ppp) REVERT: C 90 ASP cc_start: 0.4806 (OUTLIER) cc_final: 0.4561 (t0) REVERT: C 143 MET cc_start: 0.4770 (mpt) cc_final: 0.4298 (mmp) REVERT: C 467 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7850 (mmmt) REVERT: C 473 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7573 (mtt-85) REVERT: C 481 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6793 (mptt) REVERT: C 525 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7484 (mmm-85) REVERT: C 665 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7159 (mm-30) REVERT: C 671 LEU cc_start: 0.4000 (OUTLIER) cc_final: 0.3778 (tp) REVERT: C 843 ARG cc_start: 0.6554 (mpp-170) cc_final: 0.6085 (mpp80) REVERT: C 881 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8337 (mp) REVERT: C 906 MET cc_start: 0.7180 (mtt) cc_final: 0.6764 (mtp) REVERT: C 956 HIS cc_start: 0.7769 (m-70) cc_final: 0.7248 (m-70) REVERT: C 1161 PHE cc_start: 0.7855 (t80) cc_final: 0.6668 (m-80) REVERT: D 60 MET cc_start: -0.1068 (mpp) cc_final: -0.1516 (ppp) REVERT: D 90 ASP cc_start: 0.4825 (OUTLIER) cc_final: 0.4569 (t0) REVERT: D 143 MET cc_start: 0.4777 (mpt) cc_final: 0.4304 (mmp) REVERT: D 467 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7855 (mmmt) REVERT: D 473 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7567 (mtt-85) REVERT: D 481 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6829 (mptt) REVERT: D 525 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7489 (mmm-85) REVERT: D 665 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7308 (mm-30) REVERT: D 843 ARG cc_start: 0.6581 (mpp-170) cc_final: 0.6116 (mpp80) REVERT: D 906 MET cc_start: 0.7130 (mtt) cc_final: 0.6716 (mtp) REVERT: D 956 HIS cc_start: 0.7783 (m-70) cc_final: 0.7211 (m-70) REVERT: D 1161 PHE cc_start: 0.7860 (t80) cc_final: 0.6672 (m-80) outliers start: 61 outliers final: 15 residues processed: 407 average time/residue: 0.7800 time to fit residues: 381.5526 Evaluate side-chains 360 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 331 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1102 GLN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 LEU 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 1102 GLN 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 881 LEU Chi-restraints excluded: chain C residue 1102 GLN 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 481 LYS Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 1102 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 49 optimal weight: 0.9990 chunk 264 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 276 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 425 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4525 r_free = 0.4525 target = 0.221336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147089 restraints weight = 39072.606| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.44 r_work: 0.3240 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39696 Z= 0.142 Angle : 0.627 8.524 53276 Z= 0.316 Chirality : 0.042 0.218 5676 Planarity : 0.004 0.052 6364 Dihedral : 22.824 173.112 7764 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.13 % Favored : 92.68 % Rotamer: Outliers : 2.04 % Allowed : 12.08 % Favored : 85.88 % 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 are not related in a simple way. whole: -0.43 (0.13), residues: 4388 helix: 1.07 (0.10), residues: 2640 sheet: -2.62 (0.34), residues: 188 loop : -2.42 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 530 TYR 0.013 0.002 TYR A 518 PHE 0.015 0.002 PHE C 936 TRP 0.013 0.002 TRP D 78 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (39684) covalent geometry : angle 0.62624 / 0.32 (53252) SS BOND : bond 0.00463 / 0.29 ( 12) SS BOND : angle 1.19672 / 0.67 ( 24) hydrogen bonds : bond 0.04524 / 3.04 ( 1796) hydrogen bonds : angle 4.14074 / 2.86 ( 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 461 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 381 time to evaluate : 1.298 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: -0.1142 (mpp) cc_final: -0.1629 (ppp) REVERT: A 90 ASP cc_start: 0.4882 (OUTLIER) cc_final: 0.4636 (t0) REVERT: A 143 MET cc_start: 0.4852 (mpt) cc_final: 0.4293 (mmp) REVERT: A 265 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6687 (tp30) REVERT: A 467 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7919 (mmmt) REVERT: A 473 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7711 (mtt-85) REVERT: A 481 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6799 (mptt) REVERT: A 671 LEU cc_start: 0.3962 (OUTLIER) cc_final: 0.3706 (tp) REVERT: A 843 ARG cc_start: 0.7004 (mpt-90) cc_final: 0.6731 (mtt-85) REVERT: A 906 MET cc_start: 0.7170 (mtt) cc_final: 0.6822 (mtp) REVERT: A 956 HIS cc_start: 0.7953 (m-70) cc_final: 0.7396 (m-70) REVERT: A 1161 PHE cc_start: 0.7930 (t80) cc_final: 0.6772 (m-80) REVERT: A 1188 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7754 (tmmm) REVERT: A 1202 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7980 (mm-30) REVERT: A 1213 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: B 60 MET cc_start: -0.1174 (mpp) cc_final: -0.1621 (ppp) REVERT: B 90 ASP cc_start: 0.4873 (OUTLIER) cc_final: 0.4574 (t0) REVERT: B 143 MET cc_start: 0.4853 (mpt) cc_final: 0.4297 (mmp) REVERT: B 162 LYS cc_start: 0.7367 (tttp) cc_final: 0.6885 (tttp) REVERT: B 473 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7699 (mtt-85) REVERT: B 481 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6817 (mptt) REVERT: B 843 ARG cc_start: 0.7000 (mpt-90) cc_final: 0.6734 (mtt-85) REVERT: B 906 MET cc_start: 0.7150 (mtt) cc_final: 0.6798 (mtp) REVERT: B 956 HIS cc_start: 0.7876 (m-70) cc_final: 0.7309 (m-70) REVERT: B 1161 PHE cc_start: 0.7924 (t80) cc_final: 0.6754 (m-80) REVERT: B 1188 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7735 (tmmm) REVERT: B 1213 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: C 60 MET cc_start: -0.1159 (mpp) cc_final: -0.1611 (ppp) REVERT: C 90 ASP cc_start: 0.4941 (OUTLIER) cc_final: 0.4645 (t0) REVERT: C 143 MET cc_start: 0.4853 (mpt) cc_final: 0.4294 (mmp) REVERT: C 162 LYS cc_start: 0.7357 (tttp) cc_final: 0.6880 (tttp) REVERT: C 467 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7910 (mmmt) REVERT: C 473 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7689 (mtt-85) REVERT: C 481 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6816 (mptt) REVERT: C 671 LEU cc_start: 0.3965 (OUTLIER) cc_final: 0.3706 (tp) REVERT: C 843 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6182 (mpp80) REVERT: C 906 MET cc_start: 0.7138 (mtt) cc_final: 0.6794 (mtp) REVERT: C 956 HIS cc_start: 0.7934 (m-70) cc_final: 0.7411 (m-70) REVERT: C 1161 PHE cc_start: 0.7894 (t80) cc_final: 0.6744 (m-80) REVERT: C 1188 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7750 (tmmm) REVERT: C 1213 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: D 60 MET cc_start: -0.1158 (mpp) cc_final: -0.1612 (ppp) REVERT: D 90 ASP cc_start: 0.4865 (OUTLIER) cc_final: 0.4584 (t0) REVERT: D 143 MET cc_start: 0.4855 (mpt) cc_final: 0.4299 (mmp) REVERT: D 162 LYS cc_start: 0.7389 (tttp) cc_final: 0.6900 (tttp) REVERT: D 467 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7905 (mmmt) REVERT: D 473 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7680 (mtt-85) REVERT: D 481 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6812 (mptt) REVERT: D 843 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6181 (mpp80) REVERT: D 906 MET cc_start: 0.7155 (mtt) cc_final: 0.6800 (mtp) REVERT: D 956 HIS cc_start: 0.7883 (m-70) cc_final: 0.7321 (m-70) REVERT: D 1161 PHE cc_start: 0.7895 (t80) cc_final: 0.6743 (m-80) REVERT: D 1188 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7745 (tmmm) REVERT: D 1213 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6502 (tm-30) outliers start: 80 outliers final: 13 residues processed: 444 average time/residue: 0.7525 time to fit residues: 402.0247 Evaluate side-chains 379 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP 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 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 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1213 GLU 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 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain B residue 1213 GLU 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 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 671 LEU 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 C residue 1213 GLU 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 473 ARG Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 843 ARG Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Chi-restraints excluded: chain D residue 1213 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 312 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 379 optimal weight: 0.4980 chunk 318 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 391 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 435 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.221760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138659 restraints weight = 39174.103| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.04 r_work: 0.3267 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39696 Z= 0.132 Angle : 0.605 8.382 53276 Z= 0.305 Chirality : 0.042 0.243 5676 Planarity : 0.004 0.052 6364 Dihedral : 22.231 171.715 7764 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.65 % Favored : 93.16 % Rotamer: Outliers : 2.04 % Allowed : 12.97 % Favored : 84.98 % 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 are not related in a simple way. whole: -0.23 (0.13), residues: 4388 helix: 1.23 (0.10), residues: 2632 sheet: -2.75 (0.32), residues: 228 loop : -2.27 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 530 TYR 0.011 0.002 TYR C1122 PHE 0.014 0.002 PHE B 936 TRP 0.011 0.001 TRP D 78 HIS 0.006 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (39684) covalent geometry : angle 0.60508 / 0.31 (53252) SS BOND : bond 0.00367 / 0.23 ( 12) SS BOND : angle 1.05946 / 0.60 ( 24) hydrogen bonds : bond 0.04350 / 2.93 ( 1796) hydrogen bonds : angle 4.05688 / 2.80 ( 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 437 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 