Starting phenix.real_space_refine on Tue Aug 26 02:32:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx2_36688/08_2025/8jx2_36688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx2_36688/08_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_36688/08_2025/8jx2_36688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx2_36688/08_2025/8jx2_36688.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx2_36688/08_2025/8jx2_36688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx2_36688/08_2025/8jx2_36688.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.99, per 1000 atoms: 0.21 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.89 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: 5.45 Time building geometry restraints manager: 3.30 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: 0.01 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.240 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (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 ARG 0.005 0.000 ARG D 200 TYR 0.016 0.001 TYR J 65 PHE 0.008 0.001 PHE L 171 TRP 0.010 0.001 TRP C 167 HIS 0.010 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00261 (33600) covalent geometry : angle 0.49295 (45486) hydrogen bonds : bond 0.11709 ( 1560) hydrogen bonds : angle 6.49259 ( 4215) *********************** 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 : 1.120 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: 0.7083 time to fit residues: 473.8093 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 : 1.233 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.075308 restraints weight = 38804.361| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.17 r_work: 0.2726 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 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 : 0.009 0.063 33600 Z= 0.370 Angle : 0.636 6.410 45486 Z= 0.351 Chirality : 0.051 0.171 4872 Planarity : 0.004 0.045 5866 Dihedral : 7.798 59.852 4643 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.90 % Allowed : 16.18 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.13), residues: 4074 helix: -3.70 (0.18), residues: 84 sheet: 1.39 (0.10), residues: 2212 loop : -0.07 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 147 TYR 0.027 0.003 TYR M 65 PHE 0.012 0.002 PHE I 153 TRP 0.012 0.002 TRP C 167 HIS 0.012 0.002 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00861 (33600) covalent geometry : angle 0.63604 (45486) hydrogen bonds : bond 0.04381 ( 1560) hydrogen bonds : angle 5.85563 ( 4215) *********************** 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 588 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 446 time to evaluate : 1.068 Fit side-chains REVERT: A 71 GLU cc_start: 0.7144 (mp0) cc_final: 0.6821 (mp0) REVERT: A 198 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8890 (ttmm) REVERT: B 31 GLU cc_start: 0.8555 (pm20) cc_final: 0.8319 (pm20) REVERT: B 37 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.7957 (tmtt) REVERT: C 71 GLU cc_start: 0.7699 (mp0) cc_final: 0.7175 (mp0) REVERT: C 215 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8507 (mmtp) REVERT: D 58 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8774 (mtpt) REVERT: D 71 GLU cc_start: 0.7707 (mp0) cc_final: 0.7250 (mp0) REVERT: D 215 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.9010 (mttm) REVERT: E 125 THR cc_start: 0.8421 (m) cc_final: 0.8163 (t) REVERT: E 198 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8950 (ttmm) REVERT: F 71 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: G 71 GLU cc_start: 0.7642 (mp0) cc_final: 0.7265 (mp0) REVERT: H 31 GLU cc_start: 0.8335 (pm20) cc_final: 0.8023 (pm20) REVERT: H 205 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8126 (mtpp) REVERT: H 280 GLU cc_start: 0.8340 (tp30) cc_final: 0.8115 (tp30) REVERT: I 31 GLU cc_start: 0.8182 (pm20) cc_final: 0.7980 (pm20) REVERT: I 78 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8867 (tp) REVERT: I 205 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8068 (mtpp) REVERT: L 290 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7979 (tm-30) REVERT: M 164 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8493 (ttmt) REVERT: N 78 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8955 (tp) REVERT: N 257 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8646 (mt0) outliers start: 142 outliers final: 71 residues processed: 555 average time/residue: 0.7516 time to fit residues: 482.3338 Evaluate side-chains 501 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 417 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 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 159 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 230 THR 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 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 174 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 113 MET 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 113 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 250 GLU 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 205 LYS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 268 THR 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 159 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 75 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 136 ILE Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 164 LYS 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 195 LEU Chi-restraints excluded: chain N residue 205 LYS Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 257 GLN 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 60 optimal weight: 