Starting phenix.real_space_refine on Sat Mar 7 12:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj9_25159/03_2026/7sj9_25159.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj9_25159/03_2026/7sj9_25159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sj9_25159/03_2026/7sj9_25159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj9_25159/03_2026/7sj9_25159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sj9_25159/03_2026/7sj9_25159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj9_25159/03_2026/7sj9_25159.map" } resolution = 3.8 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 296 5.16 5 C 27204 2.51 5 N 7388 2.21 5 O 8304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43240 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "D" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "K" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "L" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.22, per 1000 atoms: 0.26 Number of scatterers: 43240 At special positions: 0 Unit cell: (168.36, 112.24, 212.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 296 16.00 P 36 15.00 Mg 12 11.99 O 8304 8.00 N 7388 7.00 C 27204 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: 3.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10128 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 37 sheets defined 53.0% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.575A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.656A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.750A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.703A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.530A pdb=" N HIS A 309 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.933A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.174A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.680A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.106A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.403A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 109 through 127 removed outlier: 4.612A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.695A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.610A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.535A pdb=" N ASN B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.130A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.832A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.575A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.656A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 111 through 128 removed outlier: 4.781A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.707A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.950A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.127A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.611A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 41 through 46 removed outlier: 4.022A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.344A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 109 through 127 removed outlier: 4.562A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.686A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.564A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.504A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.504A pdb=" N ASN D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 336 Processing helix chain 'D' and resid 374 through 390 Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.107A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 428 removed outlier: 3.797A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.568A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 111 through 128 removed outlier: 4.667A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.814A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 259 Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 298 through 301 removed outlier: 3.562A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.511A pdb=" N HIS E 309 " --> pdb=" O ASP E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.985A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.130A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.977A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.170A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.364A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 127 removed outlier: 4.588A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 159 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.720A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.628A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE F 242 " --> pdb=" O THR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 295 through 299 removed outlier: 3.504A pdb=" N ASN F 298 " --> pdb=" O ASP F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 336 Processing helix chain 'F' and resid 374 through 390 Processing helix chain 'F' and resid 394 through 400 removed outlier: 4.100A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 428 removed outlier: 4.146A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 Processing helix chain 'G' and resid 41 through 46 removed outlier: 4.334A pdb=" N ARG G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 69 through 79 removed outlier: 4.368A pdb=" N MET G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 109 through 127 removed outlier: 4.600A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 159 Processing helix chain 'G' and resid 180 through 196 removed outlier: 3.650A pdb=" N ASN G 184 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 Processing helix chain 'G' and resid 221 through 242 removed outlier: 3.663A pdb=" N LEU G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 285 through 294 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 322 through 336 removed outlier: 3.584A pdb=" N VAL G 326 " --> pdb=" O SER G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 390 Processing helix chain 'G' and resid 394 through 400 removed outlier: 4.165A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 427 removed outlier: 4.061A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 Processing helix chain 'H' and resid 40 through 44 Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.594A pdb=" N VAL H 49 " --> pdb=" O ARG H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.365A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 111 Processing helix chain 'H' and resid 112 through 127 Processing helix chain 'H' and resid 141 through 159 Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.687A pdb=" N ASN H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.658A pdb=" N LEU H 225 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG H 241 " --> pdb=" O THR H 237 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE H 242 " --> pdb=" O THR H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 258 Processing helix chain 'H' and resid 285 through 294 Processing helix chain 'H' and resid 295 through 299 removed outlier: 3.622A pdb=" N ASN H 298 " --> pdb=" O ASP H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 308 Processing helix chain 'H' and resid 322 through 336 Processing helix chain 'H' and resid 373 through 390 removed outlier: 4.258A pdb=" N LEU H 377 " --> pdb=" O ALA H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 400 removed outlier: 4.144A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.649A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 41 through 46 removed outlier: 4.328A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 69 through 79 removed outlier: 4.434A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 111 Processing helix chain 'I' and resid 112 through 127 Processing helix chain 'I' and resid 141 through 159 Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 221 through 242 removed outlier: 3.615A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE I 242 " --> pdb=" O THR I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.621A pdb=" N ASN I 298 " --> pdb=" O ASP I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 336 Processing helix chain 'I' and resid 373 through 390 removed outlier: 4.269A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.127A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 4.097A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 47 through 51 removed outlier: 3.676A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 81 removed outlier: 4.638A pdb=" N ILE J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 111 through 128 removed outlier: 4.625A pdb=" N ASP J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 206 through 216 Processing helix chain 'J' and resid 223 through 244 removed outlier: 3.723A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 259 Processing helix chain 'J' and resid 277 through 282 removed outlier: 4.377A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 Processing helix chain 'J' and resid 383 through 401 removed outlier: 4.025A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 410 removed outlier: 4.126A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.943A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.758A pdb=" N ASN K 50 " --> pdb=" O ASP K 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 47 through 51' Processing helix chain 'K' and resid 71 through 81 removed outlier: 4.605A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.781A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 223 through 244 removed outlier: 3.792A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 259 Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 401 removed outlier: 4.008A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 410 removed outlier: 4.125A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.734A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 47 through 51 removed outlier: 3.537A pdb=" N ASN L 50 " --> pdb=" O ASP L 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 47 through 51' Processing helix chain 'L' and resid 71 through 81 removed outlier: 4.642A pdb=" N ILE L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 111 through 128 removed outlier: 4.650A pdb=" N ASP L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 