357 time to evaluate : 1.287 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: -0.1388 (mpp) cc_final: -0.1784 (ppp) REVERT: A 143 MET cc_start: 0.4860 (mpt) cc_final: 0.4311 (mmp) REVERT: A 162 LYS cc_start: 0.7271 (tttp) cc_final: 0.6831 (tttp) REVERT: A 265 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: A 449 MET cc_start: 0.8352 (mtp) cc_final: 0.8127 (mtp) REVERT: A 467 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7873 (mmmt) REVERT: A 473 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7596 (mtt-85) REVERT: A 671 LEU cc_start: 0.3989 (OUTLIER) cc_final: 0.3672 (tp) REVERT: A 906 MET cc_start: 0.7039 (mtt) cc_final: 0.6688 (mtp) REVERT: A 956 HIS cc_start: 0.7871 (m-70) cc_final: 0.7281 (m-70) REVERT: A 1161 PHE cc_start: 0.7843 (t80) cc_final: 0.6650 (m-80) REVERT: A 1188 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7658 (tmmm) REVERT: A 1202 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7828 (mm-30) REVERT: A 1213 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: B 60 MET cc_start: -0.1459 (mpp) cc_final: -0.1854 (ppp) REVERT: B 90 ASP cc_start: 0.4862 (OUTLIER) cc_final: 0.4558 (t0) REVERT: B 143 MET cc_start: 0.4862 (mpt) cc_final: 0.4314 (mmp) REVERT: B 162 LYS cc_start: 0.7292 (tttp) cc_final: 0.6829 (tttp) REVERT: B 473 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7605 (mtt-85) REVERT: B 906 MET cc_start: 0.7034 (mtt) cc_final: 0.6687 (mtp) REVERT: B 956 HIS cc_start: 0.7860 (m-70) cc_final: 0.7259 (m-70) REVERT: B 1161 PHE cc_start: 0.7834 (t80) cc_final: 0.6654 (m-80) REVERT: B 1188 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7658 (tmmm) REVERT: B 1213 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: C 60 MET cc_start: -0.1322 (mpp) cc_final: -0.1750 (ppp) REVERT: C 90 ASP cc_start: 0.4993 (OUTLIER) cc_final: 0.4674 (t0) REVERT: C 143 MET cc_start: 0.4862 (mpt) cc_final: 0.4315 (mmp) REVERT: C 162 LYS cc_start: 0.7270 (tttp) cc_final: 0.6811 (tttp) REVERT: C 467 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7850 (mmmt) REVERT: C 473 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7597 (mtt-85) REVERT: C 843 ARG cc_start: 0.6594 (mpp-170) cc_final: 0.6083 (mpp80) REVERT: C 906 MET cc_start: 0.7031 (mtt) cc_final: 0.6681 (mtp) REVERT: C 956 HIS cc_start: 0.7838 (m-70) cc_final: 0.7273 (m-70) REVERT: C 1161 PHE cc_start: 0.7832 (t80) cc_final: 0.6658 (m-80) REVERT: C 1188 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7655 (tmmm) REVERT: C 1213 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: D 60 MET cc_start: -0.1448 (mpp) cc_final: -0.1849 (ppp) REVERT: D 90 ASP cc_start: 0.5014 (OUTLIER) cc_final: 0.4699 (t0) REVERT: D 143 MET cc_start: 0.4864 (mpt) cc_final: 0.4317 (mmp) REVERT: D 162 LYS cc_start: 0.7300 (tttp) cc_final: 0.6833 (tttp) REVERT: D 467 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7840 (mmmt) REVERT: D 473 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7609 (mtt-85) REVERT: D 843 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6077 (mpp80) REVERT: D 906 MET cc_start: 0.7036 (mtt) cc_final: 0.6687 (mtp) REVERT: D 956 HIS cc_start: 0.7859 (m-70) cc_final: 0.7259 (m-70) REVERT: D 1161 PHE cc_start: 0.7827 (t80) cc_final: 0.6644 (m-80) REVERT: D 1188 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7646 (tmmm) REVERT: D 1213 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6519 (tm-30) outliers start: 80 outliers final: 20 residues processed: 422 average time/residue: 0.7275 time to fit residues: 371.5221 Evaluate side-chains 375 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 337 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 GLU 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 671 LEU Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain B residue 90 ASP 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 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain C residue 90 ASP 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 473 ARG Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain C residue 1213 GLU Chi-restraints excluded: chain D residue 90 ASP 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 473 ARG Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 843 ARG Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Chi-restraints excluded: chain D residue 1213 GLU 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: 7.9990 chunk 301 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** 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 = 0.4502 r_free = 0.4502 target = 0.219077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133422 restraints weight = 38652.802| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.94 r_work: 0.3231 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 39696 Z= 0.262 Angle : 0.753 8.753 53276 Z= 0.376 Chirality : 0.049 0.248 5676 Planarity : 0.006 0.059 6364 Dihedral : 22.673 170.631 7764 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.50 % Favored : 92.32 % Rotamer: Outliers : 2.30 % Allowed : 13.10 % Favored : 84.60 % 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 are not related