3.9990 chunk 323 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 354 optimal weight: 6.9990 chunk 393 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 281 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN H 87 GLN I 87 GLN I 242 GLN K 87 GLN ** K 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN L 123 ASN M 242 GLN N 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.078313 restraints weight = 38552.724| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.18 r_work: 0.2770 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33600 Z= 0.146 Angle : 0.503 7.105 45486 Z= 0.277 Chirality : 0.045 0.145 4872 Planarity : 0.003 0.042 5866 Dihedral : 6.295 59.692 4544 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.05 % Allowed : 16.98 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.13), residues: 4074 helix: -3.31 (0.24), residues: 84 sheet: 1.50 (0.11), residues: 2184 loop : -0.08 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 147 TYR 0.018 0.001 TYR J 65 PHE 0.008 0.001 PHE L 171 TRP 0.010 0.001 TRP C 167 HIS 0.008 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00327 (33600) covalent geometry : angle 0.50304 (45486) hydrogen bonds : bond 0.03394 ( 1560) hydrogen bonds : angle 5.29947 ( 4215) *********************** 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 570 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 459 time to evaluate : 1.126 Fit side-chains REVERT: A 71 GLU cc_start: 0.7191 (mp0) cc_final: 0.6915 (mp0) REVERT: A 198 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8870 (ttmm) REVERT: B 31 GLU cc_start: 0.8518 (pm20) cc_final: 0.8259 (pm20) REVERT: B 37 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.7947 (tmtt) REVERT: B 78 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9194 (tp) REVERT: B 250 GLU cc_start: 0.9070 (tt0) cc_final: 0.8797 (tt0) REVERT: C 71 GLU cc_start: 0.7630 (mp0) cc_final: 0.7109 (mp0) REVERT: C 215 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8455 (mmtp) REVERT: D 58 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8715 (mtpt) REVERT: D 71 GLU cc_start: 0.7616 (mp0) cc_final: 0.7161 (mp0) REVERT: D 215 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9042 (mttm) REVERT: E 125 THR cc_start: 0.8410 (m) cc_final: 0.8182 (t) REVERT: E 198 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8919 (ttmm) REVERT: E 215 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8685 (mmtp) REVERT: G 71 GLU cc_start: 0.7623 (mp0) cc_final: 0.7201 (mp0) REVERT: H 205 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8011 (mtpp) REVERT: I 205 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7974 (mtpp) REVERT: I 283 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8273 (ttmt) REVERT: J 101 TYR cc_start: 0.9389 (OUTLIER) cc_final: 0.8379 (p90) REVERT: K 37 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.7532 (tmmm) REVERT: K 205 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8093 (mtpp) REVERT: L 154 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8609 (ptmt) REVERT: L 283 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8381 (tmmm) REVERT: L 290 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7900 (tm-30) REVERT: M 150 GLN cc_start: 0.8909 (pt0) cc_final: 0.8699 (pt0) REVERT: M 242 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7669 (mm110) REVERT: N 205 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8143 (mtpp) REVERT: N 285 ASP cc_start: 0.8026 (t70) cc_final: 0.7781 (t70) outliers start: 111 outliers final: 47 residues processed: 547 average time/residue: 0.7557 time to fit residues: 478.6190 Evaluate side-chains 499 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 434 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 B residue 230 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 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 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 78 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 106 SER 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 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 I residue 205 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 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 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 154 LYS Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 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 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 205 LYS Chi-restraints excluded: chain N residue 262 SER 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 43 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 391 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 366 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 M 123 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.076147 restraints weight = 38464.237| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.17 r_work: 0.2736 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 33600 Z= 0.282 Angle : 0.585 6.972 45486 Z= 0.321 Chirality : 0.049 0.152 4872 Planarity : 0.004 0.043 5866 Dihedral : 6.157 57.935 4517 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.99 % Allowed : 17.28 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.13), residues: 4074 helix: -3.32 (0.24), residues: 84 sheet: 1.38 (0.10), residues: 2212 loop : -0.10 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 147 TYR 0.025 0.002 TYR K 65 PHE 0.009 0.002 PHE J 153 TRP 0.011 0.001 TRP C 167 HIS 0.010 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00652 (33600) covalent geometry : angle 0.58538 (45486) hydrogen bonds : bond 0.03907 ( 1560) hydrogen bonds : angle 