Starting phenix.real_space_refine on Sat Jun 28 05:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx2_36688/06_2025/8jx2_36688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx2_36688/06_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_36688/06_2025/8jx2_36688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx2_36688/06_2025/8jx2_36688.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx2_36688/06_2025/8jx2_36688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx2_36688/06_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-5710/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: 19.34, per 1000 atoms: 0.59 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: 7.85 Conformation dependent library (CDL) restraints added in 4.3 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: 4.93 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: 13.99 Time building geometry restraints manager: 9.35 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: 0.03 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: 4.400 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: 0.030 Extract box with map and model: 1.400 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 75.780 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.930 ------------------------------------------------------------------------------- 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 : 3.972 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: 1.6618 time to fit residues: 1113.1324 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 : 3.777 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.078998 restraints weight = 38364.389| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.17 r_work: 0.2786 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 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 : 4.082 Fit side-chains REVERT: A 198 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8849 (ttmm) REVERT: B 37 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8383 (tttt) REVERT: B 78 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9178 (tp) REVERT: B 290 GLU cc_start: 0.8601 (tt0) cc_final: 0.8335 (tt0) REVERT: C 71 GLU cc_start: 0.7624 (mp0) cc_final: 0.7091 (mp0) REVERT: C 215 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8437 (mmtp) REVERT: D 71 GLU cc_start: 0.7591 (mp0) cc_final: 0.7131 (mp0) REVERT: D 215 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9033 (mttm) REVERT: E 125 THR cc_start: 0.8393 (m) cc_final: 0.8180 (t) REVERT: E 198 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8860 (ttmm) REVERT: E 205 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8298 (mtpm) REVERT: E 290 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8007 (pp20) REVERT: F 71 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: G 71 GLU cc_start: 0.7605 (mp0) cc_final: 0.7188 (mp0) REVERT: H 31 GLU cc_start: 0.8374 (pm20) cc_final: 0.8110 (pm20) REVERT: H 205 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7988 (mtpp) REVERT: H 250 GLU cc_start: 0.8733 (tt0) cc_final: 0.8500 (tt0) REVERT: H 280 GLU cc_start: 0.8322 (tp30) cc_final: 0.7999 (tp30) REVERT: I 31 GLU cc_start: 0.8269 (pm20) cc_final: 0.8044 (pm20) REVERT: I 78 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8810 (tp) REVERT: I 205 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7985 (mtpp) REVERT: I 280 GLU cc_start: 0.8334 (tp30) cc_final: 0.8046 (tp30) REVERT: K 37 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.7438 (tmmm) REVERT: K 122 SER cc_start: 0.8549 (t) cc_final: 0.8140 (p) REVERT: K 205 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8158 (mtpp) REVERT: L 235 ASP cc_start: 0.7878 (t70) cc_final: 0.7621 (t0) REVERT: L 283 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8358 (tmmm) REVERT: L 290 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7840 (tm-30) REVERT: N 74 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8060 (t0) REVERT: N 78 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8875 (tp) REVERT: N 164 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8000 (tttp) outliers start: 121 outliers final: 46 residues processed: 583 average time/residue: 1.7361 time to fit residues: 1174.4000 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 : 3.871 ------------------------------------------------------------------------------- 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: 7.9990 chunk 270 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 381 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.106749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.075018 restraints weight = 38847.572| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.17 r_work: 0.2717 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.068 33600 Z= 0.408 Angle : 0.660 6.873 45486 Z= 0.362 Chirality : 0.053 0.191 4872 Planarity : 0.005 0.047 5866 Dihedral : 6.679 59.322 4527 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.16 % Allowed : 16.68 % 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: 0.96 (0.13), residues: 4074 helix: -3.54 (0.21), residues: 84 sheet: 1.39 (0.10), residues: 2212 loop : -0.10 