in a simple way. whole: -0.63 (0.12), residues: 4388 helix: 0.90 (0.10), residues: 2632 sheet: -2.77 (0.32), residues: 228 loop : -2.41 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 843 TYR 0.022 0.003 TYR C1122 PHE 0.023 0.003 PHE A 936 TRP 0.019 0.003 TRP C 78 HIS 0.007 0.002 HIS D1039 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (39684) covalent geometry : angle 0.75283 / 0.38 (53252) SS BOND : bond 0.00447 / 0.27 ( 12) SS BOND : angle 1.51664 / 0.86 ( 24) hydrogen bonds : bond 0.05840 / 3.96 ( 1796) hydrogen bonds : angle 4.37820 / 3.02 ( 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 433 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 343 time to evaluate : 1.433 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: -0.1258 (mpp) cc_final: -0.1677 (ppp) REVERT: A 111 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7469 (mt) REVERT: A 143 MET cc_start: 0.4785 (mpt) cc_final: 0.4278 (mmp) REVERT: A 265 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6717 (tp30) REVERT: A 369 MET cc_start: 0.5813 (tpt) cc_final: 0.5454 (mtt) REVERT: A 467 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7863 (mmmt) REVERT: A 473 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7626 (mtt-85) REVERT: A 906 MET cc_start: 0.7181 (mtt) cc_final: 0.6797 (mtp) REVERT: A 956 HIS cc_start: 0.7929 (m-70) cc_final: 0.7445 (m-70) REVERT: A 1161 PHE cc_start: 0.7865 (t80) cc_final: 0.6689 (m-80) REVERT: A 1168 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6609 (tmtm) REVERT: A 1188 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7650 (tmmm) REVERT: A 1202 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7884 (mm-30) REVERT: B 60 MET cc_start: -0.1175 (mpp) cc_final: -0.1599 (ppp) REVERT: B 90 ASP cc_start: 0.4895 (OUTLIER) cc_final: 0.4379 (t0) REVERT: B 110 ARG cc_start: 0.6248 (tpt-90) cc_final: 0.5605 (tpt-90) REVERT: B 111 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7416 (mt) REVERT: B 143 MET cc_start: 0.4849 (mpt) cc_final: 0.4347 (mmp) REVERT: B 473 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7646 (mtt-85) REVERT: B 906 MET cc_start: 0.7173 (mtt) cc_final: 0.6784 (mtp) REVERT: B 956 HIS cc_start: 0.7926 (m-70) cc_final: 0.7508 (m-70) REVERT: B 1027 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: B 1161 PHE cc_start: 0.7858 (t80) cc_final: 0.6678 (m-80) REVERT: B 1168 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6617 (tmtm) REVERT: B 1188 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7647 (tmmm) REVERT: C 60 MET cc_start: -0.1266 (mpp) cc_final: -0.1678 (ppp) REVERT: C 90 ASP cc_start: 0.4895 (OUTLIER) cc_final: 0.4378 (t0) REVERT: C 110 ARG cc_start: 0.6184 (tpt-90) cc_final: 0.5543 (tpt-90) REVERT: C 111 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7448 (mt) REVERT: C 143 MET cc_start: 0.4851 (mpt) cc_final: 0.4349 (mmp) REVERT: C 467 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7854 (mmmt) REVERT: C 473 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7637 (mtt-85) REVERT: C 843 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6103 (mpp80) REVERT: C 906 MET cc_start: 0.7169 (mtt) cc_final: 0.6786 (mtp) REVERT: C 956 HIS cc_start: 0.7946 (m-70) cc_final: 0.7504 (m-70) REVERT: C 1027 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: C 1161 PHE cc_start: 0.7869 (t80) cc_final: 0.6666 (m-80) REVERT: C 1168 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6615 (tmtm) REVERT: C 1188 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7652 (tmmm) REVERT: D 60 MET cc_start: -0.1229 (mpp) cc_final: -0.1803 (ppp) REVERT: D 90 ASP cc_start: 0.4988 (OUTLIER) cc_final: 0.4650 (t0) REVERT: D 111 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7397 (mt) REVERT: D 143 MET cc_start: 0.4885 (mpt) cc_final: 0.4374 (mmp) REVERT: D 467 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7856 (mmmt) REVERT: D 473 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7643 (mtt-85) REVERT: D 843 ARG cc_start: 0.6620 (mpp-170) cc_final: 0.6113 (mpp80) REVERT: D 906 MET cc_start: 0.7179 (mtt) cc_final: 0.6795 (mtp) REVERT: D 956 HIS cc_start: 0.7929 (m-70) cc_final: 0.7514 (m-70) REVERT: D 1027 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: D 1161 PHE cc_start: 0.7857 (t80) cc_final: 0.6673 (m-80) REVERT: D 1168 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6611 (tmtm) REVERT: D 1188 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7647 (tmmm) outliers start: 90 outliers final: 44 residues processed: 411 average time/residue: 0.7326 time to fit residues: 363.9080 Evaluate side-chains 400 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 332 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU 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 372 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 737 THR 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 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 372 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 737 THR Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1168 LYS 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 737 THR Chi-restraints