5.56142 ( 4215) *********************** 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 547 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 438 time to evaluate : 1.030 Fit side-chains REVERT: A 71 GLU cc_start: 0.7195 (mp0) cc_final: 0.6796 (mp0) REVERT: A 198 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8878 (ttmm) REVERT: B 31 GLU cc_start: 0.8503 (pm20) cc_final: 0.8217 (pm20) REVERT: B 37 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.7963 (tmtt) REVERT: B 78 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9215 (tp) REVERT: B 250 GLU cc_start: 0.9063 (tt0) cc_final: 0.8799 (tt0) REVERT: C 58 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8843 (mttt) REVERT: C 71 GLU cc_start: 0.7698 (mp0) cc_final: 0.7164 (mp0) REVERT: C 215 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8496 (mmtp) REVERT: D 37 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8818 (tttt) REVERT: D 58 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8755 (mtpt) REVERT: D 71 GLU cc_start: 0.7678 (mp0) cc_final: 0.7222 (mp0) REVERT: E 37 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8616 (tmtp) REVERT: E 125 THR cc_start: 0.8432 (m) cc_final: 0.8179 (t) REVERT: E 198 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8953 (ttmm) REVERT: E 205 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8368 (mtpm) REVERT: E 215 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8663 (mmtp) REVERT: F 71 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: G 71 GLU cc_start: 0.7641 (mp0) cc_final: 0.7240 (mp0) REVERT: I 30 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8518 (tmmt) REVERT: I 283 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8314 (ttmt) REVERT: J 101 TYR cc_start: 0.9404 (OUTLIER) cc_final: 0.8494 (p90) REVERT: J 277 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7780 (ttt90) REVERT: K 37 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.7684 (tmmm) REVERT: K 205 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8110 (mtpp) REVERT: L 154 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8483 (ptmt) REVERT: N 205 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8219 (mtpp) outliers start: 109 outliers final: 60 residues processed: 521 average time/residue: 0.7587 time to fit residues: 457.5649 Evaluate side-chains 502 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 422 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 159 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 58 LYS 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 27 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 230 THR Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 215 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 142 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 204 MET 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 195 LEU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 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 230 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 101 TYR Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 159 SER Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 50 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 159 SER Chi-restraints excluded: chain N residue 205 LYS Chi-restraints excluded: chain N residue 230 THR 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 151 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 280 optimal weight: 0.1980 chunk 12 optimal weight: 9.9990 chunk 396 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 335 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 242 GLN K 87 GLN L 87 GLN L 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.079895 restraints weight = 38389.177| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.19 r_work: 0.2793 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33600 Z= 0.099 Angle : 0.463 7.537 45486 Z= 0.253 Chirality : 0.044 0.141 4872 Planarity : 0.003 0.039 5866 Dihedral : 5.213 57.666 4499 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.69 % Allowed : 17.31 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.13), residues: 4074 helix: -2.81 (0.33), residues: 84 sheet: 1.38 (0.11), residues: 2268 loop : 0.03 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 147 TYR 0.014 0.001 TYR H 65 PHE 0.007 0.001 PHE L 171 TRP 0.009 0.001 TRP C 167 HIS 0.008 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00216 (33600) covalent geometry : angle 0.46317 (45486) hydrogen bonds : bond 0.02949 ( 1560) hydrogen bonds : angle 4.97239 ( 4215) *********************** 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 534 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 436 time to evaluate : 0.969 Fit side-chains REVERT: A 71 GLU cc_start: 0.7292 (mp0) cc_final: 0.6899 (mp0) REVERT: A 125 THR cc_start: 0.8482 (p) cc_final: 0.8239 (t) REVERT: A 198 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8832 (ttmm) REVERT: B 31 GLU cc_start: 0.8610 (pm20) cc_final: 0.8317 (pm20) REVERT: B 37 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8354 (tttt) REVERT: B 78 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9150 (tt) REVERT: C 71 GLU cc_start: 0.7636 (mp0) cc_final: 0.7093 (mp0) REVERT: C 215 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8424 (mmtp) REVERT: D 71 GLU cc_start: 0.7561 (mp0) cc_final: 0.7093 (mp0) REVERT: E 125 THR cc_start: 0.8361 (m) cc_final: 0.8156 (t) REVERT: E 205 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8272 (mtpm) REVERT: E 215 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8686 (mmtp) REVERT: F 71 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: F 215 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8398 (mmtp) REVERT: G 71 GLU cc_start: 0.7550 (mp0) cc_final: 0.7127 (mp0) REVERT: H 195 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8481 (tt) REVERT: I 30 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8438 (tmmt) REVERT: I 283 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8235 (ttmt) REVERT: J 101 TYR cc_start: 0.9343 (OUTLIER) cc_final: 0.8378 (p90) REVERT: J 277 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7656 (ttt90) REVERT: K 205 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8090 (mtpp) REVERT: L 147 ARG cc_start: 0.8845 (ttp-170) cc_final: 0.8497 (ttp-110) REVERT: L 195 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8345 (tt) REVERT: L 283 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8351 (tmmm) REVERT: N 205 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8108 (mtpp) outliers start: 98 outliers final: 32 residues processed: 517 average time/residue: 0.7100 time to fit residues: 427.3022 Evaluate side-chains 475 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 426 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 E residue 205 LYS Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 78 LEU 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 283 LYS Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 136 ILE 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 262 SER Chi-restraints excluded: chain K residue 283 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 158 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 159 SER 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 159 SER Chi-restraints excluded: chain N residue 205 LYS Chi-restraints excluded: chain N residue 262 SER 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 335 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 233 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 277 optimal weight: 0.5980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.109155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.077547 restraints weight = 38426.648| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.18 r_work: 0.2758 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33600 Z= 0.199 Angle : 0.530 7.593 45486 Z= 0.288 Chirality : 0.046 0.148 4872 Planarity : 0.003 0.038 5866 Dihedral : 5.293 59.428 4483 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.17 % Allowed : 18.13 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.13), residues: 4074 helix: -2.91 (0.32), residues: 84 sheet: 1.43 (0.11), residues: 2212 loop : 0.01 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 147 TYR 0.021 0.002 TYR K 65 PHE 0.008 0.001 PHE L 171 TRP 0.009 0.001 TRP C 167 HIS 0.011 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00456 (33600) covalent geometry : angle 0.53042 (45486) hydrogen bonds : bond 0.03445 ( 1560) hydrogen bonds : angle 5.26812 ( 4215) *********************** 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 514 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 435 time to evaluate : 1.214 Fit side-chains REVERT: A 71 GLU cc_start: 0.7278 (mp0) cc_final: 0.6887 (mp0) REVERT: A 198 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8851 (ttmm) REVERT: B 31 GLU cc_start: 0.8550 (pm20) cc_final: 0.8251 (pm20) REVERT: B 37 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.7959 (tmtt) REVERT: B 78 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9216 (tp) REVERT: C 58 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8809 (mttt) REVERT: C 71 GLU cc_start: 0.7653 (mp0) cc_final: 0.7118 (mp0) REVERT: C 215 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8484 (mmtp) REVERT: D 58 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8709 (mtpt) REVERT: D 71 GLU cc_start: 0.7602 (mp0) cc_final: 0.7152 (mp0) REVERT: E 37 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8637 (tmtp) REVERT: E 204 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8419 (pmm) REVERT: E 215 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8730 (mmtp) REVERT: F 71 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: F 215 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8471 (mmtp) REVERT: G 71 GLU cc_start: 0.7587 (mp0) cc_final: 0.7176 (mp0) REVERT: I 30 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8484 (tmmt) REVERT: I 283 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: J 101 TYR cc_start: 0.9398 (OUTLIER) cc_final: 0.8389 (p90) REVERT: J 277 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7734 (ttt90) REVERT: K 205 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8145 (mtpp) REVERT: L 283 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8430 (tmmm) REVERT: N 205 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8170 (mtpp) outliers start: 79 outliers final: 39 residues processed: 494 average time/residue: 0.7544 time to fit residues: 430.2141 Evaluate side-chains 491 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 434 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 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 37 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain H residue 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 9 THR Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 145 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 159 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 159 SER Chi-restraints excluded: chain M residue 230 THR 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 159 SER Chi-restraints excluded: chain N residue 205 LYS 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 249 