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 167 HIS 0.012 0.002 HIS L 259 PHE 0.013 0.002 PHE J 153 TYR 0.028 0.003 TYR M 65 ARG 0.010 0.001 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 1560) hydrogen bonds : angle 5.78838 ( 4215) covalent geometry : bond 0.00952 (33600) covalent geometry : angle 0.65966 (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: 115 poor density : 434 time to evaluate : 4.878 Fit side-chains REVERT: A 198 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8954 (ttmm) REVERT: B 31 GLU cc_start: 0.8562 (pm20) cc_final: 0.8326 (pm20) REVERT: B 37 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.7957 (tmtt) REVERT: B 71 GLU cc_start: 0.7237 (mp0) cc_final: 0.6949 (mp0) REVERT: C 71 GLU cc_start: 0.7708 (mp0) cc_final: 0.7179 (mp0) REVERT: C 215 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8530 (mmtp) REVERT: D 58 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8769 (mtpt) REVERT: D 71 GLU cc_start: 0.7691 (mp0) cc_final: 0.7241 (mp0) REVERT: D 215 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.9029 (mttm) REVERT: E 125 THR cc_start: 0.8423 (m) cc_final: 0.8152 (t) REVERT: E 198 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8962 (ttmm) REVERT: F 71 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: F 283 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8522 (tmtt) REVERT: G 71 GLU cc_start: 0.7662 (mp0) cc_final: 0.7312 (mp0) REVERT: H 205 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: I 78 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8864 (tp) REVERT: I 205 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8070 (mtpp) REVERT: I 283 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8311 (ttmt) REVERT: J 101 TYR cc_start: 0.9409 (OUTLIER) cc_final: 0.8584 (p90) REVERT: J 292 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8368 (p) REVERT: K 205 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8173 (mtpp) REVERT: M 277 ARG cc_start: 0.8339 (ttt90) cc_final: 0.7943 (ttt90) REVERT: N 78 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8934 (tp) REVERT: N 257 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8661 (mt0) outliers start: 115 outliers final: 54 residues processed: 524 average time/residue: 2.1282 time to fit residues: 1286.3591 Evaluate side-chains 481 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 410 time to evaluate : 3.928 ------------------------------------------------------------------------------- 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 101 TYR 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 J residue 292 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 92 ASP 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 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 164 LYS Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 257 GLN 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: 0.7980 chunk 321 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 278 optimal weight: 0.1980 chunk 334 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.111528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080342 restraints weight = 38569.425| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.17 r_work: 0.2809 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33600 Z= 0.100 Angle : 0.471 7.287 45486 Z= 0.256 Chirality : 0.044 0.138 4872 Planarity : 0.003 0.040 5866 Dihedral : 5.642 57.983 4522 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.94 % Allowed : 16.59 % Favored : 80.47 % 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: 1.09 (0.13), residues: 4074 helix: -2.94 (0.31), residues: 84 sheet: 1.40 (0.11), residues: 2268 loop : 0.03 (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 0.014 0.001 TYR K 65 ARG 0.010 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 1560) hydrogen bonds : angle 5.01241 ( 4215) covalent geometry : bond 0.00216 (33600) covalent geometry : angle 0.47056 (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 569 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 462 time to evaluate : 4.952 Fit side-chains REVERT: A 198 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8840 (ttmm) REVERT: B 31 GLU cc_start: 0.8499 (pm20) cc_final: 0.8228 (pm20) REVERT: B 37 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8358 (tttt) REVERT: B 71 GLU cc_start: 0.7040 (mp0) cc_final: 0.6781 (mp0) REVERT: B 78 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9134 (tp) REVERT: C 71 GLU cc_start: 0.7619 (mp0) cc_final: 0.7095 (mp0) REVERT: C 215 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8438 (mmtp) REVERT: D 71 GLU cc_start: 0.7585 (mp0) cc_final: 0.7123 (mp0) REVERT: E 125 THR cc_start: 0.8399 (m) cc_final: 0.8179 (t) REVERT: F 106 SER cc_start: 0.9093 (m) cc_final: 0.8834 (p) REVERT: G 71 GLU cc_start: 0.7620 (mp0) cc_final: 0.7206 (mp0) REVERT: H 30 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8488 (tmtt) REVERT: H 147 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8690 (ttp-170) REVERT: H 195 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8437 (tt) REVERT: H 250 GLU cc_start: 0.8742 (tt0) cc_final: 0.8542 (tt0) REVERT: J 101 