Starting phenix.real_space_refine on Thu May 29 21:41:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx2_36688/05_2025/8jx2_36688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx2_36688/05_2025/8jx2_36688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jx2_36688/05_2025/8jx2_36688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx2_36688/05_2025/8jx2_36688.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx2_36688/05_2025/8jx2_36688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx2_36688/05_2025/8jx2_36688.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 20622 2.51 5 N 5642 2.21 5 O 6510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32872 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "B" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "C" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "D" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "E" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "F" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "G" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "H" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "I" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "J" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "K" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "L" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "M" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "N" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2348 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Time building chain proxies: 18.99, per 1000 atoms: 0.58 Number of scatterers: 32872 At special positions: 0 Unit cell: (110.32, 111.896, 211.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 6510 8.00 N 5642 7.00 C 20622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.96 Conformation dependent library (CDL) restraints added in 4.2 seconds 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 58 sheets defined 6.7% alpha, 58.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.141A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 217 through 222 removed outlier: 4.177A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.131A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 6 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 217 through 222 removed outlier: 4.144A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 6 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.160A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 6 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 217 through 222 removed outlier: 4.174A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 6 Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 212 through 216 Processing helix chain 'G' and resid 217 through 222 removed outlier: 4.173A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 6 Processing helix chain 'H' and resid 205 through 209 Processing helix chain 'H' and resid 217 through 222 removed outlier: 4.163A pdb=" N SER H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 6 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 217 through 222 removed outlier: 4.162A pdb=" N SER I 221 " --> pdb=" O SER I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 6 Processing helix chain 'J' and resid 205 through 209 Processing helix chain 'J' and resid 217 through 222 removed outlier: 4.154A pdb=" N SER J 221 " --> pdb=" O SER J 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 6 Processing helix chain 'K' and resid 205 through 209 Processing helix chain 'K' and resid 217 through 222 removed outlier: 4.167A pdb=" N SER K 221 " --> pdb=" O SER K 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 6 Processing helix chain 'L' and resid 205 through 209 Processing helix chain 'L' and resid 217 through 222 removed outlier: 4.188A pdb=" N SER L 221 " --> pdb=" O SER L 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 6 Processing helix chain 'M' and resid 205 through 209 Processing helix chain 'M' and resid 217 through 222 removed outlier: 4.136A pdb=" N SER M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 6 Processing helix chain 'N' and resid 205 through 209 Processing helix chain 'N' and resid 217 through 222 removed outlier: 4.147A pdb=" N SER N 221 " --> pdb=" O SER N 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 29 removed outlier: 6.778A pdb=" N ALA A 229 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR A 101 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70 removed outlier: 5.551A pdb=" N VAL A 67 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 79 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 69 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER A 82 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 166 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 70 removed outlier: 5.551A pdb=" N VAL A 67 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 79 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 69 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 252 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE A 84 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU A 250 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 86 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 248 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 88 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP A 246 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP A 255 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASP A 272 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLN A 257 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR A 270 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N HIS A 259 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR A 268 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 127 removed outlier: 7.518A pdb=" N THR A 109 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL A 149 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR G 109 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL G 149 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR F 109 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL F 149 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR E 109 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL E 149 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR D 109 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL D 149 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR C 109 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL C 149 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR B 109 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL B 149 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 176 removed outlier: 7.079A pdb=" N ASN A 176 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 29 removed outlier: 3.601A pdb=" N ASP B 100 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR B 233 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE B 98 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.591A pdb=" N VAL B 67 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 79 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 69 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER B 82 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.591A pdb=" N VAL B 67 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 79 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 69 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 252 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE B 84 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU B 250 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 86 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 248 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU B 88 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP B 246 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASP B 255 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASP B 272 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN B 257 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR B 270 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N HIS B 259 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR B 268 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR B 261 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS B 266 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 176 removed outlier: 7.071A pdb=" N ASN B 176 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 20 through 29 removed outlier: 6.776A pdb=" N ALA C 229 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR C 101 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 69 removed outlier: 5.557A pdb=" N VAL C 67 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 79 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 69 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER C 82 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY C 166 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 69 removed outlier: 5.557A pdb=" N VAL C 67 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 79 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 69 