206 through 216 Processing helix chain 'L' and resid 223 through 244 removed outlier: 3.718A pdb=" N LEU L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 259 Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 298 through 301 removed outlier: 3.736A pdb=" N GLN L 301 " --> pdb=" O PRO L 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 298 through 301' Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 Processing helix chain 'L' and resid 383 through 401 removed outlier: 4.014A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 410 removed outlier: 4.116A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.666A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 29 Processing helix chain 'M' and resid 34 through 40 Processing helix chain 'M' and resid 41 through 52 Processing helix chain 'M' and resid 67 through 86 Processing helix chain 'M' and resid 92 through 98 removed outlier: 4.187A pdb=" N LYS M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 125 through 131 removed outlier: 3.827A pdb=" N ALA M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 29 Processing helix chain 'N' and resid 34 through 40 Processing helix chain 'N' and resid 41 through 52 Processing helix chain 'N' and resid 67 through 86 removed outlier: 3.500A pdb=" N TYR N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 98 removed outlier: 4.169A pdb=" N LYS N 98 " --> pdb=" O GLU N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 118 removed outlier: 3.514A pdb=" N ASN N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 131 removed outlier: 3.824A pdb=" N ALA N 129 " --> pdb=" O ASN N 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.003A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.042A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.042A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 271 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.746A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.048A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 139 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.082A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.082A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 271 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LYS D 350 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL D 313 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA D 352 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR D 315 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.772A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.972A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS E 139 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'E' and resid 269 through 273 Processing sheet with id=AB7, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.043A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS F 137 " --> pdb=" O PHE F 167 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.043A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS F 137 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA F 271 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LYS F 350 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL F 313 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA F 352 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR F 315 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.904A pdb=" N LYS F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 90 through 92 removed outlier: 8.124A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA G 9 " --> pdb=" O HIS G 137 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL G 169 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS G 137 " --> pdb=" O VAL G 169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 90 through 92 removed outlier: 8.124A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA G 9 " --> pdb=" O HIS G 137 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL G 169 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS G 137 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA G 271 " --> pdb=" O SER G 365 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LYS G 350 " --> pdb=" O LEU G 311 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL G 313 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA G 352 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR G 315 " --> pdb=" O ALA G 352 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.754A pdb=" N LYS G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 90 through 92 removed outlier: 8.108A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA H 9 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL H 169 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS H 137 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 90 through 92 removed outlier: 8.108A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA H 9 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL H 169 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS H 137 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA H 271 " --> pdb=" O SER H 365 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N LYS H 350 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL H 313 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA H 352 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR H 315 " --> pdb=" O ALA H 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.872A pdb=" N LYS H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.139A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.139A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA I 271 " --> pdb=" O SER I 365 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS I 350 " --> pdb=" O LEU I 311 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL I 313 " --> pdb=" O LYS I 350 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA I 352 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR I 315 " --> pdb=" O ALA I 352 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AD1, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.102A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE J 5 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE J 138 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE J 7 " --> pdb=" O PHE J 138 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER J 140 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL J 9 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS J 139 " --> pdb=" O PHE J 169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS J 200 " --> pdb=" O LYS J 166 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.102A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE J 5 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE J 138 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE J 7 " --> pdb=" O PHE J 138 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER J 140 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL J 9 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS J 139 " --> pdb=" O PHE J 169 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AD4, first strand: chain 'J' and resid 269 through 273 Processing sheet with id=AD5, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.153A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE K 5 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE K 138 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE K 7 " --> pdb=" O PHE K 138 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N SER K 140 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL K 9 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS K 139 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'K' and resid 269 through 273 Processing sheet with id=AD8, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.104A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS L 139 " --> pdb=" O PHE L 169 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AE1, first strand: chain 'L' and resid 269 through 273 2193 hydrogen bonds defined for protein. 6381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.03 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10694 1.33 - 1.45: 9222 1.45 - 1.58: 23790 1.58 - 1.70: 60 1.70 - 1.82: 466 Bond restraints: 44232 Sorted by residual: bond pdb=" N ARG H 359 " pdb=" CA ARG H 359 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.43e+01 bond pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.40e+01 bond pdb=" CA PRO I 358 " pdb=" C PRO I 358 " ideal model delta sigma weight residual 1.529 1.554 -0.025 1.08e-02 8.57e+03 5.49e+00 bond pdb=" CA ARG I 359 " pdb=" C ARG I 359 " ideal model delta sigma weight residual 1.527 1.556 -0.029 1.30e-02 5.92e+03 5.12e+00 bond pdb=" CA PRO G 358 " pdb=" C PRO G 358 " ideal model delta sigma weight residual 1.522 1.547 -0.026 1.18e-02 7.18e+03 4.73e+00 ... (remaining 44227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 59619 3.02 - 6.04: 405 6.04 - 9.06: 22 9.06 - 12.08: 5 12.08 - 15.10: 1 Bond angle restraints: 60052 Sorted by residual: angle pdb=" N ARG I 359 " pdb=" CA ARG I 359 " pdb=" C ARG I 359 " ideal model delta sigma weight residual 111.39 126.49 -15.10 1.38e+00 5.25e-01 1.20e+02 angle pdb=" N ARG G 359 " pdb=" CA ARG G 359 " pdb=" C ARG G 359 " ideal model delta sigma weight residual 110.10 121.03 -10.93 1.49e+00 4.50e-01 5.39e+01 angle pdb=" CA PRO H 358 " pdb=" C PRO H 358 " pdb=" O PRO H 358 " ideal model delta sigma weight residual 121.38 115.94 5.44 7.70e-01 1.69e+00 4.99e+01 angle pdb=" CA PRO D 358 " pdb=" C PRO D 358 " pdb=" O PRO D 358 " ideal model delta sigma weight residual 121.38 115.97 5.41 7.70e-01 1.69e+00 4.93e+01 angle pdb=" N PRO D 358 " pdb=" CA PRO D 358 " pdb=" C PRO D 358 " ideal model delta sigma weight residual 113.12 122.57 -9.45 1.65e+00 3.67e-01 3.28e+01 ... (remaining 60047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.10: 25870 34.10 - 68.19: 326 68.19 - 102.29: 50 102.29 - 136.38: 6 136.38 - 170.48: 18 Dihedral angle restraints: 26270 sinusoidal: 10506 harmonic: 15764 Sorted by residual: dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -120.25 -170.48 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -124.18 -166.55 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -129.48 -161.25 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 26267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 6407 0.113 - 0.226: 140 0.226 - 0.340: 4 0.340 - 0.453: 0 0.453 - 0.566: 1 Chirality restraints: 6552 Sorted by residual: chirality pdb=" CA ARG I 359 " pdb=" N ARG I 359 " pdb=" C ARG I 359 " pdb=" CB ARG I 359 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CA ARG D 359 " pdb=" N ARG D 359 " pdb=" C ARG D 359 " pdb=" CB ARG D 359 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ARG F 359 " pdb=" N ARG F 359 " pdb=" C ARG F 359 " pdb=" CB ARG F 359 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 6549 not shown) Planarity restraints: 7788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO G 357 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C PRO G 357 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO G 357 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO G 358 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 357 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C PRO B 357 " -0.061 2.00e-02 2.50e+03 pdb=" O PRO B 357 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO B 358 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 357 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PRO I 357 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO I 357 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO I 358 " -0.019 2.00e-02 2.50e+03 ... (remaining 7785 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 643 2.63 - 3.20: 41552 3.20 - 3.76: 68740 3.76 - 4.33: 95319 4.33 - 4.90: 157202 Nonbonded interactions: 363456 Sorted by model distance: nonbonded pdb=" OG1 THR E 223 " pdb=" OE1 GLN G 245 " model vdw 2.061 3.040 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.065 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.067 2.170 nonbonded pdb=" O3B GTP J 501 " pdb="MG MG J 502 " model vdw 2.068 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 2.070 2.170 ... (remaining 363451 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 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = 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 group one per residue 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: 11.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 43.260 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.049 44232 Z= 0.150 Angle : 0.670 15.102 60052 Z= 0.366 Chirality : 0.047 0.566 6552 Planarity : 0.005 0.094 7788 Dihedral : 13.669 170.480 16142 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 0.13 % Allowed : 0.39 % Favored : 99.48 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 5394 helix: 1.19 (0.11), residues: 2484 sheet: -0.13 (0.19), residues: 786 loop : -1.18 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 77 TYR 0.018 0.002 TYR D 50 PHE 0.027 0.002 PHE J 343 TRP 0.024 0.003 TRP F 397 HIS 0.011 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00305 (44232) covalent geometry : angle 0.66980 (60052) hydrogen bonds : bond 0.13752 ( 2164) hydrogen bonds : angle 5.89653 ( 6381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1993 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1987 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.9237 (m110) cc_final: 0.8961 (m110) REVERT: A 155 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8631 (mt-10) REVERT: A 166 LYS cc_start: 0.9230 (mtmm) cc_final: 0.9019 (mttp) REVERT: A 169 PHE cc_start: 0.9159 (m-10) cc_final: 0.8941 (m-10) REVERT: A 202 PHE cc_start: 0.8382 (m-80) cc_final: 0.7621 (m-80) REVERT: A 211 ASP cc_start: 0.8693 (t70) cc_final: 0.8109 (t0) REVERT: A 280 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8604 (ttpp) REVERT: A 306 ASP cc_start: 0.8933 (p0) cc_final: 0.7753 (p0) REVERT: A 308 ARG cc_start: 0.8817 (mtm110) cc_final: 0.8504 (mtm-85) REVERT: A 324 VAL cc_start: 0.8996 (t) cc_final: 0.8710 (p) REVERT: A 338 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8775 (mtmt) REVERT: A 392 ASP cc_start: 0.9116 (m-30) cc_final: 0.8841 (m-30) REVERT: A 417 GLU cc_start: 0.8885 (tt0) cc_final: 0.8615 (mt-10) REVERT: B 3 GLU cc_start: 0.8130 (mp0) cc_final: 0.7561 (mp0) REVERT: B 14 ASN cc_start: 0.9044 (m110) cc_final: 0.8638 (m110) REVERT: B 31 ASP cc_start: 0.8734 (t0) cc_final: 0.8418 (t0) REVERT: B 74 ASP cc_start: 0.8890 (m-30) cc_final: 0.8681 (m-30) REVERT: B 86 ARG cc_start: 0.8443 (ttt-90) cc_final: 0.8060 (ttt-90) REVERT: B 124 CYS cc_start: 0.8997 (m) cc_final: 0.8426 (p) REVERT: B 198 GLU cc_start: 0.8622 (pt0) cc_final: 0.8362 (pt0) REVERT: B 207 LEU cc_start: 0.9666 (mm) cc_final: 0.9282 (mt) REVERT: B 252 LYS cc_start: 0.9178 (mtpp) cc_final: 0.8839 (mtpp) REVERT: B 288 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 297 LYS cc_start: 0.8913 (pttt) cc_final: 0.8683 (pttt) REVERT: B 298 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8401 (t0) REVERT: B 307 HIS cc_start: 0.9038 (m-70) cc_final: 0.8694 (m-70) REVERT: B 329 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8984 (mm-40) REVERT: B 331 LEU cc_start: 0.9485 (tp) cc_final: 0.7778 (tp) REVERT: B 375 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7101 (pp30) REVERT: B 376 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8008 (mt-10) REVERT: B 379 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8531 (mtmt) REVERT: B 404 ASP cc_start: 0.8451 (p0) cc_final: 0.7842 (p0) REVERT: B 407 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7749 (mt-10) REVERT: C 3 GLU cc_start: 0.7621 (mp0) cc_final: 0.7198 (mp0) REVERT: C 50 ASN cc_start: 0.8782 (t160) cc_final: 0.8447 (t0) REVERT: C 76 ASP cc_start: 0.9104 (m-30) cc_final: 0.8873 (m-30) REVERT: C 152 LEU cc_start: 0.9509 (tp) cc_final: 0.8998 (tp) REVERT: C 163 LYS cc_start: 0.8573 (mmpt) cc_final: 0.8038 (mmmt) REVERT: C 183 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 211 ASP cc_start: 0.8868 (t0) cc_final: 0.8658 (t0) REVERT: C 280 LYS cc_start: 0.5111 (mmtt) cc_final: 0.4520 (mmtt) REVERT: C 324 VAL cc_start: 0.8388 (t) cc_final: 0.7784 (t) REVERT: C 376 CYS cc_start: 0.9071 (t) cc_final: 0.8646 (t) REVERT: C 377 MET cc_start: 0.8554 (ttp) cc_final: 0.7973 (tmm) REVERT: C 378 LEU cc_start: 0.9541 (mt) cc_final: 0.8972 (mt) REVERT: C 423 GLU cc_start: 0.8742 (mp0) cc_final: 0.8449 (mp0) REVERT: D 41 ASP cc_start: 0.8623 (p0) cc_final: 0.7844 (p0) REVERT: D 45 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7894 (mm-30) REVERT: D 88 ASP cc_start: 0.8763 (p0) cc_final: 0.8331 (p0) REVERT: D 154 LYS cc_start: 0.9572 (mmmm) cc_final: 0.9348 (mmmm) REVERT: D 195 ASN cc_start: 0.8806 (m-40) cc_final: 0.8338 (m110) REVERT: D 198 GLU cc_start: 0.8875 (pt0) cc_final: 0.8462 (pt0) REVERT: D 252 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8528 (ttmm) REVERT: D 298 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8343 (t0) REVERT: D 307 HIS cc_start: 0.9232 (m-70) cc_final: 0.8678 (m-70) REVERT: D 327 ASP cc_start: 0.9130 (m-30) cc_final: 0.8928 (m-30) REVERT: D 379 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8877 (mtmt) REVERT: D 404 ASP cc_start: 0.8915 (p0) cc_final: 0.8672 (p0) REVERT: D 407 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 417 ASP cc_start: 0.9212 (m-30) cc_final: 0.9004 (m-30) REVERT: E 69 ASP cc_start: 0.9006 (t0) cc_final: 0.8433 (t0) REVERT: E 71 GLU cc_start: 0.7879 (pt0) cc_final: 0.7116 (pt0) REVERT: E 76 ASP cc_start: 0.9024 (m-30) cc_final: 0.8788 (m-30) REVERT: E 88 HIS cc_start: 0.8838 (t70) cc_final: 0.8254 (t70) REVERT: E 150 THR cc_start: 0.9474 (m) cc_final: 0.9077 (t) REVERT: E 152 LEU cc_start: 0.9316 (tp) cc_final: 0.9005 (tp) REVERT: E 155 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8766 (mt-10) REVERT: E 164 LYS cc_start: 0.8779 (mmmm) cc_final: 0.8505 (mmmm) REVERT: E 199 ASP cc_start: 0.8213 (m-30) cc_final: 0.7938 (m-30) REVERT: E 205 ASP cc_start: 0.8780 (t0) cc_final: 0.8535 (t0) REVERT: E 232 SER cc_start: 0.9427 (p) cc_final: 0.8931 (m) REVERT: E 245 ASP cc_start: 0.8990 (t70) cc_final: 0.8695 (t0) REVERT: E 269 LEU cc_start: 0.9084 (pp) cc_final: 0.8138 (pp) REVERT: E 284 GLU cc_start: 0.7646 (pp20) cc_final: 0.7298 (pp20) REVERT: E 293 ASN cc_start: 0.9300 (m-40) cc_final: 0.9089 (m-40) REVERT: E 324 VAL cc_start: 0.9058 (t) cc_final: 0.8818 (p) REVERT: E 341 ILE cc_start: 0.9323 (mp) cc_final: 0.8826 (mp) REVERT: E 357 TYR cc_start: 0.9060 (m-80) cc_final: 0.8809 (m-80) REVERT: E 392 ASP cc_start: 0.9444 (m-30) cc_final: 0.9057 (m-30) REVERT: E 396 ASP cc_start: 0.9025 (m-30) cc_final: 0.8746 (m-30) REVERT: E 411 GLU cc_start: 0.8124 (tp30) cc_final: 0.7808 (tp30) REVERT: E 414 GLU cc_start: 0.8430 (mp0) cc_final: 0.8144 (mp0) REVERT: E 415 GLU cc_start: 0.8005 (tt0) cc_final: 0.7719 (tt0) REVERT: E 423 GLU cc_start: 0.8858 (mp0) cc_final: 0.8518 (mp0) REVERT: E 425 MET cc_start: 0.9240 (mmm) cc_final: 0.8866 (mmt) REVERT: E 431 ASP cc_start: 0.8463 (m-30) cc_final: 0.8146 (m-30) REVERT: F 41 ASP cc_start: 0.8901 (p0) cc_final: 0.8100 (p0) REVERT: F 45 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7973 (mm-30) REVERT: F 106 TYR cc_start: 0.8924 (m-80) cc_final: 0.8644 (m-80) REVERT: F 147 MET cc_start: 0.9140 (tpp) cc_final: 0.8932 (tpp) REVERT: F 252 LYS cc_start: 0.9246 (mtpp) cc_final: 0.8726 (mtpp) REVERT: F 323 MET cc_start: 0.8420 (mmm) cc_final: 0.8080 (mmm) REVERT: F 325 GLU cc_start: 0.9146 (tt0) cc_final: 0.8870 (tt0) REVERT: F 327 ASP cc_start: 0.9062 (m-30) cc_final: 0.8852 (m-30) REVERT: F 375 GLN cc_start: 0.8345 (pp30) cc_final: 0.7383 (pp30) REVERT: F 376 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8190 (mt-10) REVERT: F 379 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8795 (mtmt) REVERT: F 404 ASP cc_start: 0.8547 (p0) cc_final: 0.8207 (p0) REVERT: F 423 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8593 (tp-100) REVERT: G 3 GLU cc_start: 0.8322 (mp0) cc_final: 0.7885 (mp0) REVERT: G 74 ASP cc_start: 0.9269 (m-30) cc_final: 0.9064 (m-30) REVERT: G 92 PHE cc_start: 0.9480 (p90) cc_final: 0.9212 (p90) REVERT: G 106 TYR cc_start: 0.9232 (m-80) cc_final: 0.8792 (m-80) REVERT: G 129 CYS cc_start: 0.8837 (t) cc_final: 0.8614 (t) REVERT: G 159 TYR cc_start: 0.9127 (m-80) cc_final: 0.8858 (m-80) REVERT: G 198 GLU cc_start: 0.8996 (pt0) cc_final: 0.8437 (pt0) REVERT: G 208 TYR cc_start: 0.9143 (m-10) cc_final: 0.8866 (m-80) REVERT: G 281 TYR cc_start: 0.9279 (m-80) cc_final: 0.9007 (m-80) REVERT: G 284 LEU cc_start: 0.9070 (mt) cc_final: 0.8387 (pt) REVERT: G 291 GLN cc_start: 0.8681 (pp30) cc_final: 0.8333 (pp30) REVERT: G 350 LYS cc_start: 0.9299 (tptp) cc_final: 0.8619 (tppt) REVERT: G 362 LYS cc_start: 0.8861 (tmmt) cc_final: 0.8445 (tmmt) REVERT: G 407 GLU cc_start: 0.8222 (pt0) cc_final: 0.7874 (pt0) REVERT: G 410 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8791 (mt-10) REVERT: G 412 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8423 (tm-30) REVERT: H 19 LYS cc_start: 0.8721 (tptm) cc_final: 0.8156 (tptt) REVERT: H 194 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7805 (mm-30) REVERT: H 209 ASP cc_start: 0.9127 (t0) cc_final: 0.8058 (t0) REVERT: H 227 HIS cc_start: 0.9115 (t70) cc_final: 0.8646 (t70) REVERT: H 284 LEU cc_start: 0.9293 (mt) cc_final: 0.8819 (pt) REVERT: H 291 GLN cc_start: 0.8555 (pp30) cc_final: 0.7967 (pp30) REVERT: H 292 GLN cc_start: 0.8790 (tt0) cc_final: 0.8512 (tt0) REVERT: H 304 ASP cc_start: 0.9272 (t70) cc_final: 0.8976 (t0) REVERT: H 307 HIS cc_start: 0.9243 (m-70) cc_final: 0.8694 (m-70) REVERT: H 320 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7620 (mmm160) REVERT: H 325 GLU cc_start: 0.9283 (tt0) cc_final: 0.8766 (tt0) REVERT: H 329 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8818 (mm-40) REVERT: H 367 PHE cc_start: 0.9112 (t80) cc_final: 0.8902 (t80) REVERT: H 383 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8674 (tm-30) REVERT: H 406 MET cc_start: 0.8610 (tpp) cc_final: 0.8335 (tpp) REVERT: H 407 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8555 (mt-10) REVERT: H 421 GLU cc_start: 0.8720 (tp30) cc_final: 0.8410 (tp30) REVERT: I 19 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8746 (tptm) REVERT: I 74 ASP cc_start: 0.9239 (m-30) cc_final: 0.9001 (m-30) REVERT: I 92 PHE cc_start: 0.9416 (p90) cc_final: 0.9127 (p90) REVERT: I 106 TYR cc_start: 0.9338 (m-80) cc_final: 0.9121 (m-80) REVERT: I 114 ASP cc_start: 0.8927 (m-30) cc_final: 0.8697 (m-30) REVERT: I 117 LEU cc_start: 0.9496 (mm) cc_final: 0.9173 (mm) REVERT: I 121 ARG cc_start: 0.9097 (ttm110) cc_final: 0.8700 (ttm110) REVERT: I 136 THR cc_start: 0.9528 (m) cc_final: 0.9044 (p) REVERT: I 159 TYR cc_start: 0.9262 (m-80) cc_final: 0.8878 (m-80) REVERT: I 164 MET cc_start: 0.8342 (mtp) cc_final: 0.8142 (mtp) REVERT: I 195 ASN cc_start: 0.8581 (m-40) cc_final: 0.8327 (p0) REVERT: I 198 GLU cc_start: 0.8883 (pt0) cc_final: 0.7935 (pt0) REVERT: I 208 TYR cc_start: 0.9007 (m-10) cc_final: 0.8802 (m-80) REVERT: I 209 ASP cc_start: 0.9221 (t0) cc_final: 0.8247 (t0) REVERT: I 291 GLN cc_start: 0.8584 (pp30) cc_final: 0.8228 (pp30) REVERT: I 293 MET cc_start: 0.7756 (mtt) cc_final: 0.7454 (mtt) REVERT: I 295 ASP cc_start: 0.8831 (p0) cc_final: 0.8269 (p0) REVERT: I 304 ASP cc_start: 0.9248 (t70) cc_final: 0.9043 (t0) REVERT: I 307 HIS cc_start: 0.9232 (m-70) cc_final: 0.8828 (m-70) REVERT: I 325 GLU cc_start: 0.9119 (tt0) cc_final: 0.8523 (tt0) REVERT: I 329 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8898 (mm-40) REVERT: I 406 MET cc_start: 0.9167 (tpp) cc_final: 0.8606 (tpp) REVERT: I 417 ASP cc_start: 0.9414 (m-30) cc_final: 0.9183 (m-30) REVERT: I 421 GLU cc_start: 0.8940 (tp30) cc_final: 0.8643 (tp30) REVERT: I 425 TYR cc_start: 0.8117 (m-10) cc_final: 0.7909 (m-10) REVERT: J 88 HIS cc_start: 0.9068 (t70) cc_final: 0.8365 (t-170) REVERT: J 128 GLN cc_start: 0.7918 (pp30) cc_final: 0.7673 (pp30) REVERT: J 150 THR cc_start: 0.9670 (m) cc_final: 0.9197 (p) REVERT: J 155 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9003 (mt-10) REVERT: J 161 TYR cc_start: 0.8539 (m-10) cc_final: 0.8301 (m-10) REVERT: J 168 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8422 (mt-10) REVERT: J 203 MET cc_start: 0.8550 (mmm) cc_final: 0.8099 (mmm) REVERT: J 293 ASN cc_start: 0.9629 (m-40) cc_final: 0.9324 (m-40) REVERT: J 313 MET cc_start: 0.8108 (mpp) cc_final: 0.7754 (mtm) REVERT: J 341 ILE cc_start: 0.9024 (mp) cc_final: 0.8695 (mp) REVERT: J 396 ASP cc_start: 0.8825 (m-30) cc_final: 0.8619 (m-30) REVERT: J 413 MET cc_start: 0.8142 (mtp) cc_final: 0.7890 (ttm) REVERT: J 417 GLU cc_start: 0.8321 (pt0) cc_final: 0.7823 (pt0) REVERT: J 420 GLU cc_start: 0.9107 (pt0) cc_final: 0.8861 (pt0) REVERT: K 1 MET cc_start: 0.6789 (tmm) cc_final: 0.6553 (tmm) REVERT: K 88 HIS cc_start: 0.9064 (t70) cc_final: 0.8590 (t-170) REVERT: K 90 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8370 (mm-30) REVERT: K 96 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8548 (mmmt) REVERT: K 112 LYS cc_start: 0.9072 (pttt) cc_final: 0.8712 (pttt) REVERT: K 150 THR cc_start: 0.9615 (m) cc_final: 0.9197 (p) REVERT: K 286 LEU cc_start: 0.9076 (mt) cc_final: 0.8678 (mt) REVERT: K 308 ARG cc_start: 0.9220 (mtm110) cc_final: 0.8910 (mtm-85) REVERT: K 343 PHE cc_start: 0.8720 (m-80) cc_final: 0.8326 (m-80) REVERT: K 417 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8544 (mt-10) REVERT: L 88 HIS cc_start: 0.8838 (t70) cc_final: 0.8399 (t-90) REVERT: L 150 THR cc_start: 0.9591 (m) cc_final: 0.9319 (p) REVERT: L 155 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8512 (mt-10) REVERT: L 290 GLU cc_start: 0.9346 (tt0) cc_final: 0.9045 (mt-10) REVERT: L 313 MET cc_start: 0.8330 (mpp) cc_final: 0.7922 (mtm) REVERT: L 377 MET cc_start: 0.9026 (ttm) cc_final: 0.8702 (ttp) REVERT: L 396 ASP cc_start: 0.8868 (m-30) cc_final: 0.8662 (m-30) REVERT: L 411 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7657 (mt-10) REVERT: L 420 GLU cc_start: 0.9137 (pt0) cc_final: 0.8901 (mm-30) REVERT: L 430 LYS cc_start: 0.9483 (pttp) cc_final: 0.9178 (pttm) REVERT: M 29 HIS cc_start: 0.9335 (t-90) cc_final: 0.8921 (t-90) REVERT: M 57 HIS cc_start: 0.7605 (t-170) cc_final: 0.7365 (t70) REVERT: M 84 LYS cc_start: 0.9422 (ttmt) cc_final: 0.9069 (ttpt) REVERT: M 109 GLN cc_start: 0.8879 (pt0) cc_final: 0.8646 (pt0) REVERT: N 29 HIS cc_start: 0.9259 (t-90) cc_final: 0.8932 (t-90) REVERT: N 57 HIS cc_start: 0.7858 (t-170) cc_final: 0.7161 (t-170) REVERT: N 60 LYS cc_start: 0.8364 (mmtm) cc_final: 0.7908 (mmtt) REVERT: N 62 LYS cc_start: 0.8457 (mttt) cc_final: 0.8214 (mttp) REVERT: N 84 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8696 (ttpt) REVERT: N 109 GLN cc_start: 0.8715 (pt0) cc_final: 0.8250 (pt0) REVERT: N 118 ASN cc_start: 0.8008 (m-40) cc_final: 0.7630 (m110) outliers start: 6 outliers final: 0 residues processed: 1992 average time/residue: 0.2762 time to fit residues: 894.3266 Evaluate side-chains 1507 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1504 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain D residue 298 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 0.0370 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN B 94 GLN B 99 ASN B 204 ASN B 247 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS B 423 GLN ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 301 GLN D 43 GLN D 94 GLN D 105 HIS D 204 ASN D 245 GLN D 247 ASN D 292 GLN D 337 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN F 99 ASN F 105 HIS F 204 ASN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN F 298 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 HIS G 57 HIS G 165 ASN G 227 HIS G 292 GLN G 298 ASN G 329 GLN G 370 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 256 ASN H 298 ASN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN I 165 ASN I 227 HIS I 245 GLN I 247 ASN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN ** I 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN K 300 ASN ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 HIS L 293 ASN M 125 ASN N 102 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.096597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.076697 restraints weight = 102711.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079291 restraints weight = 56247.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.081087 restraints weight = 36874.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082320 restraints weight = 27121.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083168 restraints weight = 21759.175| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 44232 Z= 0.197 Angle : 0.662 9.599 60052 Z= 0.343 Chirality : 0.046 0.263 6552 Planarity : 0.005 0.082 7788 Dihedral : 11.952 177.333 6075 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.39 % Allowed : 14.72 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 5394 helix: 1.48 (0.10), residues: 2518 sheet: 0.15 (0.19), residues: 786 loop : -1.19 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 359 TYR 0.030 0.002 TYR D 50 PHE 0.026 0.002 PHE I 367 TRP 0.035 0.002 TRP F 344 HIS 0.009 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00424 (44232) covalent geometry : angle 0.66161 (60052) hydrogen bonds : bond 0.04449 ( 2164) hydrogen bonds : angle 4.70852 ( 6381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1624 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7857 (mp0) cc_final: 0.7635 (mp0) REVERT: A 71 GLU cc_start: 0.7564 (pt0) cc_final: 0.7296 (pm20) REVERT: A 211 ASP cc_start: 0.8589 (t70) cc_final: 0.8051 (t0) REVERT: A 215 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8501 (ttp-110) REVERT: A 218 ASP cc_start: 0.8648 (m-30) cc_final: 0.8212 (m-30) REVERT: A 317 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9147 (mt) REVERT: A 324 VAL cc_start: 0.8752 (t) cc_final: 0.8301 (t) REVERT: A 327 ASP cc_start: 0.9065 (m-30) cc_final: 0.8842 (m-30) REVERT: A 335 ILE cc_start: 0.9760 (OUTLIER) cc_final: 0.9552 (tp) REVERT: A 411 GLU cc_start: 0.8541 (tp30) cc_final: 0.8227 (tp30) REVERT: A 430 LYS cc_start: 0.9389 (ttpt) cc_final: 0.9103 (pttm) REVERT: B 41 ASP cc_start: 0.8597 (p0) cc_final: 0.7818 (p0) REVERT: B 124 CYS cc_start: 0.8881 (m) cc_final: 0.8479 (p) REVERT: B 198 GLU cc_start: 0.8730 (pt0) cc_final: 0.8526 (pt0) REVERT: B 209 ASP cc_start: 0.8738 (t0) cc_final: 0.8246 (t0) REVERT: B 213 ARG cc_start: 0.8625 (ttm110) cc_final: 0.7891 (mtm110) REVERT: B 252 