excluded: chain C residue 843 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 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 289 ILE 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 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 737 THR Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1168 LYS 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: 2.9990 chunk 50 optimal weight: 9.9990 chunk 337 optimal weight: 0.6980 chunk 365 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 364 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 305 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.219672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134595 restraints weight = 38715.212| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.87 r_work: 0.3230 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 39696 Z= 0.211 Angle : 0.693 8.684 53276 Z= 0.350 Chirality : 0.046 0.250 5676 Planarity : 0.005 0.056 6364 Dihedral : 22.469 172.401 7764 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.02 % Favored : 92.80 % Rotamer: Outliers : 2.12 % Allowed : 13.53 % Favored : 84.35 % 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 are not related in a simple way. whole: -0.55 (0.12), residues: 4388 helix: 0.97 (0.10), residues: 2620 sheet: -2.80 (0.32), residues: 228 loop : -2.36 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 530 TYR 0.017 0.002 TYR B1122 PHE 0.020 0.002 PHE A 936 TRP 0.017 0.002 TRP C 78 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (39684) covalent geometry : angle 0.69303 / 0.35 (53252) SS BOND : bond 0.00458 / 0.28 ( 12) SS BOND : angle 1.35230 / 0.76 ( 24) hydrogen bonds : bond 0.05275 / 3.56 ( 1796) hydrogen bonds : angle 4.28330 / 2.95 ( 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 420 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 337 time to evaluate : 1.395 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: -0.1037 (mpp) cc_final: -0.1774 (pp-130) REVERT: A 110 ARG cc_start: 0.6083 (tpt-90) cc_final: 0.5427 (tpt-90) REVERT: A 111 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7463 (mt) REVERT: A 143 MET cc_start: 0.4786 (mpt) cc_final: 0.4259 (mmp) REVERT: A 265 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6735 (tp30) REVERT: A 467 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7887 (mmmt) REVERT: A 473 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7616 (mtt-85) REVERT: A 750 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7170 (mtm180) REVERT: A 843 ARG cc_start: 0.6989 (mtt-85) cc_final: 0.6777 (mtt-85) REVERT: A 906 MET cc_start: 0.7175 (mtt) cc_final: 0.6791 (mtp) REVERT: A 956 HIS cc_start: 0.7896 (m-70) cc_final: 0.7398 (m-70) REVERT: A 1161 PHE cc_start: 0.7890 (t80) cc_final: 0.6657 (m-80) REVERT: A 1168 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6573 (tmmm) REVERT: A 1188 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7652 (tmmm) REVERT: A 1202 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7832 (mm-30) REVERT: B 60 MET cc_start: -0.1033 (mpp) cc_final: -0.1774 (pp-130) REVERT: B 90 ASP cc_start: 0.4854 (OUTLIER) cc_final: 0.4374 (t0) REVERT: B 110 ARG cc_start: 0.6199 (tpt-90) cc_final: 0.5520 (tpt-90) REVERT: B 111 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7442 (mt) REVERT: B 143 MET cc_start: 0.4786 (mpt) cc_final: 0.4251 (mmp) REVERT: B 473 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7640 (mtt-85) REVERT: B 750 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7241 (mtm180) REVERT: B 843 ARG cc_start: 0.6986 (mtt-85) cc_final: 0.6779 (mtt-85) REVERT: B 906 MET cc_start: 0.7157 (mtt) cc_final: 0.6771 (mtp) REVERT: B 956 HIS cc_start: 0.7891 (m-70) cc_final: 0.7425 (m-70) REVERT: B 1161 PHE cc_start: 0.7855 (t80) cc_final: 0.6636 (m-80) REVERT: B 1168 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6571 (tmmm) REVERT: B 1188 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7657 (tmmm) REVERT: C 60 MET cc_start: -0.1280 (mpp) cc_final: -0.1750 (ppp) REVERT: C 90 ASP cc_start: 0.4914 (OUTLIER) cc_final: 0.4405 (t0) REVERT: C 110 ARG cc_start: 0.6158 (tpt-90) cc_final: 0.5422 (tpt-90) REVERT: C 111 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7477 (mt) REVERT: C 143 MET cc_start: 0.4787 (mpt) cc_final: 0.4256 (mmp) REVERT: C 467 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7888 (mmmt) REVERT: C 473 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7621 (mtt-85) REVERT: C 750 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7180 (mtm180) REVERT: C 843 ARG cc_start: 0.6608 (mpp-170) cc_final: 0.6083 (mpp80) REVERT: C 906 MET cc_start: 0.7164 (mtt) cc_final: 0.6781 (mtp) REVERT: C 956 HIS cc_start: 0.7918 (m-70) cc_final: 0.7462 (m-70) REVERT: C 1161 PHE cc_start: 0.7873 (t80) cc_final: 0.6630 (m-80) REVERT: C 1168 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6572 (tmmm) REVERT: C 1188 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7650 (tmmm) REVERT: D 60 MET cc_start: -0.1229 (mpp) cc_final: -0.1907 (pp-130) REVERT: D 90 ASP cc_start: 0.4969 (OUTLIER) cc_final: 0.4433 (t0) REVERT: D 110 ARG cc_start: 0.6153 (tpt-90) cc_final: 0.5471 (tpt-90) REVERT: D 111 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7444 (mt) REVERT: D 143 MET cc_start: 0.4828 (mpt) cc_final: 0.4290 (mmp) REVERT: D 369 MET cc_start: 0.5917 (tpt) cc_final: 0.5563 (mtt) REVERT: D 467 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7885 (mmmt) REVERT: D 473 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7636 (mtt-85) REVERT: D 750 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7179 (mtm180) REVERT: D 843 ARG cc_start: 0.6613 (mpp-170) cc_final: 0.6089 (mpp80) REVERT: D 906 MET cc_start: 0.7179 (mtt) cc_final: 0.6794 (mtp) REVERT: D 956 HIS cc_start: 0.7887 (m-70) cc_final: 0.7422 (m-70) REVERT: D 1161 PHE cc_start: 0.7885 (t80) cc_final: 0.6633 (m-80) REVERT: D 1168 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6566 (tmmm) REVERT: D 1188 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7654 (tmmm) outliers start: 83 outliers final: 42 residues processed: 404 average time/residue: 0.7587 time to fit residues: 370.7221 Evaluate side-chains 398 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 332 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 GLU 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 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 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 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 372 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 750 ARG Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1168 LYS 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 750 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 289 ILE 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 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 750 ARG Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1168 LYS 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: 7.9990 chunk 428 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 318 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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 = 0.4518 r_free = 0.4518 target = 0.220862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135842 restraints weight = 38923.770| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.95 r_work: 0.3270 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39696 Z= 0.149 Angle : 0.631 8.728 53276 Z= 0.317 Chirality : 0.043 0.235 5676 Planarity : 0.004 0.055 6364 Dihedral : 21.894 172.416 7764 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.22 % Favored : 92.59 % Rotamer: Outliers : 1.46 % Allowed : 14.56 % Favored : 83.99 % 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 are not related in a simple way. whole: -0.26 (0.13), residues: 4388 helix: 1.16 (0.10), residues: 2648 sheet: -2.64 (0.33), residues: 228 loop : -2.24 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 530 TYR 0.013 0.002 TYR B1122 PHE 0.016 0.002 PHE C 936 TRP 0.013 0.002 TRP B 747 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (39684) covalent geometry : angle 0.63015 / 0.32 (53252) SS BOND : bond 0.00434 / 0.27 ( 12) SS BOND : angle 1.18489 / 0.67 ( 24) hydrogen bonds : bond 0.04578 / 3.08 ( 1796) hydrogen bonds : angle 4.11234 / 2.83 ( 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 398 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.1023 (mpp) cc_final: -0.1675 (ppp) REVERT: A 111 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7448 (mt) REVERT: A 143 MET cc_start: 0.4827 (mpt) cc_final: 0.4308 (mmp) REVERT: A 162 LYS cc_start: 0.7272 (tttp) cc_final: 0.6827 (tttp) REVERT: A 265 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: A 449 MET cc_start: 0.8360 (mtp) cc_final: 0.8117 (mtp) REVERT: A 467 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7912 (mmmt) REVERT: A 473 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7583 (mtt-85) REVERT: A 530 ARG cc_start: 0.7099 (mmm160) cc_final: 0.6825 (mmm-85) REVERT: A 906 MET cc_start: 0.7144 (mtt) cc_final: 0.6793 (mtp) REVERT: A 956 HIS cc_start: 0.7855 (m-70) cc_final: 0.7270 (m-70) REVERT: A 1161 PHE cc_start: 0.7841 (t80) cc_final: 0.6628 (m-80) REVERT: A 1188 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7659 (tmmm) REVERT: A 1202 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7833 (mm-30) REVERT: B 60 MET cc_start: -0.0983 (mpp) cc_final: -0.1648 (ppp) REVERT: B 90 ASP cc_start: 0.4915 (OUTLIER) cc_final: 0.4425 (t0) REVERT: B 110 ARG cc_start: 0.6127 (tpt-90) cc_final: 0.5473 (tpt-90) REVERT: B 111 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7443 (mt) REVERT: B 143 MET cc_start: 0.4791 (mpt) cc_final: 0.4266 (mmp) REVERT: B 162 LYS cc_start: 0.7258 (tttp) cc_final: 0.6807 (tttp) REVERT: B 473 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7636 (mtt-85) REVERT: B 530 ARG cc_start: 0.7106 (mmm160) cc_final: 0.6828 (mmm-85) REVERT: B 906 MET cc_start: 0.7132 (mtt) cc_final: 0.6781 (mtp) REVERT: B 956 HIS cc_start: 0.7855 (m-70) cc_final: 0.7344 (m-70) REVERT: B 1161 PHE cc_start: 0.7838 (t80) cc_final: 0.6619 (m-80) REVERT: B 1188 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7627 (tmmm) REVERT: C 60 MET cc_start: -0.1144 (mpp) cc_final: -0.1801 (pp-130) REVERT: C 90 ASP cc_start: 0.4944 (OUTLIER) cc_final: 0.4420 (t0) REVERT: C 110 ARG cc_start: 0.6126 (tpt-90) cc_final: 0.5461 (tpt-90) REVERT: C 111 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7449 (mt) REVERT: C 143 MET cc_start: 0.4790 (mpt) cc_final: 0.4261 (mmp) REVERT: C 467 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7912 (mmmt) REVERT: C 473 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7587 (mtt-85) REVERT: C 843 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6069 (mpp80) REVERT: C 906 MET cc_start: 0.7125 (mtt) cc_final: 0.6772 (mtp) REVERT: C 956 HIS cc_start: 0.7946 (m-70) cc_final: 0.7395 (m-70) REVERT: C 1161 PHE cc_start: 0.7834 (t80) cc_final: 0.6614 (m-80) REVERT: C 1188 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7632 (tmmm) REVERT: D 60 MET cc_start: -0.1003 (mpp) cc_final: -0.1764 (pp-130) REVERT: D 90 ASP cc_start: 0.4945 (OUTLIER) cc_final: 0.4418 (t0) REVERT: D 110 ARG cc_start: 0.6120 (tpt-90) cc_final: 0.5459 (tpt-90) REVERT: D 111 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7446 (mt) REVERT: D 143 MET cc_start: 0.4784 (mpt) cc_final: 0.4261 (mmp) REVERT: D 162 LYS cc_start: 0.7288 (tttp) cc_final: 0.6832 (tttp) REVERT: D 467 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7918 (mmmt) REVERT: D 473 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7634 (mtt-85) REVERT: D 843 ARG cc_start: 0.6591 (mpp-170) cc_final: 0.6063 (mpp80) REVERT: D 906 MET cc_start: 0.7147 (mtt) cc_final: 0.6793 (mtp) REVERT: D 956 HIS cc_start: 0.7859 (m-70) cc_final: 0.7349 (m-70) REVERT: D 1161 PHE cc_start: 0.7836 (t80) cc_final: 0.6612 (m-80) REVERT: D 1188 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7634 (tmmm) outliers start: 57 outliers final: 31 residues processed: 386 average time/residue: 0.8170 time to fit residues: 377.7941 Evaluate side-chains 387 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 339 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 GLU 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 794 MET 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 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 473 ARG Chi-restraints excluded: chain B residue 540 LEU 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 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 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 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: 0.9980 chunk 251 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 340 optimal weight: 20.0000 chunk 312 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 chunk 250 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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** D 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.222307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147039 restraints weight = 39051.698| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.70 r_work: 0.3249 rms_B_bonded: 3.04 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: 0.8537 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39696 Z= 0.118 Angle : 0.590 8.172 53276 Z= 0.298 Chirality : 0.041 0.222 5676 Planarity : 0.004 0.053 6364 Dihedral : 21.109 172.206 7764 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.91 % Favored : 92.91 % Rotamer: Outliers : 1.07 % Allowed : 15.12 % Favored : 83.81 % 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 are not related in a simple way. whole: 0.07 (0.13), residues: 4388 helix: 1.45 (0.10), residues: 2652 sheet: -2.10 (0.39), residues: 188 loop : -2.25 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.011 0.001 TYR A 759 PHE 0.011 0.001 PHE A 936 TRP 0.017 0.001 TRP B 747 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (39684) covalent geometry : angle 0.58986 / 0.30 (53252) SS BOND : bond 0.00498 / 0.31 ( 12) SS BOND : angle 1.25203 / 0.71 ( 24) hydrogen bonds : bond 0.03993 / 2.67 ( 1796) hydrogen bonds : angle 3.94708 / 2.72 ( 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 404 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 362 time to evaluate : 1.006 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: -0.1018 (mpp) cc_final: -0.1756 (pp-130) REVERT: A 110 ARG cc_start: 0.6069 (tpt-90) cc_final: 0.5220 (tpt-90) REVERT: A 111 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7429 (mt) REVERT: A 143 MET cc_start: 0.4772 (mpt) cc_final: 0.4232 (mmp) REVERT: A 162 LYS cc_start: 0.7263 (tttp) cc_final: 0.6803 (tttp) REVERT: A 183 HIS cc_start: 0.6506 (m-70) cc_final: 0.6084 (m-70) REVERT: A 189 LYS cc_start: 0.7231 (ttmm) cc_final: 0.6861 (ttpp) REVERT: A 449 MET cc_start: 0.8433 (mtp) cc_final: 0.8204 (mtp) REVERT: A 467 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7912 (mmmt) REVERT: A 473 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7661 (mtt-85) REVERT: A 843 ARG cc_start: 0.7067 (mtt-85) cc_final: 0.6502 (mtm-85) REVERT: A 906 MET cc_start: 0.7141 (mtt) cc_final: 0.6856 (mtp) REVERT: A 956 HIS cc_start: 0.8071 (m-70) cc_final: 0.7497 (m-70) REVERT: A 1161 PHE cc_start: 0.7901 (t80) cc_final: 0.6691 (m-80) REVERT: A 1188 