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.8413 (p90) REVERT: J 141 SER cc_start: 0.8842 (m) cc_final: 0.8605 (p) REVERT: J 277 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7656 (ttt90) REVERT: K 205 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8091 (mtpp) REVERT: L 147 ARG cc_start: 0.8843 (ttp-170) cc_final: 0.8479 (ttp-110) REVERT: L 195 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8317 (tt) REVERT: L 283 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8393 (tmmm) REVERT: M 242 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7585 (mm110) REVERT: M 277 ARG cc_start: 0.8217 (ttt90) cc_final: 0.7792 (ttt90) REVERT: N 164 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8073 (tttp) REVERT: N 188 ASN cc_start: 0.7986 (t0) cc_final: 0.7661 (t0) outliers start: 107 outliers final: 33 residues processed: 545 average time/residue: 1.9636 time to fit residues: 1240.6478 Evaluate side-chains 484 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 438 time to evaluate : 3.582 ------------------------------------------------------------------------------- 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 E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F 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 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 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 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 164 LYS 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: 7.9990 chunk 388 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 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 = 0.3398 r_free = 0.3398 target = 0.107865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.076232 restraints weight = 38627.580| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.17 r_work: 0.2734 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 33600 Z= 0.297 Angle : 0.590 7.250 45486 Z= 0.322 Chirality : 0.049 0.152 4872 Planarity : 0.004 0.039 5866 Dihedral : 5.688 58.940 4488 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.34 % Allowed : 17.42 % Favored : 80.25 % 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: -3.21 (0.26), residues: 84 sheet: 1.41 (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 0.002 HIS L 259 PHE 0.010 0.002 PHE A 39 TYR 0.026 0.002 TYR K 65 ARG 0.010 0.000 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 1560) hydrogen bonds : angle 5.51386 ( 4215) covalent geometry : bond 0.00688 (33600) covalent geometry : angle 0.58967 (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 521 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 436 time to evaluate : 3.714 Fit side-chains REVERT: A 198 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8883 (ttmm) REVERT: B 31 GLU cc_start: 0.8498 (pm20) cc_final: 0.8173 (pm20) REVERT: B 37 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.7960 (tmtt) REVERT: B 71 GLU cc_start: 0.7187 (mp0) cc_final: 0.6896 (mp0) REVERT: B 78 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9215 (tp) REVERT: C 71 GLU cc_start: 0.7683 (mp0) cc_final: 0.7156 (mp0) REVERT: C 215 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8504 (mmtp) REVERT: D 37 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8820 (tttt) REVERT: D 58 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8752 (mtpt) REVERT: D 71 GLU cc_start: 0.7655 (mp0) cc_final: 0.7202 (mp0) REVERT: E 205 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8371 (mtpm) REVERT: F 71 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: F 215 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8515 (mmtp) REVERT: F 283 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8508 (tmtt) REVERT: G 71 GLU cc_start: 0.7637 (mp0) cc_final: 0.7239 (mp0) REVERT: H 30 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8544 (tmtt) REVERT: I 283 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8307 (ttmt) REVERT: J 101 TYR cc_start: 0.9406 (OUTLIER) cc_final: 0.8492 (p90) REVERT: J 277 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7782 (ttt90) REVERT: K 205 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8088 (mtpp) REVERT: L 283 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8393 (tmmm) REVERT: M 277 ARG cc_start: 0.8307 (ttt90) cc_final: 0.7903 (ttt90) REVERT: N 164 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8160 (tttp) REVERT: N 285 ASP cc_start: 0.8067 (t70) cc_final: 0.7795 (t70) outliers start: 85 outliers final: 43 residues processed: 498 average time/residue: 1.8553 time to fit residues: 1068.2114 Evaluate side-chains 487 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 427 time to evaluate : 3.551 ------------------------------------------------------------------------------- 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 A residue 230 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 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 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 58 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 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 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 