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8787 (ttmm) REVERT: B 282 ARG cc_start: 0.7033 (tmm-80) cc_final: 0.6231 (ptm-80) REVERT: B 298 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8573 (t0) REVERT: B 324 LYS cc_start: 0.9614 (OUTLIER) cc_final: 0.9226 (ptmm) REVERT: B 329 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8861 (mm-40) REVERT: B 367 PHE cc_start: 0.9275 (t80) cc_final: 0.8840 (t80) REVERT: B 375 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7873 (pp30) REVERT: B 403 MET cc_start: 0.8993 (mtp) cc_final: 0.8610 (mtm) REVERT: B 407 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 412 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8110 (tm-30) REVERT: C 120 ASP cc_start: 0.8671 (t70) cc_final: 0.8464 (t0) REVERT: C 150 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9235 (m) REVERT: C 198 SER cc_start: 0.8671 (p) cc_final: 0.7944 (p) REVERT: C 218 ASP cc_start: 0.9056 (m-30) cc_final: 0.8633 (m-30) REVERT: C 256 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8808 (tt0) REVERT: C 280 LYS cc_start: 0.5060 (mmtt) cc_final: 0.4275 (mtmm) REVERT: C 338 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8335 (mtmt) REVERT: C 376 CYS cc_start: 0.8984 (t) cc_final: 0.8681 (t) REVERT: C 377 MET cc_start: 0.8814 (ttp) cc_final: 0.7943 (tmm) REVERT: C 378 LEU cc_start: 0.9508 (mt) cc_final: 0.9016 (mt) REVERT: D 19 LYS cc_start: 0.8957 (tptt) cc_final: 0.8264 (tptm) REVERT: D 41 ASP cc_start: 0.8618 (p0) cc_final: 0.7714 (p0) REVERT: D 45 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7815 (mm-30) REVERT: D 58 LYS cc_start: 0.8851 (tttm) cc_final: 0.8076 (tttm) REVERT: D 124 CYS cc_start: 0.8900 (m) cc_final: 0.8487 (p) REVERT: D 164 MET cc_start: 0.8007 (ptp) cc_final: 0.7709 (pmm) REVERT: D 213 ARG cc_start: 0.8755 (ttm110) cc_final: 0.8186 (ttm170) REVERT: D 252 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8737 (ttmm) REVERT: D 307 HIS cc_start: 0.9261 (m-70) cc_final: 0.8912 (m-70) REVERT: D 323 MET cc_start: 0.8286 (mmm) cc_final: 0.7934 (mmm) REVERT: D 327 ASP cc_start: 0.9022 (m-30) cc_final: 0.8732 (m-30) REVERT: D 375 GLN cc_start: 0.8385 (pp30) cc_final: 0.6960 (pp30) REVERT: D 379 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8609 (mtmt) REVERT: D 383 GLU cc_start: 0.9011 (tt0) cc_final: 0.8771 (tm-30) REVERT: D 412 GLU cc_start: 0.8884 (tm-30) cc_final: 0.7726 (tm-30) REVERT: E 20 CYS cc_start: 0.8347 (m) cc_final: 0.7951 (m) REVERT: E 88 HIS cc_start: 0.8718 (t70) cc_final: 0.8378 (t-170) REVERT: E 90 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8300 (mm-30) REVERT: E 152 LEU cc_start: 0.9443 (tp) cc_final: 0.8885 (tp) REVERT: E 163 LYS cc_start: 0.7635 (mmtt) cc_final: 0.6671 (mmpt) REVERT: E 215 ARG cc_start: 0.8849 (mtm110) cc_final: 0.8631 (mtm110) REVERT: E 232 SER cc_start: 0.9479 (p) cc_final: 0.9075 (m) REVERT: E 245 ASP cc_start: 0.8757 (t70) cc_final: 0.8447 (t0) REVERT: E 326 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8917 (ttpt) REVERT: E 357 TYR cc_start: 0.8976 (m-80) cc_final: 0.8771 (m-80) REVERT: E 361 THR cc_start: 0.9005 (m) cc_final: 0.8622 (t) REVERT: E 417 GLU cc_start: 0.7993 (pm20) cc_final: 0.7424 (pm20) REVERT: E 430 LYS cc_start: 0.9444 (ttpt) cc_final: 0.9209 (pttm) REVERT: F 3 GLU cc_start: 0.8622 (mp0) cc_final: 0.8230 (mp0) REVERT: F 41 ASP cc_start: 0.8747 (p0) cc_final: 0.7944 (t0) REVERT: F 45 GLU cc_start: 0.8345 (mm-30) cc_final: 0.6955 (mm-30) REVERT: F 123 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8883 (mm-30) REVERT: F 147 MET cc_start: 0.9073 (tpp) cc_final: 0.8786 (tpp) REVERT: F 209 ASP cc_start: 0.8684 (t0) cc_final: 0.8450 (t0) REVERT: F 211 CYS cc_start: 0.9069 (t) cc_final: 0.8732 (p) REVERT: F 252 LYS cc_start: 0.9309 (mtpp) cc_final: 0.9047 (ttmm) REVERT: F 257 MET cc_start: 0.8866 (mmp) cc_final: 0.8022 (mmt) REVERT: F 291 GLN cc_start: 0.8652 (pp30) cc_final: 0.8344 (pp30) REVERT: F 341 PHE cc_start: 0.8991 (m-80) cc_final: 0.8610 (m-80) REVERT: F 375 GLN cc_start: 0.8182 (pp30) cc_final: 0.7959 (pp30) REVERT: F 403 MET cc_start: 0.8024 (mtp) cc_final: 0.7799 (mtp) REVERT: F 423 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8527 (tp-100) REVERT: G 3 GLU cc_start: 0.8592 (mp0) cc_final: 0.8332 (mp0) REVERT: G 14 ASN cc_start: 0.9068 (m-40) cc_final: 0.8833 (m110) REVERT: G 53 GLU cc_start: 0.8476 (tp30) cc_final: 0.7696 (tp30) REVERT: G 164 MET cc_start: 0.8630 (ttm) cc_final: 0.8149 (mtp) REVERT: G 208 TYR cc_start: 0.9078 (m-10) cc_final: 0.8824 (m-80) REVERT: G 284 LEU cc_start: 0.8988 (mt) cc_final: 0.8395 (pt) REVERT: G 292 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8584 (tt0) REVERT: G 375 GLN cc_start: 0.8882 (pt0) cc_final: 0.8164 (pp30) REVERT: G 406 MET cc_start: 0.8459 (tpt) cc_final: 0.7949 (tpt) REVERT: G 407 GLU cc_start: 0.8512 (pt0) cc_final: 0.7860 (pt0) REVERT: G 410 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8599 (mt-10) REVERT: G 412 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8573 (tp30) REVERT: G 421 GLU cc_start: 0.8521 (tp30) cc_final: 0.8277 (tp30) REVERT: H 3 GLU cc_start: 0.8923 (mp0) cc_final: 0.8635 (mp0) REVERT: H 14 ASN cc_start: 0.9086 (m-40) cc_final: 0.8786 (m110) REVERT: H 121 ARG cc_start: 0.8396 (mtt90) cc_final: 0.8182 (mtt90) REVERT: H 194 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7813 (mm-30) REVERT: H 200 TYR cc_start: 0.9235 (m-10) cc_final: 0.9033 (m-80) REVERT: H 209 ASP cc_start: 0.9085 (t0) cc_final: 0.8738 (t0) REVERT: H 298 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8791 (t0) REVERT: H 307 HIS cc_start: 0.9375 (m-70) cc_final: 0.8999 (m-70) REVERT: H 375 GLN cc_start: 0.8838 (pt0) cc_final: 0.8304 (pp30) REVERT: H 383 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8351 (tm-30) REVERT: H 406 MET cc_start: 0.8325 (tpp) cc_final: 0.8065 (tpp) REVERT: H 421 GLU cc_start: 0.8395 (tp30) cc_final: 0.7611 (tp30) REVERT: I 3 GLU cc_start: 0.8529 (mp0) cc_final: 0.7899 (mp0) REVERT: I 51 TYR cc_start: 0.9245 (m-80) cc_final: 0.8893 (m-80) REVERT: I 69 GLU cc_start: 0.8204 (pp20) cc_final: 0.7986 (pp20) REVERT: I 83 HIS cc_start: 0.8733 (m90) cc_final: 0.8300 (m90) REVERT: I 194 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7764 (mm-30) REVERT: I 205 GLU cc_start: 0.8767 (tp30) cc_final: 0.8318 (tt0) REVERT: I 209 ASP cc_start: 0.9168 (t0) cc_final: 0.8890 (t70) REVERT: I 213 ARG cc_start: 0.8969 (ttm110) cc_final: 0.8323 (ttp80) REVERT: I 291 GLN cc_start: 0.8453 (pp30) cc_final: 0.8136 (pp30) REVERT: I 295 ASP cc_start: 0.9187 (p0) cc_final: 0.8894 (p0) REVERT: I 325 GLU cc_start: 0.9080 (tt0) cc_final: 0.8798 (tt0) REVERT: I 329 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8787 (mm-40) REVERT: I 362 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8729 (tmmt) REVERT: I 363 MET cc_start: 0.8890 (ptt) cc_final: 0.8648 (ptt) REVERT: I 423 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8626 (tp-100) REVERT: J 88 HIS cc_start: 0.8718 (t70) cc_final: 0.8213 (t-170) REVERT: J 90 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8716 (mm-30) REVERT: J 128 GLN cc_start: 0.8051 (pp30) cc_final: 0.7752 (pp30) REVERT: J 150 THR cc_start: 0.9481 (m) cc_final: 0.9135 (p) REVERT: J 154 MET cc_start: 0.9153 (mmp) cc_final: 0.8902 (mmp) REVERT: J 155 GLU cc_start: 0.9384 (mt-10) cc_final: 0.8964 (mt-10) REVERT: J 168 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7730 (mt-10) REVERT: J 170 SER cc_start: 0.9287 (m) cc_final: 0.8765 (t) REVERT: J 202 PHE cc_start: 0.8705 (m-80) cc_final: 0.8406 (m-10) REVERT: J 293 ASN cc_start: 0.9658 (m-40) cc_final: 0.9395 (m-40) REVERT: J 308 ARG cc_start: 0.9393 (mtm110) cc_final: 0.9076 (mtm-85) REVERT: J 313 MET cc_start: 0.8464 (mpp) cc_final: 0.7879 (mtm) REVERT: J 377 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8560 (ttm) REVERT: J 388 TRP cc_start: 0.9070 (m100) cc_final: 0.8812 (m100) REVERT: J 396 ASP cc_start: 0.8540 (m-30) cc_final: 0.8289 (m-30) REVERT: J 420 GLU cc_start: 0.9094 (pt0) cc_final: 0.8880 (pt0) REVERT: K 88 HIS cc_start: 0.9136 (t70) cc_final: 0.8772 (t70) REVERT: K 128 GLN cc_start: 0.7750 (pp30) cc_final: 0.7417 (pp30) REVERT: K 150 THR cc_start: 0.9366 (m) cc_final: 0.9090 (p) REVERT: K 155 GLU cc_start: 0.9160 (pt0) cc_final: 0.8616 (pt0) REVERT: K 204 VAL cc_start: 0.9001 (t) cc_final: 0.8791 (p) REVERT: K 205 ASP cc_start: 0.8352 (t0) cc_final: 0.8103 (t0) REVERT: K 308 ARG cc_start: 0.9118 (mtm110) cc_final: 0.8902 (mtm-85) REVERT: K 313 MET cc_start: 0.9144 (mtm) cc_final: 0.8135 (mtm) REVERT: K 336 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8787 (mmmm) REVERT: L 76 ASP cc_start: 0.9395 (m-30) cc_final: 0.9190 (m-30) REVERT: L 150 THR cc_start: 0.9457 (m) cc_final: 0.9127 (p) REVERT: L 155 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8871 (mt-10) REVERT: L 156 ARG cc_start: 0.9059 (mmp80) cc_final: 0.8753 (mmp80) REVERT: L 214 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7994 (ttp80) REVERT: L 286 LEU cc_start: 0.9163 (mt) cc_final: 0.8940 (pp) REVERT: L 290 GLU cc_start: 0.9374 (tt0) cc_final: 0.9042 (mt-10) REVERT: L 293 ASN cc_start: 0.9502 (m110) cc_final: 0.9115 (p0) REVERT: L 313 MET cc_start: 0.8607 (mpp) cc_final: 0.8117 (mtm) REVERT: L 361 THR cc_start: 0.8560 (m) cc_final: 0.8275 (p) REVERT: L 377 MET cc_start: 0.9038 (ttm) cc_final: 0.8794 (ttp) REVERT: L 396 ASP cc_start: 0.8617 (m-30) cc_final: 0.8399 (m-30) REVERT: L 413 MET cc_start: 0.8519 (ttm) cc_final: 0.8125 (ttm) REVERT: L 425 MET cc_start: 0.8955 (tpp) cc_final: 0.8571 (tpt) REVERT: M 29 HIS cc_start: 0.9148 (t-90) cc_final: 0.8753 (t-90) REVERT: M 57 HIS cc_start: 0.7788 (t-170) cc_final: 0.6743 (t70) REVERT: M 60 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7923 (mmtt) REVERT: M 84 LYS cc_start: 0.9443 (ttmt) cc_final: 0.9193 (ttpt) REVERT: M 118 ASN cc_start: 0.7815 (m-40) cc_final: 0.7543 (m110) REVERT: N 17 ARG cc_start: 0.8937 (mtm-85) cc_final: 0.8728 (mtm-85) REVERT: N 29 HIS cc_start: 0.9109 (t-90) cc_final: 0.8735 (t-90) REVERT: N 57 HIS cc_start: 0.7817 (t-170) cc_final: 0.6582 (t-170) REVERT: N 60 LYS cc_start: 0.8174 (mmtm) cc_final: 0.7965 (mmtt) REVERT: N 84 LYS cc_start: 0.9277 (ttmt) cc_final: 0.8762 (ttpt) REVERT: N 100 LYS cc_start: 0.7941 (mmmm) cc_final: 0.7321 (mmtp) REVERT: N 104 ASN cc_start: 0.8665 (m-40) cc_final: 0.8382 (m-40) REVERT: N 118 ASN cc_start: 0.8193 (m-40) cc_final: 0.7647 (m110) outliers start: 111 outliers final: 65 residues processed: 1668 average time/residue: 0.2681 time to fit residues: 725.6787 Evaluate side-chains 1455 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1379 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain N residue 55 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 19 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 392 optimal weight: 5.9990 chunk 527 optimal weight: 7.9990 chunk 322 optimal weight: 9.9990 chunk 475 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 305 optimal weight: 0.3980 chunk 142 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 293 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 347 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 139 HIS E 301 GLN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN G 126 ASN G 227 HIS G 292 GLN G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 126 ASN H 247 ASN H 256 ASN H 279 GLN H 292 GLN H 298 ASN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 ASN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 139 HIS ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 HIS K 300 ASN ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.095739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.075826 restraints weight = 101198.