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 326 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 403 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 K 242 GLN L 87 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.075783 restraints weight = 38737.272| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.18 r_work: 0.2733 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 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 : 0.008 0.056 33600 Z= 0.324 Angle : 0.608 7.063 45486 Z= 0.333 Chirality : 0.050 0.153 4872 Planarity : 0.004 0.042 5866 Dihedral : 5.590 57.527 4481 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.31 % Allowed : 18.13 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.13), residues: 4074 helix: -3.24 (0.26), residues: 84 sheet: 1.39 (0.10), residues: 2212 loop : -0.08 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 147 TYR 0.026 0.002 TYR M 65 PHE 0.010 0.002 PHE H 153 TRP 0.011 0.001 TRP L 260 HIS 0.011 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00754 (33600) covalent geometry : angle 0.60815 (45486) hydrogen bonds : bond 0.03977 ( 1560) hydrogen bonds : angle 5.56279 ( 4215) *********************** 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 517 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 433 time to evaluate : 1.371 Fit side-chains REVERT: A 71 GLU cc_start: 0.7216 (mp0) cc_final: 0.6818 (mp0) REVERT: A 198 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8950 (ttmm) REVERT: B 31 GLU cc_start: 0.8506 (pm20) cc_final: 0.8192 (pm20) REVERT: B 37 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.7971 (tmtt) REVERT: B 78 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9226 (tp) REVERT: C 58 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8856 (mttt) REVERT: C 71 GLU cc_start: 0.7693 (mp0) cc_final: 0.7162 (mp0) REVERT: C 215 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8497 (mmtp) REVERT: D 58 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8757 (mtpt) REVERT: D 71 GLU cc_start: 0.7673 (mp0) cc_final: 0.7225 (mp0) REVERT: E 37 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8633 (tmtp) REVERT: E 205 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8362 (mtpm) REVERT: E 215 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8685 (mmtp) REVERT: F 31 GLU cc_start: 0.8541 (pm20) cc_final: 0.8210 (pm20) REVERT: F 71 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: F 280 GLU cc_start: 0.8626 (tt0) cc_final: 0.8408 (tt0) REVERT: G 71 GLU cc_start: 0.7633 (mp0) cc_final: 0.7241 (mp0) REVERT: I 30 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8526 (tmmt) REVERT: I 283 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8302 (ttmt) REVERT: J 101 TYR cc_start: 0.9410 (OUTLIER) cc_final: 0.8495 (p90) REVERT: J 277 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7808 (ttt90) REVERT: K 205 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8155 (mtpp) REVERT: N 205 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8242 (mtpp) outliers start: 84 outliers final: 48 residues processed: 497 average time/residue: 0.7864 time to fit residues: 450.2024 Evaluate side-chains 479 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 415 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 215 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 37 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 159 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 195 LEU Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 30 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 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 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 158 GLU Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 283 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 159 SER Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 159 SER Chi-restraints excluded: chain N residue 205 LYS Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 283 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 218 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 378 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 327 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 H 87 GLN I 87 GLN I 242 GLN K 87 GLN L 87 GLN M 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.078021 restraints weight = 38255.761| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.20 r_work: 0.2758 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33600 Z= 0.140 Angle : 0.503 7.573 45486 Z= 0.273 Chirality : 0.045 0.142 4872 Planarity : 0.003 0.037 5866 Dihedral : 5.192 59.849 4481 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.98 % Allowed : 18.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.13), residues: 4074 helix: -2.90 (0.32), residues: 84 sheet: 1.39 (0.11), residues: 2212 loop : -0.00 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 147 TYR 0.018 0.001 TYR H 65 PHE 0.007 0.001 PHE L 171 TRP 0.010 0.001 TRP C 167 HIS 0.009 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00313 (33600) covalent geometry : angle 0.50296 (45486) hydrogen bonds : bond 0.03238 ( 1560) hydrogen bonds : angle 5.16055 ( 4215) *********************** 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 506 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 434 time to evaluate : 1.099 Fit side-chains REVERT: A 71 GLU cc_start: 0.7273 (mp0) cc_final: 0.6857 (mp0) REVERT: A 125 THR cc_start: 0.8474 (p) cc_final: 0.8233 (t) REVERT: A 198 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8848 (ttmm) REVERT: B 31 GLU cc_start: 0.8581 (pm20) cc_final: 0.8273 (pm20) REVERT: B 37 