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 252 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE C 84 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU C 250 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL C 86 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 248 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 88 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP C 246 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP C 255 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP C 272 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLN C 257 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR C 270 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS C 259 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR C 268 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 174 through 176 removed outlier: 7.077A pdb=" N ASN C 176 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLY C 180 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 29 removed outlier: 3.568A pdb=" N ASP D 100 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR D 233 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE D 98 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 66 through 69 removed outlier: 5.560A pdb=" N VAL D 67 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA D 79 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 69 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER D 82 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 66 through 69 removed outlier: 5.560A pdb=" N VAL D 67 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA D 79 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 69 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 252 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE D 84 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU D 250 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL D 86 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 248 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU D 88 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP D 246 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASP D 255 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP D 272 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLN D 257 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR D 270 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS D 259 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR D 268 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 174 through 176 removed outlier: 7.059A pdb=" N ASN D 176 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLY D 180 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 20 through 29 removed outlier: 3.598A pdb=" N ASP E 100 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR E 233 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE E 98 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 66 through 71 removed outlier: 5.572A pdb=" N VAL E 67 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA E 79 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER E 69 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 71 removed outlier: 5.572A pdb=" N VAL E 67 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA E 79 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER E 69 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL E 252 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE E 84 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU E 250 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL E 86 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE E 248 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU E 88 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP E 246 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 174 through 176 removed outlier: 7.098A pdb=" N ASN E 176 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 20 through 29 removed outlier: 6.799A pdb=" N ALA F 229 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR F 101 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL F 231 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 66 through 69 removed outlier: 5.574A pdb=" N VAL F 67 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA F 79 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER F 69 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 66 through 69 removed outlier: 5.574A pdb=" N VAL F 67 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA F 79 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER F 69 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL F 252 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE F 84 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU F 250 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL F 86 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE F 248 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU F 88 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP F 246 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR F 261 " --> pdb=" O LYS F 266 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS F 266 " --> pdb=" O THR F 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 176 removed outlier: 7.095A pdb=" N ASN F 176 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLY F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 20 through 29 removed outlier: 6.791A pdb=" N ALA G 229 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR G 101 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL G 231 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 66 through 69 removed outlier: 5.575A pdb=" N VAL G 67 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA G 79 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G 69 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER G 82 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 66 through 69 removed outlier: 5.575A pdb=" N VAL G 67 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA G 79 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G 69 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL G 252 " --> pdb=" O SER G 82 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE G 84 " --> pdb=" O GLU G 250 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU G 250 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL G 86 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 248 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU G 88 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP G 246 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP G 255 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP G 272 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLN G 257 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR G 270 " --> pdb=" O GLN G 257 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS G 259 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR G 268 " --> pdb=" O HIS G 259 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 174 through 176 removed outlier: 7.059A pdb=" N ASN G 176 " --> pdb=" O GLY G 180 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY G 180 " --> pdb=" O ASN G 176 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 20 through 29 removed outlier: 6.706A pdb=" N ALA H 229 " --> pdb=" O TYR H 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR H 101 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL H 231 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.534A pdb=" N GLY H 77 " --> pdb=" O TYR H 68 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU H 70 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS H 75 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER H 82 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY H 166 " --> pdb=" O GLU H 158 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.534A pdb=" N GLY H 77 " --> pdb=" O TYR H 68 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU H 70 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS H 75 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS H 75 " --> pdb=" O TRP H 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP H 260 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLY H 77 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU H 258 " --> pdb=" O GLY H 77 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA H 79 " --> pdb=" O TYR H 256 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR H 256 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP H 254 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASP H 255 " --> pdb=" O ASP H 272 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP H 272 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLN H 257 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR H 270 " --> pdb=" O GLN H 257 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS H 259 " --> pdb=" O THR H 268 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR H 268 " --> pdb=" O HIS H 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 109 through 127 removed outlier: 7.486A pdb=" N THR H 109 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL H 149 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR N 109 " --> pdb=" O VAL N 149 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL N 149 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR M 109 " --> pdb=" O VAL M 149 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL M 149 " --> pdb=" O THR M 109 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR L 109 " --> pdb=" O VAL L 149 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL L 149 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR K 109 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL K 149 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR J 109 " --> pdb=" O VAL J 149 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL J 149 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR I 109 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL I 149 " --> pdb=" O THR I 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 174 through 176 removed outlier: 7.099A pdb=" N ASN H 176 " --> pdb=" O GLY H 180 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY H 180 " --> pdb=" O ASN H 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 20 through 29 removed outlier: 6.743A pdb=" N ALA I 229 " --> pdb=" O TYR I 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR I 101 " --> pdb=" O ALA I 229 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL I 231 " --> pdb=" O SER I 99 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 66 through 71 removed outlier: 6.520A pdb=" N GLY I 77 " --> pdb=" O TYR I 68 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU I 70 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS I 75 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER I 82 " --> pdb=" O PHE I 171 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY I 166 " --> pdb=" O GLU I 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 66 through 71 removed outlier: 6.520A pdb=" N GLY I 77 " --> pdb=" O TYR I 68 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU I 70 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS I 75 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS I 75 " --> pdb=" O TRP I 260 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TRP I 260 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLY I 77 " --> pdb=" O LEU I 258 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU I 258 " --> pdb=" O GLY I 77 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA I 79 " --> pdb=" O TYR I 256 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR I 256 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP I 254 " --> pdb=" O PRO I 81 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP I 255 " --> pdb=" O ASP I 272 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASP I 272 " --> pdb=" O ASP I 255 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLN I 257 " --> pdb=" O THR I 270 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR I 270 " --> pdb=" O GLN I 257 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N HIS I 259 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR I 268 " --> pdb=" O HIS I 259 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 174 through 176 removed outlier: 7.088A pdb=" N ASN I 176 " --> pdb=" O GLY I 180 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY I 180 " --> pdb=" O ASN I 176 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 20 through 29 removed outlier: 6.753A pdb=" N ALA J 229 " --> pdb=" O TYR J 101 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR J 101 " --> pdb=" O ALA J 229 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL J 231 " --> pdb=" O SER J 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 66 through 71 removed outlier: 6.467A pdb=" N GLY J 77 " --> pdb=" O TYR J 68 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU J 70 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS J 75 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER J 82 " --> pdb=" O PHE J 171 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY J 166 " --> pdb=" O GLU J 158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 66 through 71 removed outlier: 6.467A pdb=" N GLY J 77 " --> pdb=" O TYR J 68 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU J 70 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS J 75 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS J 75 " --> pdb=" O TRP J 260 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TRP J 260 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY J 77 " --> pdb=" O LEU J 258 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU J 258 " --> pdb=" O GLY J 77 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA J 79 " --> pdb=" O TYR J 256 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR J 256 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP J 254 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP J 255 " --> pdb=" O ASP J 272 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP J 272 " --> pdb=" O ASP J 255 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLN J 257 " --> pdb=" O THR J 270 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR J 270 " --> pdb=" O GLN J 257 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N HIS J 259 " --> pdb=" O THR J 268 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR J 268 " --> pdb=" O HIS J 259 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 174 through 176 removed outlier: 7.100A pdb=" N ASN J 176 " --> pdb=" O GLY J 180 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLY J 180 " --> pdb=" O ASN J 176 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 20 through 29 removed outlier: 6.724A pdb=" N ALA K 229 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR K 101 " --> pdb=" O ALA K 229 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL K 231 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.514A pdb=" N GLY K 77 " --> pdb=" O TYR K 68 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU K 70 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS K 75 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N SER K 82 " --> pdb=" O PHE K 171 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY K 166 " --> pdb=" O GLU K 158 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.514A pdb=" N GLY K 77 " --> pdb=" O TYR K 68 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU K 70 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS K 75 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS K 75 " --> pdb=" O TRP K 260 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP K 260 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLY K 77 " --> pdb=" O LEU K 258 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU K 258 " --> pdb=" O GLY K 77 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA K 79 " --> pdb=" O TYR K 256 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR K 256 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP K 254 " --> pdb=" O PRO K 81 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP K 255 " --> pdb=" O ASP K 272 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP K 272 " --> pdb=" O ASP K 255 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLN K 257 " --> pdb=" O THR K 270 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR K 270 " --> pdb=" O GLN K 257 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N HIS K 259 " --> pdb=" O THR K 268 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR K 268 " --> pdb=" O HIS K 259 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 174 through 176 removed outlier: 7.113A pdb=" N ASN K 176 " --> pdb=" O GLY K 180 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLY K 180 " --> pdb=" O ASN K 176 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 20 through 29 removed outlier: 3.517A pdb=" N PHE L 228 " --> pdb=" O THR L 57 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA L 229 " --> pdb=" O TYR L 101 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR L 101 " --> pdb=" O ALA L 229 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL L 231 " --> pdb=" O SER L 99 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 66 through 71 removed outlier: 6.543A pdb=" N GLY L 77 " --> pdb=" O TYR L 68 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU L 70 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYS L 75 " --> pdb=" O GLU L 70 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N SER L 82 " --> pdb=" O PHE L 171 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY L 166 " --> pdb=" O GLU L 158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 66 through 71 removed outlier: 6.543A pdb=" N GLY L 77 " --> pdb=" O TYR L 68 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU L 70 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYS L 75 " --> pdb=" O GLU L 70 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS L 75 " --> pdb=" O TRP L 260 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N TRP L 260 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLY L 77 " --> pdb=" O LEU L 258 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU L 258 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA L 79 " --> pdb=" O TYR L 256 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR L 256 " --> pdb=" O ALA L 79 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASP L 254 " --> pdb=" O PRO L 81 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP L 255 " --> pdb=" O ASP L 272 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASP L 272 " --> pdb=" O ASP L 255 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN L 257 " --> pdb=" O THR L 270 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N THR L 270 " --> pdb=" O GLN L 257 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N HIS L 259 " --> pdb=" O THR L 268 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR L 268 " --> pdb=" O HIS L 259 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 174 through 176 removed outlier: 7.089A pdb=" N ASN L 176 " --> pdb=" O GLY L 180 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY L 180 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 20 through 29 removed outlier: 6.717A pdb=" N ALA M 229 " --> pdb=" O TYR M 101 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR M 101 " --> pdb=" O ALA M 229 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL M 231 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 66 through 71 removed outlier: 6.528A pdb=" N GLY M 77 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU M 70 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LYS M 75 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N SER M 82 " --> pdb=" O PHE M 171 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY M 166 " --> pdb=" O GLU M 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 66 through 71 removed outlier: 6.528A pdb=" N GLY M 77 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU M 70 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LYS M 75 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS M 75 " --> pdb=" O TRP M 260 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TRP M 260 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLY M 77 " --> pdb=" O LEU M 258 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU M 258 " --> pdb=" O GLY M 77 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA M 79 " --> pdb=" O TYR M 256 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR M 256 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP M 254 " --> pdb=" O PRO M 81 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP M 255 " --> pdb=" O ASP M 272 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASP M 272 " --> pdb=" O ASP M 255 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLN M 257 " --> pdb=" O THR M 270 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR M 270 " --> pdb=" O GLN M 257 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS M 259 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR M 268 " --> pdb=" O HIS M 259 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 174 through 176 removed outlier: 7.098A pdb=" N ASN M 176 " --> pdb=" O GLY M 180 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY M 180 " --> pdb=" O ASN M 176 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 20 through 29 removed outlier: 6.719A pdb=" N ALA N 229 " --> pdb=" O TYR N 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR N 101 " --> pdb=" O ALA N 229 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL N 231 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 66 through 71 removed outlier: 6.541A pdb=" N GLY N 77 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU N 70 " --> pdb=" O LYS N 75 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS N 75 " --> pdb=" O GLU N 70 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N SER N 82 " --> pdb=" O PHE N 171 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY N 166 " --> pdb=" O GLU N 158 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 66 through 71 removed outlier: 6.541A pdb=" N GLY N 77 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU N 70 " --> pdb=" O LYS N 75 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS N 75 " --> pdb=" O GLU N 70 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS N 75 " --> pdb=" O TRP N 260 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TRP N 260 " --> pdb=" O LYS N 75 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLY N 77 " --> pdb=" O LEU N 258 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU N 258 " --> pdb=" O GLY N 77 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA N 79 " --> pdb=" O TYR N 256 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR N 256 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP N 254 " --> pdb=" O PRO N 81 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP N 255 " --> pdb=" O ASP N 272 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP N 272 " --> pdb=" O ASP N 255 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN N 257 " --> pdb=" O THR N 270 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR N 270 " --> pdb=" O GLN N 257 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N HIS N 259 " --> pdb=" O THR N 268 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N THR N 268 " --> pdb=" O HIS N 259 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 174 through 176 removed outlier: 7.117A pdb=" N ASN N 176 " --> pdb=" O GLY N 180 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY N 180 " --> pdb=" O ASN N 176 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4215 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: 11.64 Time building geometry restraints manager: 8.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10745 1.34 - 1.46: 7633 1.46 - 1.57: 15026 1.57 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 33600 Sorted by residual: bond pdb=" N THR A 261 " pdb=" CA THR A 261 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.41e+00 bond pdb=" N THR D 261 " pdb=" CA THR D 261 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.28e+00 bond pdb=" C LYS L 58 " pdb=" N GLY L 59 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.12e-02 7.97e+03 1.04e+00 bond pdb=" CG PRO D 181 " pdb=" CD PRO D 181 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.04e+00 bond pdb=" CG PRO C 181 " pdb=" CD PRO C 181 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 1.01e+00 ... (remaining 33595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 44341 1.34 - 2.67: 1014 2.67 - 4.01: 103 4.01 - 5.34: 17 5.34 - 6.68: 11 Bond angle restraints: 45486 Sorted by residual: angle pdb=" C THR D 261 " pdb=" CA THR D 261 " pdb=" CB THR D 261 " ideal model delta sigma weight residual 110.42 115.26 -4.84 1.99e+00 2.53e-01 5.91e+00 angle pdb=" CA TYR J 65 " pdb=" CB TYR J 65 " pdb=" CG TYR J 65 " ideal model delta sigma weight residual 113.90 118.27 -4.37 1.80e+00 3.09e-01 5.90e+00 angle pdb=" CA TYR I 65 " pdb=" CB TYR I 65 " pdb=" CG TYR I 65 " ideal model delta sigma weight residual 113.90 118.16 -4.26 1.80e+00 3.09e-01 5.59e+00 angle pdb=" CA TYR H 65 " pdb=" CB TYR H 65 " pdb=" CG TYR H 65 " ideal model delta sigma weight residual 113.90 118.14 -4.24 1.80e+00 3.09e-01 5.56e+00 angle pdb=" CA TYR L 65 " pdb=" CB TYR L 65 " pdb=" CG TYR L 65 " ideal model delta sigma weight residual 113.90 118.13 -4.23 1.80e+00 3.09e-01 5.52e+00 ... (remaining 45481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17178 17.95 - 35.91: 1986 35.91 - 53.86: 631 53.86 - 71.81: 110 71.81 - 89.76: 73 Dihedral angle restraints: 19978 sinusoidal: 8078 harmonic: 11900 Sorted by residual: dihedral pdb=" CA ASP J 185 " pdb=" CB ASP J 185 " pdb=" CG ASP J 185 " pdb=" OD1 ASP J 185 " ideal model delta sinusoidal sigma weight residual -30.00 -89.67 59.67 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " pdb=" CG ASP F 24 " pdb=" OD1 ASP F 24 " ideal model delta sinusoidal sigma weight residual -30.00 -89.29 59.29 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP N 235 " pdb=" CB ASP N 235 " pdb=" CG ASP N 235 " pdb=" OD1 ASP N 235 " ideal model delta sinusoidal sigma weight residual -30.00 -86.32 56.32 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 19975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2803 0.028 - 0.056: 1267 0.056 - 0.085: 340 0.085 - 0.113: 331 0.113 - 0.141: 131 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA ILE K 284 " pdb=" N ILE K 284 " pdb=" C ILE K 284 " pdb=" CB ILE K 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE F 142 " pdb=" N ILE F 142 " pdb=" C ILE F 142 " pdb=" CB ILE F 142 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE J 284 " pdb=" N ILE J 284 " pdb=" C ILE J 284 " pdb=" CB ILE J 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 4869 not shown) Planarity restraints: 5866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 90 " -0.030 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO H 91 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 91 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 91 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 188 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO K 189 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 90 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO K 91 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO K 91 