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7699 (tmmm) REVERT: A 1202 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8016 (mm-30) REVERT: B 60 MET cc_start: -0.1011 (mpp) cc_final: -0.1755 (pp-130) REVERT: B 90 ASP cc_start: 0.5036 (OUTLIER) cc_final: 0.4509 (t0) REVERT: B 110 ARG cc_start: 0.6084 (tpt-90) cc_final: 0.5263 (tpt-90) REVERT: B 111 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7423 (mt) REVERT: B 143 MET cc_start: 0.4769 (mpt) cc_final: 0.4227 (mmp) REVERT: B 162 LYS cc_start: 0.7291 (tttp) cc_final: 0.6816 (tttp) REVERT: B 473 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7713 (mtt-85) REVERT: B 763 LEU cc_start: 0.7847 (tp) cc_final: 0.7637 (tm) REVERT: B 843 ARG cc_start: 0.7057 (mtt-85) cc_final: 0.6504 (mtm-85) REVERT: B 906 MET cc_start: 0.7150 (mtt) cc_final: 0.6858 (mtp) REVERT: B 956 HIS cc_start: 0.8052 (m-70) cc_final: 0.7543 (m-70) REVERT: B 1161 PHE cc_start: 0.7904 (t80) cc_final: 0.6685 (m-80) REVERT: B 1188 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7705 (tmmm) REVERT: C 60 MET cc_start: -0.1258 (mpp) cc_final: -0.1938 (pp-130) REVERT: C 90 ASP cc_start: 0.5069 (OUTLIER) cc_final: 0.4541 (t0) REVERT: C 110 ARG cc_start: 0.6042 (tpt-90) cc_final: 0.5225 (tpt-90) REVERT: C 111 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7418 (mt) REVERT: C 143 MET cc_start: 0.4804 (mpt) cc_final: 0.4243 (mmp) REVERT: C 162 LYS cc_start: 0.7257 (tttp) cc_final: 0.6783 (tttp) REVERT: C 467 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7915 (mmmt) REVERT: C 473 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7657 (mtt-85) REVERT: C 763 LEU cc_start: 0.7855 (tp) cc_final: 0.7643 (tm) REVERT: C 843 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6139 (mpp80) REVERT: C 906 MET cc_start: 0.7158 (mtt) cc_final: 0.6874 (mtp) REVERT: C 956 HIS cc_start: 0.8066 (m-70) cc_final: 0.7556 (m-70) REVERT: C 1161 PHE cc_start: 0.7914 (t80) cc_final: 0.6696 (m-80) REVERT: C 1188 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7670 (tmmm) REVERT: D 60 MET cc_start: -0.1202 (mpp) cc_final: -0.1908 (pp-130) REVERT: D 90 ASP cc_start: 0.5065 (OUTLIER) cc_final: 0.4537 (t0) REVERT: D 110 ARG cc_start: 0.6041 (tpt-90) cc_final: 0.5223 (tpt-90) REVERT: D 111 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7446 (mt) REVERT: D 143 MET cc_start: 0.4777 (mpt) cc_final: 0.4244 (mmp) REVERT: D 162 LYS cc_start: 0.7299 (tttp) cc_final: 0.6840 (tttp) REVERT: D 467 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7918 (mmmt) REVERT: D 473 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7713 (mtt-85) REVERT: D 843 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6144 (mpp80) REVERT: D 906 MET cc_start: 0.7156 (mtt) cc_final: 0.6858 (mtp) REVERT: D 956 HIS cc_start: 0.8062 (m-70) cc_final: 0.7548 (m-70) REVERT: D 1161 PHE cc_start: 0.7899 (t80) cc_final: 0.6681 (m-80) REVERT: D 1188 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7686 (tmmm) outliers start: 42 outliers final: 24 residues processed: 396 average time/residue: 0.7235 time to fit residues: 346.7930 Evaluate side-chains 386 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 372 MET Chi-restraints excluded: chain A residue 473 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 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 473 ARG Chi-restraints excluded: chain B residue 540 LEU 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 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 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: 5.9990 chunk 166 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 412 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 417 optimal weight: 0.0670 chunk 303 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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 329 HIS ** 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 = 0.4516 r_free = 0.4516 target = 0.220561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135740 restraints weight = 38790.474| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.04 r_work: 0.3237 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 39696 Z= 0.163 Angle : 0.644 9.758 53276 Z= 0.322 Chirality : 0.044 0.229 5676 Planarity : 0.005 0.054 6364 Dihedral : 21.217 171.104 7764 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 1.10 % Allowed : 15.19 % Favored : 83.71 % 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 are not related in a simple way. whole: -0.08 (0.13), residues: 4388 helix: 1.29 (0.10), residues: 2652 sheet: -2.05 (0.39), residues: 188 loop : -2.26 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.016 0.002 TYR B1122 PHE 0.016 0.002 PHE A 936 TRP 0.013 0.002 TRP B 857 HIS 0.007 0.001 HIS D 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (39684) covalent geometry : angle 0.64305 / 0.32 (53252) SS BOND : bond 0.00434 / 0.27 ( 12) SS BOND : angle 1.35688 / 0.76 ( 24) hydrogen bonds : bond 0.04769 / 3.21 ( 1796) hydrogen bonds : angle 4.08140 / 2.81 ( 5232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25193.23 seconds wall clock time: 426 minutes 40.45 seconds (25600.45 seconds total)