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8335 (tttt) REVERT: B 78 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9175 (tp) REVERT: C 71 GLU cc_start: 0.7628 (mp0) cc_final: 0.7085 (mp0) REVERT: C 147 ARG cc_start: 0.8950 (ttp-110) cc_final: 0.8743 (ttp-110) REVERT: C 215 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8423 (mmtp) REVERT: D 71 GLU cc_start: 0.7584 (mp0) cc_final: 0.7118 (mp0) REVERT: E 37 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8685 (tmtp) REVERT: E 205 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8339 (mtpm) REVERT: E 215 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8663 (mmtp) REVERT: F 71 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: G 71 GLU cc_start: 0.7544 (mp0) cc_final: 0.7127 (mp0) REVERT: I 30 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8431 (tmmt) REVERT: I 56 ARG cc_start: 0.8912 (mtt90) cc_final: 0.8669 (mtt90) REVERT: I 277 ARG cc_start: 0.8228 (ttt90) cc_final: 0.7938 (ttt90) REVERT: I 283 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8243 (ttmt) REVERT: J 101 TYR cc_start: 0.9365 (OUTLIER) cc_final: 0.8362 (p90) REVERT: J 277 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7701 (ttt90) REVERT: K 205 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8116 (mtpp) REVERT: L 283 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8366 (tmmm) REVERT: N 205 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8142 (mtpp) outliers start: 72 outliers final: 39 residues processed: 493 average time/residue: 0.7988 time to fit residues: 454.1621 Evaluate side-chains 484 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 430 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 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 37 LYS Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU 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 30 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 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 78 LEU Chi-restraints excluded: chain L residue 101 TYR 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 159 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 159 SER Chi-restraints excluded: chain N residue 205 LYS 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 316 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 K 242 GLN L 87 GLN M 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.075894 restraints weight = 38536.499| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.17 r_work: 0.2735 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 33600 Z= 0.321 Angle : 0.609 7.890 45486 Z= 0.332 Chirality : 0.049 0.151 4872 Planarity : 0.004 0.039 5866 Dihedral : 5.579 56.998 4481 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.03 % Allowed : 18.54 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.13), residues: 4074 helix: -3.24 (0.26), residues: 84 sheet: 1.36 (0.10), residues: 2212 loop : -0.09 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 147 TYR 0.026 0.002 TYR M 65 PHE 0.010 0.002 PHE N 153 TRP 0.012 0.001 TRP L 260 HIS 0.012 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00746 (33600) covalent geometry : angle 0.60901 (45486) hydrogen bonds : bond 0.03946 ( 1560) hydrogen bonds : angle 5.54834 ( 4215) *********************** 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 503 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 429 time to evaluate : 1.132 Fit side-chains REVERT: A 71 GLU cc_start: 0.7223 (mp0) cc_final: 0.6846 (mp0) REVERT: A 125 THR cc_start: 0.8531 (p) cc_final: 0.8246 (t) REVERT: A 198 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8944 (ttmm) REVERT: B 31 GLU cc_start: 0.8505 (pm20) cc_final: 0.8166 (pm20) REVERT: B 37 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.7976 (tmtt) REVERT: B 78 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9222 (tp) REVERT: C 58 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8867 (mttt) REVERT: C 71 GLU cc_start: 0.7707 (mp0) cc_final: 0.7177 (mp0) REVERT: C 215 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8497 (mmtp) REVERT: D 71 GLU cc_start: 0.7679 (mp0) cc_final: 0.7230 (mp0) REVERT: E 37 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8641 (tmtp) REVERT: E 147 ARG cc_start: 0.9109 (ttp80) cc_final: 0.8884 (ttp-110) REVERT: E 205 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8414 (mtpm) REVERT: E 215 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8677 (mmtp) REVERT: F 31 GLU cc_start: 0.8542 (pm20) cc_final: 0.8203 (pm20) REVERT: F 71 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: G 71 GLU cc_start: 0.7639 (mp0) cc_final: 0.7248 (mp0) REVERT: I 30 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8524 (tmmt) REVERT: I 283 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8298 (ttmt) REVERT: J 101 TYR cc_start: 0.9412 (OUTLIER) cc_final: 0.8496 (p90) REVERT: J 277 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7807 (ttt90) REVERT: K 205 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8155 (mtpp) outliers start: 74 outliers final: 44 residues processed: 486 average time/residue: 0.7932 time to fit residues: 444.4673 Evaluate side-chains 494 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 436 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 58 LYS 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 37 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 250 GLU 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 159 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 195 LEU Chi-restraints excluded: chain H residue 283 LYS Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 159 SER 