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO K 91 " -0.022 5.00e-02 4.00e+02 ... (remaining 5863 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8000 2.80 - 3.32: 26083 3.32 - 3.85: 57656 3.85 - 4.37: 68954 4.37 - 4.90: 120369 Nonbonded interactions: 281062 Sorted by model distance: nonbonded pdb=" OD1 ASP L 183 " pdb=" OG SER L 186 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASP J 183 " pdb=" OG SER J 186 " model vdw 2.278 3.040 nonbonded pdb=" O ASN A 32 " pdb=" NH2 ARG A 251 " model vdw 2.279 3.120 nonbonded pdb=" OE1 GLU E 111 " pdb=" NH1 ARG E 147 " model vdw 2.282 3.120 nonbonded pdb=" OD2 ASP N 127 " pdb=" OG1 THR N 129 " model vdw 2.288 3.040 ... (remaining 281057 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 68.730 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.160 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:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 : 0.003 0.031 33600 Z= 0.123 Angle : 0.493 6.679 45486 Z= 0.278 Chirality : 0.044 0.141 4872 Planarity : 0.003 0.046 5866 Dihedral : 17.910 89.765 12362 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.38 % Allowed : 18.13 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4074 helix: -3.56 (0.20), residues: 84 sheet: 1.39 (0.11), residues: 2212 loop : 0.05 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 167 HIS 0.010 0.001 HIS K 259 PHE 0.008 0.001 PHE L 171 TYR 0.016 0.001 TYR J 65 ARG 0.005 0.000 ARG D 200 Details of bonding type rmsd hydrogen bonds : bond 0.11709 ( 1560) hydrogen bonds : angle 6.49259 ( 4215) covalent geometry : bond 0.00261 (33600) covalent geometry : angle 0.49295 (45486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 455 time to evaluate : 3.818 Fit side-chains REVERT: C 71 GLU cc_start: 0.7333 (mp0) cc_final: 0.6959 (mp0) REVERT: D 71 GLU cc_start: 0.7317 (mp0) cc_final: 0.6990 (mp0) REVERT: G 71 GLU cc_start: 0.7260 (mp0) cc_final: 0.7032 (mp0) REVERT: L 290 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7260 (tm-30) outliers start: 123 outliers final: 101 residues processed: 574 average time/residue: 1.5937 time to fit residues: 1066.9046 Evaluate side-chains 543 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 442 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 215 LYS Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 281 ARG Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 75 LYS Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 159 SER Chi-restraints excluded: chain M residue 164 LYS Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain N residue 131 LYS Chi-restraints excluded: chain N residue 142 ILE Chi-restraints excluded: chain N residue 159 SER Chi-restraints excluded: chain N residue 164 LYS Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 205 LYS Chi-restraints excluded: chain N residue 261 THR Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 0.5980 chunk 307 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 164 optimal weight: 0.4980 chunk 318 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 368 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN D 242 GLN E 242 GLN H 87 GLN H 178 ASN I 87 GLN I 178 ASN I 242 GLN J 178 ASN K 87 GLN K 89 GLN ** K 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 GLN L 87 GLN L 242 GLN M 178 ASN M 241 GLN M 242 GLN N 178 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079024 restraints weight = 38364.391| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.16 r_work: 0.2785 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33600 Z= 0.139 Angle : 0.494 6.663 45486 Z= 0.272 Chirality : 0.045 0.144 4872 Planarity : 0.003 0.043 5866 Dihedral : 7.044 59.911 4643 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.32 % Allowed : 16.18 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.13), residues: 4074 helix: -3.23 (0.26), residues: 84 sheet: 1.53 (0.11), residues: 2184 loop : -0.00 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.011 0.001 HIS K 259 PHE 0.007 0.001 PHE N 84 TYR 0.018 0.001 TYR G 65 ARG 0.004 0.000 ARG E 147 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 1560) hydrogen bonds : angle 5.31926 ( 4215) covalent geometry : bond 0.00313 (33600) covalent geometry : angle 0.49405 (45486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 489 time to evaluate : 3.605 Fit side-chains REVERT: A 198 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8850 (ttmm) REVERT: B 37 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8382 (tttt) REVERT: B 78 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9179 (tp) REVERT: B 290 GLU cc_start: 0.8601 (tt0) cc_final: 0.8335 (tt0) REVERT: C 71 GLU cc_start: 0.7630 (mp0) cc_final: 0.7097 (mp0) REVERT: C 215 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8435 (mmtp) REVERT: D 71 GLU cc_start: 0.7598 (mp0) cc_final: 0.7139 (mp0) REVERT: D 215 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9034 (mttm) REVERT: E 125 THR cc_start: 0.8382 (m) cc_final: 0.8168 (t) REVERT: E 198 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8861 (ttmm) REVERT: E 205 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8306 (mtpm) REVERT: E 290 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8008 (pp20) REVERT: F 71 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: G 71 GLU cc_start: 0.7612 (mp0) cc_final: 0.7196 (mp0) REVERT: H 31 GLU cc_start: 0.8378 (pm20) cc_final: 0.8114 (pm20) REVERT: H 205 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7986 (mtpp) REVERT: H 250 GLU cc_start: 0.8734 (tt0) cc_final: 0.8501 (tt0) REVERT: H 280 GLU cc_start: 0.8322 (tp30) cc_final: 0.8000 (tp30) REVERT: I 31 GLU cc_start: 0.8272 (pm20) cc_final: 0.8047 (pm20) REVERT: I 78 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8813 (tp) REVERT: I 205 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7982 (mtpp) REVERT: I 280 GLU cc_start: 0.8336 (tp30) cc_final: 0.8048 (tp30) REVERT: K 37 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.7439 (tmmm) REVERT: K 122 SER cc_start: 0.8541 (t) cc_final: 0.8134 (p) REVERT: K 205 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8157 (mtpp) REVERT: L 235 ASP cc_start: 0.7883 (t70) cc_final: 0.7627 (t0) REVERT: L 283 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8361 (tmmm) REVERT: L 290 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7841 (tm-30) REVERT: N 74 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8062 (t0) REVERT: N 78 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8879 (tp) REVERT: N 164 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8010 (tttp) outliers start: 121 outliers final: 46 residues processed: 583 average time/residue: 1.7130 time to fit residues: 1156.2641 Evaluate side-chains 509 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 445 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 164 LYS Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 262 SER Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 404 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 381 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 293 ASN C 89 GLN D 89 GLN D 242 GLN E 242 GLN H 87 GLN H 150 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN L 242 GLN M 242 GLN N 242 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.075334 restraints weight = 38828.085| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.17 r_work: 0.2726 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 33600 Z= 0.378 Angle : 0.639 6.797 45486 Z= 0.351 Chirality : 0.052 0.177 4872 Planarity : 0.004 0.045 5866 Dihedral : 6.613 58.958 4527 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.99 % Allowed : 16.84 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4074 helix: -3.48 (0.22), residues: 84 sheet: 1.41 (0.10), residues: 2212 loop : -0.09 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 167 HIS 0.011 0.002 HIS L 259 PHE 0.012 0.002 PHE J 153 TYR 0.027 0.003 TYR M 65 ARG 0.010 0.001 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 1560) hydrogen bonds : angle 5.73342 ( 4215) covalent geometry : bond 0.00881 (33600) covalent geometry : angle 0.63929 (45486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 440 time to evaluate : 4.050 Fit side-chains REVERT: A 198 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8955 (ttmm) REVERT: B 31 GLU cc_start: 0.8551 (pm20) cc_final: 0.8311 (pm20) REVERT: B 37 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.7984 (tmtt) REVERT: B 71 GLU cc_start: 0.7173 (mp0) cc_final: 0.6930 (mp0) REVERT: C 71 GLU cc_start: 0.7704 (mp0) cc_final: 0.7173 (mp0) REVERT: C 215 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8508 (mmtp) REVERT: D 58 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8779 (mtpt) REVERT: D 71 GLU cc_start: 0.7687 (mp0) cc_final: 0.7231 (mp0) REVERT: D 215 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.9012 (mttm) REVERT: E 125 THR cc_start: 0.8425 (m) cc_final: 0.8157 (t) REVERT: E 198 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8960 (ttmm) REVERT: F 71 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: F 283 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8521 (tmtt) REVERT: G 71 GLU cc_start: 0.7645 (mp0) cc_final: 0.7278 (mp0) REVERT: H 205 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: I 78 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8870 (tp) REVERT: I 205 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: I 283 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8312 (ttmt) REVERT: K 205 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8123 (mtpp) REVERT: L 154 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8523 (ptmt) REVERT: L 290 GLU cc_start: 0.8219 (tm-30) cc_final: 0.8000 (tm-30) REVERT: M 277 ARG cc_start: 0.8324 (ttt90) cc_final: 0.7922 (ttt90) REVERT: N 78 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8945 (tp) outliers start: 109 outliers final: 53 residues processed: 525 average time/residue: 1.8638 time to fit residues: 1126.0194 Evaluate side-chains 495 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 427 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 151 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 321 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 278 optimal weight: 0.9980 chunk 334 optimal weight: 0.7980 chunk 203 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN E 242 GLN F 259 HIS H 87 GLN I 87 GLN I 150 GLN I 242 GLN K 87 GLN L 87 GLN M 242 GLN N 242 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.080042 restraints weight = 38567.367| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.17 r_work: 0.2802 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33600 Z= 0.105 Angle : 0.475 7.213 45486 Z= 0.258 Chirality : 0.044 0.139 4872 Planarity : 0.003 0.040 5866 Dihedral : 5.628 58.062 4518 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.75 % Allowed : 16.90 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 4074 helix: -2.94 (0.31), residues: 84 sheet: 1.40 (0.11), residues: 2268 loop : 0.02 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.008 0.001 HIS K 259 PHE 0.007 0.001 PHE L 171 TYR 0.015 0.001 TYR K 65 ARG 0.009 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 1560) hydrogen bonds : angle 5.04620 ( 4215) covalent geometry : bond 0.00229 (33600) covalent geometry : angle 0.47470 (45486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 473 time to evaluate : 4.048 Fit side-chains REVERT: A 198 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8847 (ttmm) REVERT: A 290 GLU cc_start: 0.8319 (pp20) cc_final: 0.7883 (pp20) REVERT: B 31 GLU cc_start: 0.8506 (pm20) cc_final: 0.8243 (pm20) REVERT: B 37 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8361 (tttt) REVERT: B 71 GLU cc_start: 0.7044 (mp0) cc_final: 0.6788 (mp0) REVERT: B 78 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9145 (tp) REVERT: C 71 GLU cc_start: 0.7617 (mp0) cc_final: 0.7089 (mp0) REVERT: C 215 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8445 (mmtp) REVERT: D 71 GLU cc_start: 0.7586 (mp0) cc_final: 0.7127 (mp0) REVERT: E 125 THR cc_start: 0.8389 (m) cc_final: 0.8168 (t) REVERT: E 198 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8911 (ttmm) REVERT: G 71 GLU cc_start: 0.7618 (mp0) cc_final: 0.7176 (mp0) REVERT: H 30 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8488 (tmtt) REVERT: H 195 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8427 (tt) REVERT: H 250 GLU cc_start: 0.8729 (tt0) cc_final: 0.8524 (tt0) REVERT: J 101 TYR cc_start: 0.9373 (OUTLIER) cc_final: 0.8458 (p90) REVERT: J 141 SER cc_start: 0.8862 (m) cc_final: 0.8592 (p) REVERT: J 277 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7653 (ttt90) REVERT: K 37 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7480 (tmmm) REVERT: K 205 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8109 (mtpp) REVERT: L 250 GLU cc_start: 0.8706 (tt0) cc_final: 0.8438 (tt0) REVERT: L 283 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8390 (tmmm) REVERT: M 242 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7590 (mm110) REVERT: M 277 ARG cc_start: 0.8224 (ttt90) cc_final: 0.7801 (ttt90) REVERT: N 188 ASN cc_start: 0.7988 (t0) cc_final: 0.7663 (t0) outliers start: 100 outliers final: 36 residues processed: 550 average time/residue: 1.7583 time to fit residues: 1117.1993 Evaluate side-chains 481 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 432 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 242 GLN Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 262 SER Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 172 optimal weight: 0.0270 chunk 388 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 overall best weight: 3.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN E 242 GLN E 293 ASN I 87 GLN I 242 GLN K 87 GLN L 87 GLN N 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.076861 restraints weight = 38605.478| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.16 r_work: 0.2747 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 33600 Z= 0.252 Angle : 0.563 7.333 45486 Z= 0.307 Chirality : 0.048 0.150 4872 Planarity : 0.004 0.039 5866 Dihedral : 5.593 59.756 4490 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.58 % Allowed : 17.42 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4074 helix: -3.11 (0.28), residues: 84 sheet: 1.43 (0.11), residues: 2212 loop : -0.03 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 167 HIS 0.011 0.001 HIS L 259 PHE 0.009 0.002 PHE A 39 TYR 0.024 0.002 TYR K 65 ARG 0.010 0.000 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 1560) hydrogen bonds : angle 5.41603 ( 4215) covalent geometry : bond 0.00581 (33600) covalent geometry : angle 0.56297 (45486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 438 time to evaluate : 3.779 Fit side-chains REVERT: A 198 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8875 (ttmm) REVERT: A 290 GLU cc_start: 0.8443 (pp20) cc_final: 0.7990 (pp20) REVERT: B 31 GLU cc_start: 0.8515 (pm20) cc_final: 0.8190 (pm20) REVERT: B 37 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.7961 (tmtt) REVERT: B 71 GLU cc_start: 0.7129 (mp0) cc_final: 0.6853 (mp0) REVERT: B 78 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9201 (tp) REVERT: C 71 GLU cc_start: 0.7684 (mp0) cc_final: 0.7152 (mp0) REVERT: C 215 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8484 (mmtp) REVERT: D 37 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8817 (tttt) REVERT: D 71 GLU cc_start: 0.7611 (mp0) cc_final: 0.7164 (mp0) REVERT: E 198 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8935 (ttmm) REVERT: E 204 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8460 (pmm) REVERT: E 205 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8387 (mtpm) REVERT: F 283 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8491 (tmtt) REVERT: G 37 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8241 (tmtt) REVERT: G 71 GLU cc_start: 0.7629 (mp0) cc_final: 0.7228 (mp0) REVERT: H 30 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8527 (tmtt) REVERT: I 283 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8311 (ttmt) REVERT: J 101 TYR cc_start: 0.9407 (OUTLIER) cc_final: 0.8493 (p90) REVERT: J 277 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7745 (ttt90) REVERT: K 37 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.7644 (tmmm) REVERT: K 205 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8103 (mtpp) REVERT: L 283 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8416 (tmmm) REVERT: M 277 ARG cc_start: 0.8297 (ttt90) cc_final: 0.7894 (ttt90) REVERT: N 285 ASP cc_start: 0.8073 (t70) cc_final: 0.7797 (t70) outliers start: 94 outliers final: 46 residues processed: 508 average time/residue: 1.7620 time to fit residues: 1036.5736 Evaluate side-chains 485 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 422 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain G residue 37 LYS Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 298 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 355 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 357 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 376 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN H 87 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN N 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.077525 restraints weight = 38700.165| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.16 r_work: 0.2757 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 33600 Z= 0.198 Angle : 0.532 7.269 45486 Z= 0.291 Chirality : 0.046 0.145 4872 Planarity : 0.003 0.038 5866 Dihedral : 5.444 59.992 4489 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.42 % Allowed : 17.50 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4074 helix: -2.99 (0.30), residues: 84 sheet: 1.41 (0.11), residues: 2212 loop : -0.04 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 167 HIS 0.009 0.001 HIS K 259 PHE 0.009 0.001 PHE L 171 TYR 0.022 0.002 TYR J 65 ARG 0.011 0.000 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 1560) hydrogen bonds : angle 5.31271 ( 4215) covalent geometry : bond 0.00452 (33600) covalent geometry : angle 0.53228 (45486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 421 time to evaluate : 3.829 Fit side-chains REVERT: A 125 THR cc_start: 0.8554 (p) cc_final: 0.8262 (t) REVERT: A 198 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8861 (ttmm) REVERT: A 290 GLU cc_start: 0.8432 (pp20) cc_final: 0.7957 (pp20) REVERT: B 31 GLU cc_start: 0.8489 (pm20) cc_final: 0.8148 (pm20) REVERT: B 37 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.7954 (tmtt) REVERT: B 71 GLU cc_start: 0.7123 (mp0) cc_final: 0.6838 (mp0) REVERT: B 78 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9185 (tp) REVERT: C 71 GLU cc_start: 0.7661 (mp0) cc_final: 0.7137 (mp0) REVERT: C 215 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8485 (mmtp) REVERT: D 71 GLU cc_start: 0.7618 (mp0) cc_final: 0.7168 (mp0) REVERT: E 198 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8923 (ttmm) REVERT: E 204 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8430 (pmm) REVERT: E 205 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8375 (mtpm) REVERT: F 71 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: F 215 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8475 (mmtp) REVERT: F 283 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8472 (tmtt) REVERT: G 37 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8199 (tmtt) REVERT: G 71 GLU cc_start: 0.7627 (mp0) cc_final: 0.7232 (mp0) REVERT: H 30 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8544 (tmtt) REVERT: I 283 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8296 (ttmt) REVERT: J 101 TYR cc_start: 0.9400 (OUTLIER) cc_final: 0.8389 (p90) REVERT: J 277 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7736 (ttt90) REVERT: K 37 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.7600 (tmmm) REVERT: K 205 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8142 (mtpp) REVERT: L 154 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8696 (ptpt) REVERT: L 283 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8423 (tmmm) REVERT: M 277 ARG cc_start: 0.8276 (ttt90) cc_final: 0.7858 (ttt90) REVERT: N 285 ASP cc_start: 0.8085 (t70) cc_final: 0.7836 (t70) outliers start: 88 outliers final: 48 residues processed: 491 average time/residue: 1.7112 time to fit residues: 971.9807 Evaluate side-chains 482 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 415 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain G residue 37 LYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 262 SER Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 227 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 367 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN H 87 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.078084 restraints weight = 38189.052| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.20 r_work: 0.2760 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33600 Z= 0.143 Angle : 0.498 7.884 45486 Z= 0.271 Chirality : 0.045 0.142 4872 Planarity : 0.003 0.038 5866 Dihedral : 5.241 58.570 4487 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.17 % Allowed : 17.91 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.13), residues: 4074 helix: -2.82 (0.33), residues: 84 sheet: 1.41 (0.11), residues: 2212 loop : 0.01 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.010 0.001 HIS K 259 PHE 0.007 0.001 PHE L 171 TYR 0.019 0.001 TYR J 65 ARG 0.011 0.000 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 1560) hydrogen bonds : angle 5.14449 ( 4215) covalent geometry : bond 0.00323 (33600) covalent geometry : angle 0.49783 (45486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 429 time to evaluate : 3.725 Fit side-chains REVERT: A 125 THR cc_start: 0.8486 (p) cc_final: 0.8246 (t) REVERT: A 198 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8848 (ttmm) REVERT: A 290 GLU cc_start: 0.8387 (pp20) cc_final: 0.7891 (pp20) REVERT: B 31 GLU cc_start: 0.8537 (pm20) cc_final: 0.8187 (pm20) REVERT: B 37 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8342 (tttt) REVERT: B 71 GLU cc_start: 0.7060 (mp0) cc_final: 0.6776 (mp0) REVERT: B 78 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9170 (tp) REVERT: C 71 GLU cc_start: 0.7647 (mp0) cc_final: 0.7105 (mp0) REVERT: C 215 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8463 (mmtp) REVERT: D 71 GLU cc_start: 0.7561 (mp0) cc_final: 0.7096 (mp0) REVERT: E 198 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8894 (ttmm) REVERT: E 205 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8282 (mtpm) REVERT: F 71 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: F 215 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8436 (mmtp) REVERT: G 71 GLU cc_start: 0.7549 (mp0) cc_final: 0.7130 (mp0) REVERT: H 30 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8481 (tmtt) REVERT: I 283 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8274 (ttmt) REVERT: J 101 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.8378 (p90) REVERT: J 277 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7698 (ttt90) REVERT: K 37 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.7497 (tmmm) REVERT: K 205 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8120 (mtpp) REVERT: L 50 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8427 (ptpp) REVERT: L 154 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8662 (ptpt) REVERT: L 235 ASP cc_start: 0.7922 (t70) cc_final: 0.7649 (t0) REVERT: L 283 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8392 (tmmm) REVERT: M 277 ARG cc_start: 0.8245 (ttt90) cc_final: 0.7812 (ttt90) REVERT: N 113 MET cc_start: 0.8864 (ttp) cc_final: 0.8517 (ttt) outliers start: 79 outliers final: 40 residues processed: 494 average time/residue: 1.7374 time to fit residues: 996.5155 Evaluate side-chains 488 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 431 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 218 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 348 optimal weight: 6.9990 chunk 334 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 1 optimal weight: 0.0470 chunk 24 optimal weight: 8.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN H 87 GLN I 87 GLN I 150 GLN I 242 GLN K 87 GLN L 87 GLN M 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.077196 restraints weight = 38248.799| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.19 r_work: 0.2743 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33600 Z= 0.189 Angle : 0.529 8.101 45486 Z= 0.288 Chirality : 0.046 0.146 4872 Planarity : 0.003 0.040 5866 Dihedral : 5.340 59.038 4485 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.34 % Allowed : 17.83 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4074 helix: -2.89 (0.31), residues: 84 sheet: 1.41 (0.11), residues: 2212 loop : -0.02 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.011 0.001 HIS K 259 PHE 0.008 0.001 PHE L 171 TYR 0.021 0.002 TYR J 65 ARG 0.011 0.000 ARG M 147 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 1560) hydrogen bonds : angle 5.26558 ( 4215) covalent geometry : bond 0.00433 (33600) covalent geometry : angle 0.52920 (45486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 444 time to evaluate : 3.645 Fit side-chains REVERT: A 125 THR cc_start: 0.8483 (p) cc_final: 0.8202 (t) REVERT: A 198 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8848 (ttmm) REVERT: A 290 GLU cc_start: 0.8418 (pp20) cc_final: 0.7905 (pp20) REVERT: B 31 GLU cc_start: 0.8532 (pm20) cc_final: 0.8164 (pm20) REVERT: B 37 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.7953 (tmtt) REVERT: B 71 GLU cc_start: 0.7091 (mp0) cc_final: 0.6805 (mp0) REVERT: B 78 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9198 (tp) REVERT: C 71 GLU cc_start: 0.7652 (mp0) cc_final: 0.7116 (mp0) REVERT: C 215 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8461 (mmtp) REVERT: D 71 GLU cc_start: 0.7571 (mp0) cc_final: 0.7110 (mp0) REVERT: E 198 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8891 (ttmm) REVERT: E 204 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8358 (pmm) REVERT: E 205 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8345 (mtpm) REVERT: F 71 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: F 215 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8444 (mmtp) REVERT: G 71 GLU cc_start: 0.7569 (mp0) cc_final: 0.7162 (mp0) REVERT: H 30 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8502 (tmtt) REVERT: I 56 ARG cc_start: 0.8927 (mtt90) cc_final: 0.8578 (mtt90) REVERT: I 277 ARG cc_start: 0.8239 (ttt90) cc_final: 0.7960 (ttt90) REVERT: I 283 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8262 (ttmt) REVERT: J 101 TYR cc_start: 0.9371 (OUTLIER) cc_final: 0.8360 (p90) REVERT: J 277 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7709 (ttt90) REVERT: K 37 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.7528 (tmmm) REVERT: K 205 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8130 (mtpp) REVERT: L 154 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8698 (ptpt) REVERT: L 235 ASP cc_start: 0.7977 (t70) cc_final: 0.7696 (t0) REVERT: L 283 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8403 (tmmm) REVERT: M 242 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7699 (mm110) REVERT: M 277 ARG cc_start: 0.8264 (ttt90) cc_final: 0.7838 (ttt90) outliers start: 85 outliers final: 