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 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 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 283 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 164 LYS 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: 1.9990 chunk 311 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 160 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 357 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 376 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 G 264 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 = 0.3429 r_free = 0.3429 target = 0.110685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.078961 restraints weight = 38313.956| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.20 r_work: 0.2774 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33600 Z= 0.117 Angle : 0.480 7.539 45486 Z= 0.261 Chirality : 0.044 0.140 4872 Planarity : 0.003 0.039 5866 Dihedral : 5.142 58.020 4486 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.06 % Allowed : 17.75 % Favored : 80.19 % 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: 1.07 (0.13), residues: 4074 helix: -2.78 (0.34), residues: 84 sheet: 1.38 (0.11), residues: 2268 loop : 0.03 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.009 0.001 HIS K 259 PHE 0.006 0.001 PHE L 171 TYR 0.017 0.001 TYR J 65 ARG 0.011 0.000 ARG J 147 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 1560) hydrogen bonds : angle 5.04112 ( 4215) covalent geometry : bond 0.00258 (33600) covalent geometry : angle 0.48005 (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 520 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 445 time to evaluate : 3.688 Fit side-chains REVERT: A 125 THR cc_start: 0.8502 (p) cc_final: 0.8260 (t) REVERT: A 198 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8836 (ttmm) REVERT: B 31 GLU cc_start: 0.8542 (pm20) cc_final: 0.8205 (pm20) REVERT: B 37 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8364 (tttt) REVERT: B 71 GLU cc_start: 0.7055 (mp0) cc_final: 0.6780 (mp0) REVERT: B 78 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9148 (tp) REVERT: C 71 GLU cc_start: 0.7610 (mp0) cc_final: 0.7073 (mp0) REVERT: C 215 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8427 (mmtp) REVERT: D 71 GLU cc_start: 0.7564 (mp0) cc_final: 0.7096 (mp0) REVERT: F 71 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: G 71 GLU cc_start: 0.7559 (mp0) cc_final: 0.7141 (mp0) REVERT: H 30 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8484 (tmtt) REVERT: H 195 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8328 (tt) REVERT: I 283 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8269 (ttmt) REVERT: J 101 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.8298 (p90) REVERT: J 277 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7684 (ttt90) REVERT: K 205 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8118 (mtpp) REVERT: L 283 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8364 (tmmm) REVERT: M 277 ARG cc_start: 0.8233 (ttt90) cc_final: 0.7795 (ttt90) REVERT: N 164 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8064 (tttp) REVERT: N 285 ASP cc_start: 0.8048 (t70) cc_final: 0.7793 (t70) outliers start: 75 outliers final: 33 residues processed: 505 average time/residue: 1.8026 time to fit residues: 1051.2164 Evaluate side-chains 474 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 428 time to evaluate : 3.777 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 27 THR 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 F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU 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 283 LYS 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 78 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 136 ILE 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 78 LEU Chi-restraints excluded: chain M residue 101 TYR 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 164 LYS 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: 0.8980 chunk 154 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 367 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 I 87 GLN I 242 GLN K 87 GLN L 87 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.077560 restraints weight = 38192.097| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.19 r_work: 0.2750 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 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 : 0.004 0.033 33600 Z= 0.171 Angle : 0.516 7.945 45486 Z= 0.280 Chirality : 0.046 0.147 4872 Planarity : 0.003 0.037 5866 Dihedral : 5.230 58.463 4483 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.95 % Allowed : 18.16 % Favored : 79.89 % 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: 1.07 (0.13), residues: 4074 helix: -2.85 (0.32), residues: 84 sheet: 1.42 (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 0.011 0.000 ARG J 147 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 1560) hydrogen bonds : angle 5.19454 ( 4215) covalent geometry : bond 0.00391 (33600) covalent geometry : angle 0.51589 (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: 71 poor density : 437 time to evaluate : 3.630 Fit side-chains REVERT: A 125 THR cc_start: 0.8492 (p) cc_final: 0.8247 (t) REVERT: A 198 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8854 (ttmm) REVERT: B 31 GLU cc_start: 0.8531 (pm20) cc_final: 0.8168 (pm20) REVERT: B 37 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.7974 (tmtt) REVERT: B 71 GLU cc_start: 0.7099 (mp0) cc_final: 0.6815 (mp0) REVERT: B 78 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9187 (tp) REVERT: C 71 GLU cc_start: 0.7608 (mp0) cc_final: 0.7057 (mp0) REVERT: C 215 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8455 (mmtp) REVERT: D 71 GLU cc_start: 0.7562 (mp0) cc_final: 0.7101 (mp0) REVERT: F 71 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: F 215 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8434 (mmtp) REVERT: G 71 GLU cc_start: 0.7544 (mp0) cc_final: 0.7127 (mp0) REVERT: H 30 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8489 (tmtt) REVERT: I 283 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8262 (ttmt) REVERT: J 101 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.8378 (p90) REVERT: J 277 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7713 (ttt90) REVERT: K 205 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8132 (mtpp) REVERT: L 235 ASP cc_start: 0.7941 (t70) cc_final: 0.7652 (t0) REVERT: L 283 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8391 (tmmm) REVERT: M 277 ARG cc_start: 0.8260 (ttt90) cc_final: 0.7822 (ttt90) REVERT: N 164 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8091 (tttp) outliers start: 71 outliers final: 38 residues processed: 490 average time/residue: 1.8775 time to fit residues: 1061.9395 Evaluate side-chains 480 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 429 time to evaluate : 4.029 ------------------------------------------------------------------------------- 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 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 230 THR 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 283 LYS 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 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 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 101 TYR Chi-restraints excluded: chain N residue 164 LYS 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: 0.8980 chunk 223 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 348 optimal weight: 5.9990 chunk 334 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 24 optimal weight: 7.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- 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 I 87 GLN I 242 GLN K 87 GLN L 87 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.077894 restraints weight = 38225.566| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.20 r_work: 0.2755 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33600 Z= 0.158 Angle : 0.508 8.040 45486 Z= 0.276 Chirality : 0.045 0.145 4872 Planarity : 0.003 0.040 5866 Dihedral : 5.188 58.171 4483 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.95 % Allowed : 18.19 % Favored : 79.86 % 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: 1.07 (0.13), residues: 4074 helix: -2.80 (0.33), residues: 84 sheet: 1.42 (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 0.010 0.001 HIS K 259 PHE 0.008 0.001 PHE L 171 TYR 0.020 0.002 TYR H 65 ARG 0.011 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 1560) hydrogen bonds : angle 5.15254 ( 4215) covalent geometry : bond 0.00359 (33600) covalent geometry : angle 0.50838 (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 503 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 432 time to evaluate : 4.616 Fit side-chains REVERT: A 125 THR cc_start: 0.8501 (p) cc_final: 0.8250 (t) REVERT: A 198 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8839 (ttmm) REVERT: B 31 GLU cc_start: 0.8538 (pm20) cc_final: 0.8181 (pm20) REVERT: B 37 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.7969 (tmtt) REVERT: B 71 GLU cc_start: 0.7103 (mp0) cc_final: 0.6808 (mp0) REVERT: B 78 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9178 (tp) REVERT: B 290 GLU cc_start: 0.8523 (tt0) cc_final: 0.8258 (tt0) REVERT: C 71 GLU cc_start: 0.7612 (mp0) cc_final: 0.7064 (mp0) REVERT: C 215 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8450 (mmtp) REVERT: D 71 GLU cc_start: 0.7558 (mp0) cc_final: 0.7092 (mp0) REVERT: F 71 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: F 215 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8439 (mmtp) REVERT: F 283 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8439 (tmtt) REVERT: G 71 GLU cc_start: 0.7531 (mp0) cc_final: 0.7114 (mp0) REVERT: H 30 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8487 (tmtt) REVERT: I 283 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8271 (ttmt) REVERT: J 101 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.8375 (p90) REVERT: J 277 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7707 (ttt90) REVERT: K 205 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8118 (mtpp) REVERT: L 235 ASP cc_start: 0.7984 (t70) cc_final: 0.7714 (t0) REVERT: L 283 