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 78 LEU Chi-restraints excluded: chain L residue 101 TYR 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 159 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 159 SER 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 192 optimal weight: 0.2980 chunk 347 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 350 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 152 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- 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 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.078886 restraints weight = 38404.844| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.20 r_work: 0.2774 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33600 Z= 0.118 Angle : 0.491 8.409 45486 Z= 0.265 Chirality : 0.045 0.140 4872 Planarity : 0.003 0.037 5866 Dihedral : 5.067 59.991 4477 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.57 % Allowed : 19.07 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.13), residues: 4074 helix: -2.86 (0.33), residues: 84 sheet: 1.36 (0.11), residues: 2268 loop : 0.01 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 147 TYR 0.016 0.001 TYR C 65 PHE 0.006 0.001 PHE L 171 TRP 0.010 0.001 TRP C 167 HIS 0.010 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00262 (33600) covalent geometry : angle 0.49063 (45486) hydrogen bonds : bond 0.03079 ( 1560) hydrogen bonds : angle 5.05322 ( 4215) ********************** 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: 57 poor density : 440 time to evaluate : 1.311 Fit side-chains REVERT: A 71 GLU cc_start: 0.7296 (mp0) cc_final: 0.6891 (mp0) REVERT: A 125 THR cc_start: 0.8406 (p) cc_final: 0.8169 (t) REVERT: A 198 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8845 (ttmm) REVERT: B 31 GLU cc_start: 0.8592 (pm20) cc_final: 0.8320 (pm20) REVERT: B 37 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8334 (tttt) REVERT: B 78 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9158 (tp) REVERT: B 290 GLU cc_start: 0.8485 (tt0) cc_final: 0.8189 (tt0) REVERT: C 71 GLU cc_start: 0.7644 (mp0) cc_final: 0.7109 (mp0) REVERT: C 215 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8420 (mmtp) REVERT: D 71 GLU cc_start: 0.7570 (mp0) cc_final: 0.7106 (mp0) REVERT: E 37 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8661 (tmtp) REVERT: E 215 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8687 (mmtp) REVERT: F 71 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: G 71 GLU cc_start: 0.7525 (mp0) cc_final: 0.7109 (mp0) REVERT: H 147 ARG cc_start: 0.8939 (ttp80) cc_final: 0.8695 (ttp80) REVERT: H 195 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8193 (tt) REVERT: I 30 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8415 (tmmt) REVERT: I 56 ARG cc_start: 0.8890 (mtt90) cc_final: 0.8644 (mtt90) REVERT: I 277 ARG cc_start: 0.8213 (ttt90) cc_final: 0.7918 (ttt90) REVERT: I 283 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8240 (ttmt) REVERT: J 101 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8352 (p90) REVERT: J 277 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7689 (ttt90) REVERT: K 122 SER cc_start: 0.8562 (t) cc_final: 0.8101 (p) REVERT: K 205 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8119 (mtpp) REVERT: L 283 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8359 (tmmm) REVERT: M 242 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7684 (mm110) outliers start: 57 outliers final: 33 residues processed: 487 average time/residue: 0.7678 time to fit residues: 430.7458 Evaluate side-chains 472 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 424 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 E residue 37 LYS Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 LEU 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 30 LYS Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 145 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 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 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 159 SER Chi-restraints excluded: chain M residue 242 GLN Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 101 TYR Chi-restraints excluded: chain N residue 159 SER 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 73 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 295 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 393 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 I 87 GLN I 242 GLN K 87 GLN K 242 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 = 0.3397 r_free = 0.3397 target = 0.108628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.076701 restraints weight = 38311.321| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.19 r_work: 0.2735 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33600 Z= 0.215 Angle : 0.554 8.133 45486 Z= 0.301 Chirality : 0.047 0.148 4872 Planarity : 0.004 0.046 5866 Dihedral : 5.314 58.499 4477 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.65 % Allowed : 18.96 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.13), residues: 4074 helix: -2.99 (0.30), residues: 84 sheet: 1.39 (0.11), residues: 2212 loop : -0.03 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 147 TYR 0.023 0.002 TYR J 65 PHE 0.009 0.002 PHE E 84 TRP 0.010 0.001 TRP C 167 HIS 0.012 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00495 (33600) covalent geometry : angle 0.55438 (45486) hydrogen bonds : bond 0.03531 ( 1560) hydrogen bonds : angle 5.31477 ( 4215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14200.62 seconds wall clock time: 241 minutes 52.10 seconds (14512.10 seconds total)