51 residues processed: 508 average time/residue: 1.7940 time to fit residues: 1047.7721 Evaluate side-chains 496 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 427 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 242 GLN Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 257 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 337 optimal weight: 0.4980 chunk 148 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 306 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN H 87 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.077033 restraints weight = 38579.062| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.18 r_work: 0.2747 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33600 Z= 0.234 Angle : 0.557 7.917 45486 Z= 0.304 Chirality : 0.047 0.152 4872 Planarity : 0.004 0.048 5866 Dihedral : 5.463 59.398 4485 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.25 % Allowed : 17.99 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 4074 helix: -3.01 (0.30), residues: 84 sheet: 1.40 (0.11), residues: 2212 loop : -0.05 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 167 HIS 0.011 0.001 HIS K 259 PHE 0.009 0.002 PHE H 153 TYR 0.023 0.002 TYR K 65 ARG 0.011 0.000 ARG J 147 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 1560) hydrogen bonds : angle 5.38182 ( 4215) covalent geometry : bond 0.00540 (33600) covalent geometry : angle 0.55739 (45486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 435 time to evaluate : 3.860 Fit side-chains REVERT: A 125 THR cc_start: 0.8512 (p) cc_final: 0.8229 (t) REVERT: A 198 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8885 (ttmm) REVERT: A 290 GLU cc_start: 0.8454 (pp20) cc_final: 0.7951 (pp20) REVERT: B 31 GLU cc_start: 0.8475 (pm20) cc_final: 0.8115 (pm20) REVERT: B 37 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.7947 (tmtt) REVERT: B 71 GLU cc_start: 0.7153 (mp0) cc_final: 0.6857 (mp0) REVERT: B 78 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9202 (tp) REVERT: C 71 GLU cc_start: 0.7689 (mp0) cc_final: 0.7164 (mp0) REVERT: C 215 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8490 (mmtp) REVERT: D 71 GLU cc_start: 0.7614 (mp0) cc_final: 0.7168 (mp0) REVERT: E 198 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8928 (ttmm) REVERT: E 205 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8356 (mtpm) REVERT: F 71 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: F 215 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8507 (mmtp) REVERT: F 283 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8489 (tmtt) REVERT: G 37 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8214 (tmtt) REVERT: G 71 GLU cc_start: 0.7635 (mp0) cc_final: 0.7240 (mp0) REVERT: H 30 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8552 (tmtt) REVERT: I 56 ARG cc_start: 0.8959 (mtt90) cc_final: 0.8645 (mtt90) REVERT: I 277 ARG cc_start: 0.8272 (ttt90) cc_final: 0.7998 (ttt90) REVERT: I 283 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8299 (ttmt) REVERT: J 101 TYR cc_start: 0.9406 (OUTLIER) cc_final: 0.8487 (p90) REVERT: J 277 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7757 (ttt90) REVERT: K 37 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.7621 (tmmm) REVERT: K 205 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8230 (mtpp) REVERT: L 154 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8719 (ptpt) REVERT: L 235 ASP cc_start: 0.8023 (t70) cc_final: 0.7713 (t0) REVERT: L 283 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8407 (tmmm) REVERT: M 242 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7757 (mm-40) REVERT: M 277 ARG cc_start: 0.8289 (ttt90) cc_final: 0.7870 (ttt90) REVERT: N 113 MET cc_start: 0.8880 (ttp) cc_final: 0.8548 (ttt) outliers start: 82 outliers final: 53 residues processed: 502 average time/residue: 1.7656 time to fit residues: 1030.4592 Evaluate side-chains 498 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 426 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain G residue 37 LYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 242 GLN Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 203 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN F 89 GLN H 87 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN L 123 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.077428 restraints weight = 38197.592| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.20 r_work: 0.2748 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33600 Z= 0.174 Angle : 0.524 8.194 45486 Z= 0.285 Chirality : 0.046 0.144 4872 Planarity : 0.003 0.043 5866 Dihedral : 5.327 59.899 4485 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.06 % Allowed : 18.32 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4074 helix: -2.90 (0.32), residues: 84 sheet: 1.40 (0.11), residues: 2212 loop : -0.02 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.011 0.001 HIS K 259 PHE 0.008 0.001 PHE L 171 TYR 0.020 0.002 TYR H 65 ARG 0.010 0.000 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 1560) hydrogen bonds : angle 5.24477 ( 4215) covalent geometry : bond 0.00397 (33600) covalent geometry : angle 0.52422 (45486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 436 time to evaluate : 3.593 Fit side-chains REVERT: A 125 THR cc_start: 0.8436 (p) cc_final: 0.8167 (t) REVERT: A 198 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8920 (ttmm) REVERT: A 290 GLU cc_start: 0.8424 (pp20) cc_final: 0.7904 (pp20) REVERT: B 31 GLU cc_start: 0.8536 (pm20) cc_final: 0.8152 (pm20) REVERT: B 37 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.7944 (tmtt) REVERT: B 71 GLU cc_start: 0.7090 (mp0) cc_final: 0.6802 (mp0) REVERT: B 78 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9191 (tp) REVERT: C 71 GLU cc_start: 0.7644 (mp0) cc_final: 0.7109 (mp0) REVERT: C 215 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8453 (mmtp) REVERT: D 71 GLU cc_start: 0.7584 (mp0) cc_final: 0.7125 (mp0) REVERT: E 198 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8897 (ttmm) REVERT: E 205 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8295 (mtpm) REVERT: F 71 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: F 215 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8436 (mmtp) REVERT: G 37 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8224 (tmtt) REVERT: G 71 GLU cc_start: 0.7537 (mp0) cc_final: 0.7127 (mp0) REVERT: H 30 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8499 (tmtt) REVERT: I 56 ARG cc_start: 0.8929 (mtt90) cc_final: 0.8580 (mtt90) REVERT: I 277 ARG cc_start: 0.8238 (ttt90) cc_final: 0.7958 (ttt90) REVERT: I 283 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8258 (ttmt) REVERT: J 101 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.8363 (p90) REVERT: J 277 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7718 (ttt90) REVERT: K 37 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.7544 (tmmm) REVERT: K 205 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8185 (mtpp) REVERT: L 154 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8659 (ptpt) REVERT: L 283 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8364 (tmmm) REVERT: M 242 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7667 (mm110) REVERT: M 277 ARG cc_start: 0.8254 (ttt90) cc_final: 0.7827 (ttt90) REVERT: N 113 MET cc_start: 0.8852 (ttp) cc_final: 0.8519 (ttt) outliers start: 75 outliers final: 50 residues processed: 498 average time/residue: 1.7341 time to fit residues: 994.9962 Evaluate side-chains 496 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 428 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 37 LYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 242 GLN Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 72 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 327 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 285 optimal weight: 4.9990 chunk 386 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 358 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 264 ASN C 89 GLN D 89 GLN H 87 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN L 242 GLN M 123 ASN M 242 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.077185 restraints weight = 38150.207| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.19 r_work: 0.2743 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33600 Z= 0.188 Angle : 0.537 8.102 45486 Z= 0.291 Chirality : 0.046 0.146 4872 Planarity : 0.004 0.050 5866 Dihedral : 5.363 59.637 4485 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.06 % Allowed : 18.43 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 4074 helix: -2.94 (0.31), residues: 84 sheet: 1.39 (0.11), residues: 2212 loop : -0.03 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.011 0.001 HIS K 259 PHE 0.008 0.001 PHE L 171 TYR 0.021 0.002 TYR J 65 ARG 0.013 0.001 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 1560) hydrogen bonds : angle 5.28180 ( 4215) covalent geometry : bond 0.00430 (33600) covalent geometry : angle 0.53676 (45486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31327.29 seconds wall clock time: 539 minutes 51.04 seconds (32391.04 seconds total)