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8387 (tmmm) REVERT: M 277 ARG cc_start: 0.8253 (ttt90) cc_final: 0.7813 (ttt90) REVERT: N 164 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8075 (tttp) outliers start: 71 outliers final: 43 residues processed: 486 average time/residue: 1.8588 time to fit residues: 1043.7479 Evaluate side-chains 486 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 429 time to evaluate : 3.573 ------------------------------------------------------------------------------- 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 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 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 113 MET 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 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 283 LYS 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 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 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 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 164 LYS 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: 7.9990 chunk 291 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 331 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 H 87 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN L 242 GLN M 123 ASN 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 = 0.3387 r_free = 0.3387 target = 0.107100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.075446 restraints weight = 38833.849| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.17 r_work: 0.2724 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1093 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= 0.376 Angle : 0.643 7.603 45486 Z= 0.351 Chirality : 0.051 0.177 4872 Planarity : 0.004 0.049 5866 Dihedral : 5.700 57.115 4483 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.23 % Allowed : 17.94 % 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: 0.95 (0.13), residues: 4074 helix: -3.34 (0.24), residues: 84 sheet: 1.37 (0.10), residues: 2212 loop : -0.09 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 260 HIS 0.013 0.002 HIS K 259 PHE 0.012 0.002 PHE F 39 TYR 0.028 0.003 TYR M 65 ARG 0.012 0.001 ARG J 147 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 1560) hydrogen bonds : angle 5.63973 ( 4215) covalent geometry : bond 0.00876 (33600) covalent geometry : angle 0.64316 (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: 81 poor density : 436 time to evaluate : 3.496 Fit side-chains REVERT: A 31 GLU cc_start: 0.8507 (pm20) cc_final: 0.8194 (pm20) REVERT: A 198 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8957 (ttmm) REVERT: B 31 GLU cc_start: 0.8468 (pm20) cc_final: 0.8086 (pm20) REVERT: B 37 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.7960 (tmtt) REVERT: B 71 GLU cc_start: 0.7246 (mp0) cc_final: 0.6933 (mp0) REVERT: B 78 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9225 (tp) REVERT: C 71 GLU cc_start: 0.7672 (mp0) cc_final: 0.7147 (mp0) REVERT: C 215 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8511 (mmtp) REVERT: D 71 GLU cc_start: 0.7685 (mp0) cc_final: 0.7236 (mp0) REVERT: E 147 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8907 (ttp-110) REVERT: E 205 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8352 (mtpm) REVERT: F 71 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: F 280 GLU cc_start: 0.8645 (tt0) cc_final: 0.8432 (tt0) REVERT: F 283 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8529 (tmtt) REVERT: G 37 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8234 (tmtt) REVERT: G 71 GLU cc_start: 0.7633 (mp0) cc_final: 0.7259 (mp0) REVERT: H 30 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8649 (tmtt) REVERT: I 283 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8312 (ttmt) REVERT: J 101 TYR cc_start: 0.9419 (OUTLIER) cc_final: 0.8594 (p90) REVERT: J 277 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7832 (ttt90) REVERT: K 205 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8144 (mtpp) REVERT: L 235 ASP cc_start: 0.8058 (t70) cc_final: 0.7740 (t0) REVERT: M 277 ARG cc_start: 0.8338 (ttt90) cc_final: 0.7935 (ttt90) outliers start: 81 outliers final: 49 residues processed: 495 average time/residue: 1.8849 time to fit residues: 1080.9719 Evaluate side-chains 498 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 436 time to evaluate : 3.724 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain B residue 263 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 174 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 78 LEU 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 113 MET 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 195 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS 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 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 113 MET 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 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 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: 8.9990 chunk 121 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 308 optimal weight: 0.1980 chunk 149 optimal weight: 3.9990 chunk 184 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 H 87 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN L 123 ASN M 242 GLN N 242 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.079331 restraints weight = 38192.259| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.19 r_work: 0.2783 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33600 Z= 0.108 Angle : 0.488 8.312 45486 Z= 0.264 Chirality : 0.044 0.140 4872 Planarity : 0.003 0.038 5866 Dihedral : 5.072 59.127 4479 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.48 % Allowed : 19.04 % Favored : 79.48 % 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: 1.05 (0.13), residues: 4074 helix: -2.86 (0.32), residues: 84 sheet: 1.35 (0.11), residues: 2268 loop : 0.03 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.009 0.001 HIS K 259 PHE 0.006 0.001 PHE L 171 TYR 0.016 0.001 TYR H 65 ARG 0.012 0.001 ARG J 147 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 1560) hydrogen bonds : angle 5.03567 ( 4215) covalent geometry : bond 0.00236 (33600) covalent geometry : angle 0.48846 (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 497 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 443 time to evaluate : 5.402 Fit side-chains REVERT: A 31 GLU cc_start: 0.8564 (pm20) cc_final: 0.8184 (pm20) REVERT: A 125 THR cc_start: 0.8401 (p) cc_final: 0.8166 (t) REVERT: A 198 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8847 (ttmm) REVERT: A 290 GLU cc_start: 0.8297 (pp20) cc_final: 0.7996 (pp20) REVERT: B 31 GLU cc_start: 0.8547 (pm20) cc_final: 0.8205 (pm20) REVERT: B 37 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8332 (tttt) REVERT: B 71 GLU cc_start: 0.7049 (mp0) cc_final: 0.6788 (mp0) REVERT: B 78 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9144 (tp) REVERT: B 290 GLU cc_start: 0.8487 (tt0) cc_final: 0.8224 (tt0) REVERT: C 71 GLU cc_start: 0.7621 (mp0) cc_final: 0.7104 (mp0) REVERT: C 215 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8417 (mmtp) REVERT: D 71 GLU cc_start: 0.7573 (mp0) cc_final: 0.7106 (mp0) REVERT: E 113 MET cc_start: 0.8955 (mtt) cc_final: 0.8743 (mmt) REVERT: G 71 GLU cc_start: 0.7531 (mp0) cc_final: 0.7119 (mp0) REVERT: H 30 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8462 (tmtt) REVERT: H 147 ARG cc_start: 0.8932 (ttp80) cc_final: 0.8704 (ttp80) REVERT: H 195 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8325 (tt) REVERT: I 283 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8262 (ttmt) REVERT: J 101 TYR cc_start: 0.9366 (OUTLIER) cc_final: 0.8306 (p90) REVERT: J 277 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7686 (ttt90) REVERT: K 205 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8112 (mtpp) REVERT: L 235 ASP cc_start: 0.7948 (t70) cc_final: 0.7670 (t0) REVERT: L 283 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8349 (tmmm) REVERT: M 242 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7730 (mm110) REVERT: M 277 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7781 (ttt90) outliers start: 54 outliers final: 29 residues processed: 487 average time/residue: 1.9628 time to fit residues: 1102.2472 Evaluate side-chains 471 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 430 time to evaluate : 3.997 ------------------------------------------------------------------------------- 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 C residue 159 SER Chi-restraints excluded: chain C residue 215 LYS 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 F residue 78 LEU 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 283 LYS Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 78 LEU 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 113 MET 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 242 GLN 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 283 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 72 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 327 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 386 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 358 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 89 GLN H 87 GLN H 241 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN L 242 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.077864 restraints weight = 38149.304| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.20 r_work: 0.2756 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33600 Z= 0.160 Angle : 0.521 8.397 45486 Z= 0.281 Chirality : 0.045 0.146 4872 Planarity : 0.003 0.043 5866 Dihedral : 5.160 59.434 4479 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.29 % Allowed : 19.26 % Favored : 79.45 % 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: -2.86 (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 0.010 0.001 TRP C 167 HIS 0.012 0.001 HIS K 259 PHE 0.007 0.001 PHE L 171 TYR 0.020 0.002 TYR H 65 ARG 0.013 0.001 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 1560) hydrogen bonds : angle 5.14875 ( 4215) covalent geometry : bond 0.00363 (33600) covalent geometry : angle 0.52127 (45486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33483.91 seconds wall clock time: 581 minutes 32.68 seconds (34892.68 seconds total)