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078311 restraints weight = 55667.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080069 restraints weight = 36376.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081315 restraints weight = 26838.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082166 restraints weight = 21526.233| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44232 Z= 0.136 Angle : 0.619 9.254 60052 Z= 0.317 Chirality : 0.045 0.220 6552 Planarity : 0.004 0.059 7788 Dihedral : 11.809 179.612 6073 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 3.18 % Allowed : 17.45 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.12), residues: 5394 helix: 1.54 (0.10), residues: 2542 sheet: 0.48 (0.19), residues: 774 loop : -1.06 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 320 TYR 0.023 0.001 TYR E 172 PHE 0.023 0.001 PHE I 92 TRP 0.019 0.002 TRP I 344 HIS 0.012 0.001 HIS G 190 Details of bonding type rmsd covalent geometry : bond 0.00302 (44232) covalent geometry : angle 0.61942 (60052) hydrogen bonds : bond 0.04074 ( 2164) hydrogen bonds : angle 4.57049 ( 6381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1544 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.7693 (t0) REVERT: A 176 GLN cc_start: 0.7880 (tm-30) cc_final: 0.6969 (tm-30) REVERT: A 211 ASP cc_start: 0.8693 (t70) cc_final: 0.7961 (t70) REVERT: A 214 ARG cc_start: 0.8809 (tmm-80) cc_final: 0.8459 (ttp80) REVERT: A 218 ASP cc_start: 0.8679 (m-30) cc_final: 0.8257 (m-30) REVERT: A 317 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9043 (mt) REVERT: A 324 VAL cc_start: 0.8802 (t) cc_final: 0.8338 (t) REVERT: A 327 ASP cc_start: 0.9064 (m-30) cc_final: 0.8848 (m-30) REVERT: A 335 ILE cc_start: 0.9751 (tp) cc_final: 0.9518 (tp) REVERT: A 361 THR cc_start: 0.9147 (m) cc_final: 0.8712 (t) REVERT: A 377 MET cc_start: 0.9020 (tmm) cc_final: 0.8578 (tmm) REVERT: A 425 MET cc_start: 0.8793 (tpp) cc_final: 0.8484 (mpp) REVERT: B 41 ASP cc_start: 0.8494 (p0) cc_final: 0.8171 (p0) REVERT: B 124 CYS cc_start: 0.8847 (m) cc_final: 0.8452 (p) REVERT: B 134 GLN cc_start: 0.8735 (pt0) cc_final: 0.8485 (pt0) REVERT: B 156 ARG cc_start: 0.8853 (ttm-80) cc_final: 0.8494 (tpp-160) REVERT: B 161 ASP cc_start: 0.8776 (p0) cc_final: 0.8469 (p0) REVERT: B 213 ARG cc_start: 0.8770 (ttm170) cc_final: 0.8192 (ttm170) REVERT: B 252 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8833 (ttmm) REVERT: B 298 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8708 (t0) REVERT: B 329 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8770 (mm-40) REVERT: B 367 PHE cc_start: 0.9259 (t80) cc_final: 0.8807 (t80) REVERT: B 375 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7495 (pp30) REVERT: B 407 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7961 (mt-10) REVERT: B 415 MET cc_start: 0.8282 (mmp) cc_final: 0.7990 (mmp) REVERT: C 3 GLU cc_start: 0.7975 (mp0) cc_final: 0.7649 (mp0) REVERT: C 150 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9192 (m) REVERT: C 183 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8380 (mt-10) REVERT: C 215 ARG cc_start: 0.8591 (mtm110) cc_final: 0.8360 (mtm110) REVERT: C 218 ASP cc_start: 0.9055 (m-30) cc_final: 0.8827 (m-30) REVERT: C 256 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8771 (tt0) REVERT: C 280 LYS cc_start: 0.5240 (mmtt) cc_final: 0.4279 (mmmt) REVERT: C 377 MET cc_start: 0.8553 (ttp) cc_final: 0.7930 (tmm) REVERT: C 378 LEU cc_start: 0.9515 (mt) cc_final: 0.9188 (mt) REVERT: C 414 GLU cc_start: 0.8685 (mp0) cc_final: 0.8375 (mp0) REVERT: C 425 MET cc_start: 0.9008 (mmm) cc_final: 0.8733 (mmm) REVERT: D 19 LYS cc_start: 0.8740 (tptt) cc_final: 0.8524 (tptm) REVERT: D 41 ASP cc_start: 0.8578 (p0) cc_final: 0.8276 (p0) REVERT: D 124 CYS cc_start: 0.8869 (m) cc_final: 0.8487 (p) REVERT: D 164 MET cc_start: 0.7669 (ptp) cc_final: 0.7213 (pmm) REVERT: D 209 ASP cc_start: 0.8785 (t0) cc_final: 0.8155 (t0) REVERT: D 213 ARG cc_start: 0.8808 (ttm110) cc_final: 0.8452 (mtm110) REVERT: D 252 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8735 (ttmm) REVERT: D 327 ASP cc_start: 0.9004 (m-30) cc_final: 0.8764 (m-30) REVERT: D 350 LYS cc_start: 0.8721 (tptm) cc_final: 0.8218 (tppt) REVERT: E 88 HIS cc_start: 0.8494 (t70) cc_final: 0.8045 (t-170) REVERT: E 90 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8201 (mm-30) REVERT: E 150 THR cc_start: 0.9395 (m) cc_final: 0.9188 (p) REVERT: E 203 MET cc_start: 0.8471 (mmp) cc_final: 0.8153 (mmp) REVERT: E 214 ARG cc_start: 0.9046 (tmm-80) cc_final: 0.8572 (tmm-80) REVERT: E 280 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8422 (mtmm) REVERT: E 326 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8922 (ttpt) REVERT: E 361 THR cc_start: 0.9083 (m) cc_final: 0.8696 (t) REVERT: E 377 MET cc_start: 0.9011 (ttp) cc_final: 0.8250 (tmm) REVERT: E 398 MET cc_start: 0.9048 (mtp) cc_final: 0.8770 (ttm) REVERT: F 41 ASP cc_start: 0.8764 (p0) cc_final: 0.8438 (p0) REVERT: F 147 MET cc_start: 0.9012 (tpp) cc_final: 0.8784 (tpp) REVERT: F 168 SER cc_start: 0.9403 (p) cc_final: 0.9059 (p) REVERT: F 174 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8902 (mtmt) REVERT: F 205 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8433 (mp0) REVERT: F 252 LYS cc_start: 0.9307 (mtpp) cc_final: 0.9077 (ttmm) REVERT: F 257 MET cc_start: 0.8903 (mmp) cc_final: 0.8292 (mmt) REVERT: F 291 GLN cc_start: 0.8638 (pp30) cc_final: 0.8305 (pp30) REVERT: F 307 HIS cc_start: 0.9401 (m-70) cc_final: 0.9194 (m-70) REVERT: F 375 GLN cc_start: 0.8276 (pp30) cc_final: 0.7827 (pp30) REVERT: F 376 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7993 (mt-10) REVERT: F 406 MET cc_start: 0.8277 (tmm) cc_final: 0.7951 (tmm) REVERT: G 53 GLU cc_start: 0.8574 (tp30) cc_final: 0.7806 (tp30) REVERT: G 164 MET cc_start: 0.8623 (ttm) cc_final: 0.8055 (mtp) REVERT: G 282 ARG cc_start: 0.7845 (ptm-80) cc_final: 0.7610 (ptm-80) REVERT: G 284 LEU cc_start: 0.8911 (mt) cc_final: 0.8612 (mt) REVERT: G 292 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: G 304 ASP cc_start: 0.8956 (t0) cc_final: 0.8714 (t0) REVERT: G 307 HIS cc_start: 0.9454 (m-70) cc_final: 0.9020 (m170) REVERT: G 362 LYS cc_start: 0.8644 (tmmt) cc_final: 0.8249 (tmmt) REVERT: G 375 GLN cc_start: 0.8819 (pt0) cc_final: 0.7628 (pp30) REVERT: G 406 MET cc_start: 0.8389 (tpt) cc_final: 0.7794 (tpt) REVERT: G 407 GLU cc_start: 0.8472 (pt0) cc_final: 0.7555 (pt0) REVERT: G 410 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8471 (mt-10) REVERT: G 412 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8162 (tp30) REVERT: G 416 ASN cc_start: 0.9260 (m-40) cc_final: 0.8942 (m-40) REVERT: G 421 GLU cc_start: 0.8402 (tp30) cc_final: 0.8106 (tp30) REVERT: G 425 TYR cc_start: 0.8071 (m-10) cc_final: 0.7245 (m-10) REVERT: H 50 TYR cc_start: 0.8896 (m-10) cc_final: 0.8563 (m-10) REVERT: H 209 ASP cc_start: 0.9100 (t0) cc_final: 0.8813 (t70) REVERT: H 213 ARG cc_start: 0.8873 (ttm110) cc_final: 0.8416 (ttp-110) REVERT: H 304 ASP cc_start: 0.9118 (t0) cc_final: 0.8527 (t0) REVERT: H 307 HIS cc_start: 0.9373 (m-70) cc_final: 0.8975 (m-70) REVERT: H 331 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9148 (tp) REVERT: H 362 LYS cc_start: 0.8749 (pptt) cc_final: 0.8435 (pptt) REVERT: H 363 MET cc_start: 0.8793 (ptt) cc_final: 0.8242 (ptt) REVERT: H 375 GLN cc_start: 0.8788 (pt0) cc_final: 0.8298 (pp30) REVERT: H 383 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8366 (tm-30) REVERT: H 421 GLU cc_start: 0.8311 (tp30) cc_final: 0.7938 (tp30) REVERT: H 425 TYR cc_start: 0.7888 (m-10) cc_final: 0.7273 (m-10) REVERT: I 194 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7620 (mm-30) REVERT: I 198 GLU cc_start: 0.9000 (pt0) cc_final: 0.8667 (pt0) REVERT: I 203 ASP cc_start: 0.7883 (t0) cc_final: 0.7547 (t0) REVERT: I 209 ASP cc_start: 0.9112 (t0) cc_final: 0.8881 (t0) REVERT: I 213 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8210 (ttp80) REVERT: I 299 MET cc_start: 0.8952 (tpp) cc_final: 0.8108 (mpp) REVERT: I 304 ASP cc_start: 0.9136 (t0) cc_final: 0.8894 (t70) REVERT: I 325 GLU cc_start: 0.9029 (tt0) cc_final: 0.8763 (tt0) REVERT: I 329 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8716 (mm-40) REVERT: I 362 LYS cc_start: 0.8945 (tmmt) cc_final: 0.8629 (tmmt) REVERT: I 406 MET cc_start: 0.8301 (tpt) cc_final: 0.8039 (tpt) REVERT: I 423 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8496 (tp-100) REVERT: J 88 HIS cc_start: 0.8756 (t70) cc_final: 0.8199 (t70) REVERT: J 90 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8615 (mm-30) REVERT: J 128 GLN cc_start: 0.7974 (pp30) cc_final: 0.7678 (pp30) REVERT: J 150 THR cc_start: 0.9460 (m) cc_final: 0.9175 (p) REVERT: J 155 GLU cc_start: 0.9418 (mt-10) cc_final: 0.8908 (mt-10) REVERT: J 161 TYR cc_start: 0.8526 (m-10) cc_final: 0.8263 (m-10) REVERT: J 163 LYS cc_start: 0.7319 (mmpt) cc_final: 0.7097 (mmpt) REVERT: J 170 SER cc_start: 0.9160 (m) cc_final: 0.8614 (t) REVERT: J 203 MET cc_start: 0.8904 (mmm) cc_final: 0.8635 (mmm) REVERT: J 214 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7949 (ttp80) REVERT: J 293 ASN cc_start: 0.9654 (m-40) cc_final: 0.9322 (m-40) REVERT: J 306 ASP cc_start: 0.8899 (p0) cc_final: 0.8482 (p0) REVERT: J 308 ARG cc_start: 0.9443 (mtm110) cc_final: 0.9059 (mtm-85) REVERT: J 309 HIS cc_start: 0.8851 (m170) cc_final: 0.8563 (m170) REVERT: J 313 MET cc_start: 0.8390 (mpp) cc_final: 0.7830 (mtm) REVERT: J 357 TYR cc_start: 0.9125 (m-80) cc_final: 0.8362 (m-80) REVERT: J 377 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8652 (ttm) REVERT: J 388 TRP cc_start: 0.9107 (m100) cc_final: 0.8547 (m100) REVERT: J 396 ASP cc_start: 0.8569 (m-30) cc_final: 0.8355 (m-30) REVERT: J 413 MET cc_start: 0.8567 (mtp) cc_final: 0.8217 (ttm) REVERT: J 420 GLU cc_start: 0.9142 (pt0) cc_final: 0.8764 (pt0) REVERT: K 1 MET cc_start: 0.6662 (tmm) cc_final: 0.6391 (tmm) REVERT: K 108 TYR cc_start: 0.8790 (m-80) cc_final: 0.8458 (m-10) REVERT: K 150 THR cc_start: 0.9391 (m) cc_final: 0.9100 (p) REVERT: K 155 GLU cc_start: 0.9090 (pt0) cc_final: 0.8801 (pt0) REVERT: K 166 LYS cc_start: 0.8302 (ptpt) cc_final: 0.7583 (pttt) REVERT: K 204 VAL cc_start: 0.8915 (t) cc_final: 0.8617 (p) REVERT: K 205 ASP cc_start: 0.8205 (t0) cc_final: 0.7873 (t0) REVERT: K 214 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8174 (ttp80) REVERT: K 286 LEU cc_start: 0.9115 (mp) cc_final: 0.8819 (pp) REVERT: K 290 GLU cc_start: 0.9364 (pt0) cc_final: 0.8983 (pt0) REVERT: K 313 MET cc_start: 0.9129 (mtm) cc_final: 0.8597 (mtm) REVERT: L 22 GLU cc_start: 0.9171 (pt0) cc_final: 0.8910 (pt0) REVERT: L 76 ASP cc_start: 0.9364 (m-30) cc_final: 0.9162 (m-30) REVERT: L 84 ARG cc_start: 0.9171 (ttp-110) cc_final: 0.8763 (ttm110) REVERT: L 124 LYS cc_start: 0.9563 (mtpt) cc_final: 0.9327 (mtpp) REVERT: L 150 THR cc_start: 0.9508 (m) cc_final: 0.9243 (p) REVERT: L 155 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8819 (mt-10) REVERT: L 156 ARG cc_start: 0.9107 (mmp80) cc_final: 0.8809 (mmp80) REVERT: L 214 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8202 (ttp80) REVERT: L 286 LEU cc_start: 0.9243 (mt) cc_final: 0.9002 (pp) REVERT: L 290 GLU cc_start: 0.9381 (tt0) cc_final: 0.9008 (mt-10) REVERT: L 293 ASN cc_start: 0.9483 (m110) cc_final: 0.9085 (p0) REVERT: L 308 ARG cc_start: 0.9205 (mtm-85) cc_final: 0.8884 (mtm-85) REVERT: L 313 MET cc_start: 0.8597 (mpp) cc_final: 0.8195 (mtm) REVERT: L 361 THR cc_start: 0.8605 (m) cc_final: 0.8254 (p) REVERT: L 396 ASP cc_start: 0.8621 (m-30) cc_final: 0.8392 (m-30) REVERT: M 14 ASN cc_start: 0.7958 (p0) cc_final: 0.7740 (p0) REVERT: M 29 HIS cc_start: 0.9183 (t-90) cc_final: 0.8735 (t-90) REVERT: M 57 HIS cc_start: 0.7853 (t-170) cc_final: 0.6593 (t70) REVERT: M 60 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7874 (mmtt) REVERT: M 84 LYS cc_start: 0.9417 (ttmt) cc_final: 0.9168 (ttpt) REVERT: M 100 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7744 (mmtp) REVERT: M 110 TRP cc_start: 0.9391 (t60) cc_final: 0.9172 (t60) REVERT: M 118 ASN cc_start: 0.7786 (m-40) cc_final: 0.7255 (m110) REVERT: N 29 HIS cc_start: 0.9156 (t-90) cc_final: 0.8700 (t-90) REVERT: N 84 LYS cc_start: 0.9294 (ttmt) cc_final: 0.8776 (ttpt) REVERT: N 100 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7576 (mmtt) REVERT: N 114 PHE cc_start: 0.9052 (t80) cc_final: 0.8767 (t80) REVERT: N 118 ASN cc_start: 0.8061 (m-40) cc_final: 0.7545 (m110) outliers start: 148 outliers final: 90 residues processed: 1597 average time/residue: 0.2864 time to fit residues: 741.5676 Evaluate side-chains 1526 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 1425 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain H residue 83 HIS Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 376 GLU Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 334 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 128 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 472 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 498 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN C 61 HIS D 35 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 15 GLN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 ASN ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 89 ASN H 245 GLN H 292 GLN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 57 HIS I 165 ASN I 227 HIS ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 HIS ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS N 57 HIS N 104 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.091436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072045 restraints weight = 104195.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074478 restraints weight = 57386.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076208 restraints weight = 37518.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077360 restraints weight = 27573.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078151 restraints weight = 22240.983| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 44232 Z= 0.233 Angle : 0.653 11.016 60052 Z= 0.335 Chirality : 0.046 0.203 6552 Planarity : 0.004 0.062 7788 Dihedral : 11.940 179.418 6073 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 4.60 % Allowed : 18.65 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 5394 helix: 1.60 (0.11), residues: 2530 sheet: 0.51 (0.19), residues: 774 loop : -1.03 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 77 TYR 0.020 0.002 TYR E 172 PHE 0.023 0.002 PHE D 260 TRP 0.016 0.002 TRP I 344 HIS 0.023 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00515 (44232) covalent geometry : angle 0.65273 (60052) hydrogen bonds : bond 0.04232 ( 2164) hydrogen bonds : angle 4.61620 ( 6381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1673 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 1459 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 211 ASP cc_start: 0.8776 (t70) cc_final: 0.8365 (t70) REVERT: A 215 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8355 (ttp80) REVERT: A 218 ASP cc_start: 0.8833 (m-30) cc_final: 0.8504 (m-30) REVERT: A 300 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8382 (t0) REVERT: A 324 VAL cc_start: 0.8978 (t) cc_final: 0.8517 (t) REVERT: A 327 ASP cc_start: 0.9037 (m-30) cc_final: 0.8825 (m-30) REVERT: A 335 ILE cc_start: 0.9792 (OUTLIER) cc_final: 0.9523 (tp) REVERT: A 361 THR cc_start: 0.9223 (m) cc_final: 0.8810 (t) REVERT: A 377 MET cc_start: 0.9036 (tmm) cc_final: 0.8561 (tmm) REVERT: A 430 LYS cc_start: 0.9257 (ttpp) cc_final: 0.9011 (pttm) REVERT: B 22 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7759 (mt-10) REVERT: B 41 ASP cc_start: 0.8596 (p0) cc_final: 0.8236 (p0) REVERT: B 124 CYS cc_start: 0.8859 (m) cc_final: 0.8405 (p) REVERT: B 161 ASP cc_start: 0.8909 (p0) cc_final: 0.8615 (p0) REVERT: B 164 MET cc_start: 0.7044 (pmm) cc_final: 0.6644 (pmm) REVERT: B 213 ARG cc_start: 0.8726 (ttm170) cc_final: 0.8525 (mtm110) REVERT: B 252 LYS cc_start: 0.9167 (mtpp) cc_final: 0.8881 (mtpp) REVERT: B 282 ARG cc_start: 0.7727 (tmm-80) cc_final: 0.7380 (ttp80) REVERT: B 307 HIS cc_start: 0.9332 (m-70) cc_final: 0.9002 (m90) REVERT: B 320 ARG cc_start: 0.8428 (mmm160) cc_final: 0.8128 (mmp80) REVERT: B 329 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8696 (mm-40) REVERT: B 367 PHE cc_start: 0.9429 (t80) cc_final: 0.9136 (t80) REVERT: B 375 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7800 (pp30) REVERT: C 3 GLU cc_start: 0.8093 (mp0) cc_final: 0.7555 (mp0) REVERT: C 124 LYS cc_start: 0.9369 (ttmm) cc_final: 0.8925 (ttmm) REVERT: C 150 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9205 (m) REVERT: C 215 ARG cc_start: 0.8561 (mtm110) cc_final: 0.8233 (mtm-85) REVERT: C 218 ASP cc_start: 0.9177 (m-30) cc_final: 0.8766 (m-30) REVERT: C 256 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: C 280 LYS cc_start: 0.4540 (mmtt) cc_final: 0.3667 (mtmm) REVERT: C 304 LYS cc_start: 0.9118 (tppt) cc_final: 0.8734 (tppt) REVERT: C 319 TYR cc_start: 0.8971 (m-80) cc_final: 0.8766 (m-80) REVERT: C 377 MET cc_start: 0.8618 (ttp) cc_final: 0.7646 (tmm) REVERT: C 378 LEU cc_start: 0.9534 (mt) cc_final: 0.9118 (mt) REVERT: C 414 GLU cc_start: 0.8687 (mp0) cc_final: 0.8473 (mp0) REVERT: D 19 LYS cc_start: 0.8838 (tptt) cc_final: 0.8546 (tptp) REVERT: D 41 ASP cc_start: 0.8689 (p0) cc_final: 0.8354 (p0) REVERT: D 124 CYS cc_start: 0.8922 (m) cc_final: 0.8580 (p) REVERT: D 164 MET cc_start: 0.7627 (ptp) cc_final: 0.7258 (pmm) REVERT: D 213 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8615 (mtm110) REVERT: D 252 LYS cc_start: 0.9173 (mtpp) cc_final: 0.8692 (ttmm) REVERT: D 323 MET cc_start: 0.8225 (mmp) cc_final: 0.7981 (mmp) REVERT: D 327 ASP cc_start: 0.8993 (m-30) cc_final: 0.8713 (m-30) REVERT: D 375 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.6748 (pp30) REVERT: D 379 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8802 (mtmt) REVERT: D 423 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8476 (tp-100) REVERT: E 22 GLU cc_start: 0.8780 (pt0) cc_final: 0.8449 (pt0) REVERT: E 88 HIS cc_start: 0.8788 (t70) cc_final: 0.8330 (t-170) REVERT: E 90 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 214 ARG cc_start: 0.9095 (tmm-80) cc_final: 0.8586 (tmm-80) REVERT: E 230 LEU cc_start: 0.9608 (mp) cc_final: 0.9372 (mp) REVERT: E 280 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8644 (mtmm) REVERT: E 361 THR cc_start: 0.9205 (m) cc_final: 0.8856 (t) REVERT: E 377 MET cc_start: 0.9053 (ttp) cc_final: 0.8272 (tmm) REVERT: E 392 ASP cc_start: 0.8998 (m-30) cc_final: 0.8679 (m-30) REVERT: E 396 ASP cc_start: 0.8708 (m-30) cc_final: 0.8410 (m-30) REVERT: E 398 MET cc_start: 0.9137 (mtp) cc_final: 0.8832 (ttm) REVERT: E 430 LYS cc_start: 0.9440 (ttpt) cc_final: 0.9233 (ttpp) REVERT: E 438 ASP cc_start: 0.8709 (t0) cc_final: 0.8158 (t0) REVERT: F 41 ASP cc_start: 0.8826 (p0) cc_final: 0.8473 (p0) REVERT: F 50 TYR cc_start: 0.8932 (m-10) cc_final: 0.8716 (m-80) REVERT: F 108 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8098 (tp30) REVERT: F 168 SER cc_start: 0.9444 (p) cc_final: 0.9189 (p) REVERT: F 257 MET cc_start: 0.8956 (mmp) cc_final: 0.8589 (mmt) REVERT: F 266 PHE cc_start: 0.8982 (m-10) cc_final: 0.8631 (m-10) REVERT: F 291 GLN cc_start: 0.8767 (pp30) cc_final: 0.8468 (pp30) REVERT: F 307 HIS cc_start: 0.9435 (m-70) cc_final: 0.9165 (m-70) REVERT: F 321 MET cc_start: 0.8150 (pmm) cc_final: 0.7837 (pmm) REVERT: F 327 ASP cc_start: 0.8942 (m-30) cc_final: 0.8700 (m-30) REVERT: F 363 MET cc_start: 0.8927 (ptt) cc_final: 0.8609 (ptt) REVERT: F 375 GLN cc_start: 0.8106 (pp30) cc_final: 0.7734 (pp30) REVERT: G 164 MET cc_start: 0.8578 (ttm) cc_final: 0.8043 (mtp) REVERT: G 197 ASP cc_start: 0.8723 (m-30) cc_final: 0.8490 (m-30) REVERT: G 203 ASP cc_start: 0.8014 (t70) cc_final: 0.7602 (t0) REVERT: G 266 PHE cc_start: 0.9157 (m-10) cc_final: 0.8933 (m-10) REVERT: G 282 ARG cc_start: 0.7873 (ptm-80) cc_final: 0.7600 (ptm-80) REVERT: G 284 LEU cc_start: 0.9081 (mt) cc_final: 0.8547 (mt) REVERT: G 292 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: G 307 HIS cc_start: 0.9491 (m-70) cc_final: 0.9061 (m170) REVERT: G 362 LYS cc_start: 0.8727 (tmmt) cc_final: 0.8494 (tmmt) REVERT: G 407 GLU cc_start: 0.8458 (pt0) cc_final: 0.8231 (pt0) REVERT: G 416 ASN cc_start: 0.9266 (m-40) cc_final: 0.9062 (m-40) REVERT: G 421 GLU cc_start: 0.8388 (tp30) cc_final: 0.8115 (tp30) REVERT: G 427 ASP cc_start: 0.8362 (p0) cc_final: 0.8142 (p0) REVERT: H 45 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: H 164 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8401 (mtt) REVERT: H 209 ASP cc_start: 0.9134 (t0) cc_final: 0.8870 (t70) REVERT: H 213 ARG cc_start: 0.8874 (ttm110) cc_final: 0.8438 (ttp-110) REVERT: H 282 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7457 (ptm-80) REVERT: H 304 ASP cc_start: 0.9083 (t0) cc_final: 0.8621 (t0) REVERT: H 307 HIS cc_start: 0.9419 (m-70) cc_final: 0.9104 (m-70) REVERT: H 362 LYS cc_start: 0.8779 (pptt) cc_final: 0.8492 (pptt) REVERT: H 375 GLN cc_start: 0.8852 (pt0) cc_final: 0.8326 (pp30) REVERT: H 383 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8430 (tm-30) REVERT: I 14 ASN cc_start: 0.9029 (m-40) cc_final: 0.8806 (m110) REVERT: I 51 TYR cc_start: 0.9177 (m-80) cc_final: 0.8886 (m-80) REVERT: I 194 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7722 (mm-30) REVERT: I 203 ASP cc_start: 0.8193 (t0) cc_final: 0.7934 (t0) REVERT: I 213 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8445 (tmm-80) REVERT: I 293 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8220 (mtt) REVERT: I 299 MET cc_start: 0.9003 (tpp) cc_final: 0.8066 (mpp) REVERT: I 315 THR cc_start: 0.9700 (m) cc_final: 0.9249 (p) REVERT: I 325 GLU cc_start: 0.9092 (tt0) cc_final: 0.8852 (tt0) REVERT: I 329 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8673 (mm-40) REVERT: I 362 LYS cc_start: 0.8906 (tmmt) cc_final: 0.8507 (ttpp) REVERT: I 363 MET cc_start: 0.8996 (ptt) cc_final: 0.8746 (ptt) REVERT: I 406 MET cc_start: 0.8376 (tpt) cc_final: 0.7718 (tpp) REVERT: I 423 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8426 (tp40) REVERT: I 427 ASP cc_start: 0.8011 (p0) cc_final: 0.7762 (p0) REVERT: J 67 PHE cc_start: 0.8730 (m-80) cc_final: 0.8518 (m-10) REVERT: J 88 HIS cc_start: 0.8846 (t70) cc_final: 0.8209 (t70) REVERT: J 90 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8704 (mm-30) REVERT: J 128 GLN cc_start: 0.8040 (pp30) cc_final: 0.7763 (pp30) REVERT: J 155 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9004 (mt-10) REVERT: J 156 ARG cc_start: 0.8890 (mmp80) cc_final: 0.8667 (mmp80) REVERT: J 168 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8118 (mt-10) REVERT: J 170 SER cc_start: 0.9153 (m) cc_final: 0.8709 (t) REVERT: J 214 ARG cc_start: 0.8410 (ttp80) cc_final: 0.8006 (ttp80) REVERT: J 293 ASN cc_start: 0.9630 (m-40) cc_final: 0.9321 (m-40) REVERT: J 308 ARG cc_start: 0.9437 (mtm110) cc_final: 0.9070 (mtm-85) REVERT: J 313 MET cc_start: 0.8461 (mpp) cc_final: 0.7912 (mtm) REVERT: J 388 TRP cc_start: 0.9093 (m100) cc_final: 0.8782 (m100) REVERT: J 396 ASP cc_start: 0.8622 (m-30) cc_final: 0.8374 (m-30) REVERT: J 413 MET cc_start: 0.8759 (mtp) cc_final: 0.8404 (ttm) REVERT: K 96 LYS cc_start: 0.9112 (mmmt) cc_final: 0.8877 (mmmt) REVERT: K 108 TYR cc_start: 0.8777 (m-80) cc_final: 0.8478 (m-10) REVERT: K 150 THR cc_start: 0.9350 (m) cc_final: 0.9049 (p) REVERT: K 155 GLU cc_start: 0.9173 (pt0) cc_final: 0.8897 (pt0) REVERT: K 172 TYR cc_start: 0.8132 (t80) cc_final: 0.7425 (t80) REVERT: K 203 MET cc_start: 0.8855 (mmm) cc_final: 0.8319 (mmm) REVERT: K 205 ASP cc_start: 0.8158 (t0) cc_final: 0.7679 (t0) REVERT: K 214 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8234 (ttp80) REVERT: K 290 GLU cc_start: 0.9408 (pt0) cc_final: 0.8988 (pt0) REVERT: K 293 ASN cc_start: 0.9471 (m110) cc_final: 0.9264 (p0) REVERT: K 313 MET cc_start: 0.9134 (mtm) cc_final: 0.8693 (mtm) REVERT: K 336 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8865 (mmmm) REVERT: L 22 GLU cc_start: 0.9156 (pt0) cc_final: 0.8902 (pt0) REVERT: L 76 ASP cc_start: 0.9378 (m-30) cc_final: 0.9166 (m-30) REVERT: L 150 THR cc_start: 0.9500 (m) cc_final: 0.9232 (p) REVERT: L 155 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8756 (mt-10) REVERT: L 156 ARG cc_start: 0.9155 (mmp80) cc_final: 0.8866 (mmp80) REVERT: L 205 ASP cc_start: 0.8394 (t70) cc_final: 0.8054 (t0) REVERT: L 214 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8208 (ttp80) REVERT: L 286 LEU cc_start: 0.9280 (mt) cc_final: 0.9017 (pp) REVERT: L 290 GLU cc_start: 0.9391 (tt0) cc_final: 0.9130 (mt-10) REVERT: L 313 MET cc_start: 0.8616 (mpp) cc_final: 0.8271 (mtm) REVERT: L 361 THR cc_start: 0.8664 (m) cc_final: 0.8206 (p) REVERT: L 377 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8738 (ttm) REVERT: L 388 TRP cc_start: 0.9194 (m100) cc_final: 0.8994 (m100) REVERT: L 396 ASP cc_start: 0.8698 (m-30) cc_final: 0.8479 (m-30) REVERT: L 413 MET cc_start: 0.8515 (ttm) cc_final: 0.8106 (ttm) REVERT: L 425 MET cc_start: 0.9062 (tpp) cc_final: 0.8656 (tpt) REVERT: L 430 LYS cc_start: 0.9487 (ptmm) cc_final: 0.9272 (pttm) REVERT: M 14 ASN cc_start: 0.8019 (p0) cc_final: 0.7602 (p0) REVERT: M 20 MET cc_start: 0.9121 (mtt) cc_final: 0.8852 (mtp) REVERT: M 29 HIS cc_start: 0.9160 (t-90) cc_final: 0.8659 (t-90) REVERT: M 57 HIS cc_start: 0.7854 (t-170) cc_final: 0.6769 (t70) REVERT: M 60 LYS cc_start: 0.8349 (mmtm) cc_final: 0.7921 (mmtt) REVERT: M 84 LYS cc_start: 0.9416 (ttmt) cc_final: 0.9164 (ttpt) REVERT: M 112 LYS cc_start: 0.9199 (tptp) cc_final: 0.8780 (tppt) REVERT: M 118 ASN cc_start: 0.7816 (m-40) cc_final: 0.7507 (m110) REVERT: N 29 HIS cc_start: 0.9135 (t-90) cc_final: 0.8670 (t-90) REVERT: N 84 LYS cc_start: 0.9302 (ttmt) cc_final: 0.8768 (ttpt) REVERT: N 100 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7476 (mmtp) REVERT: N 104 ASN cc_start: 0.8426 (m-40) cc_final: 0.8164 (m110) REVERT: N 118 ASN cc_start: 0.7961 (m-40) cc_final: 0.7353 (m110) outliers start: 214 outliers final: 134 residues processed: 1539 average time/residue: 0.2689 time to fit residues: 671.9529 Evaluate side-chains 1473 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1326 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 334 THR Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 377 MET Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 67 optimal weight: 20.0000 chunk 465 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 428 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 478 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 423 GLN E 41 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 126 ASN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 227 HIS I 291 GLN ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS L 8 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 285 GLN N 14 ASN N 57 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071702 restraints weight = 103187.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074156 restraints weight = 56067.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075871 restraints weight = 36721.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077001 restraints weight = 27085.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077781 restraints weight = 21910.555| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 44232 Z= 0.191 Angle : 0.636 12.340 60052 Z= 0.326 Chirality : 0.045 0.182 6552 Planarity : 0.004 0.056 7788 Dihedral : 11.899 177.155 6071 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 4.24 % Allowed : 20.27 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 5394 helix: 1.64 (0.11), residues: 2536 sheet: 0.58 (0.19), residues: 774 loop : -1.01 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 77 TYR 0.017 0.001 TYR D 340 PHE 0.022 0.001 PHE D 260 TRP 0.018 0.002 TRP A 21 HIS 0.013 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00425 (44232) covalent geometry : angle 0.63622 (60052) hydrogen bonds : bond 0.04095 ( 2164) hydrogen bonds : angle 4.58656 ( 6381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 1413 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8817 (t70) cc_final: 0.8333 (t70) REVERT: A 215 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8285 (ttp80) REVERT: A 218 ASP cc_start: 0.8860 (m-30) cc_final: 0.8550 (m-30) REVERT: A 324 VAL cc_start: 0.8986 (t) cc_final: 0.8509 (t) REVERT: A 361 THR cc_start: 0.9236 (m) cc_final: 0.8823 (t) REVERT: A 377 MET cc_start: 0.9008 (tmm) cc_final: 0.8489 (tmm) REVERT: B 19 LYS cc_start: 0.8817 (tptm) cc_final: 0.8428 (tptm) REVERT: B 41 ASP cc_start: 0.8584 (p0) cc_final: 0.8209 (p0) REVERT: B 161 ASP cc_start: 0.8926 (p0) cc_final: 0.8613 (p0) REVERT: B 164 MET cc_start: 0.7091 (pmm) cc_final: 0.6676 (pmm) REVERT: B 213 ARG cc_start: 0.8675 (ttm170) cc_final: 0.8011 (mtm110) REVERT: B 297 LYS cc_start: 0.8861 (pttt) cc_final: 0.8604 (tttt) REVERT: B 298 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8777 (t0) REVERT: B 299 MET cc_start: 0.8721 (mmm) cc_final: 0.8340 (mmm) REVERT: B 329 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8667 (mm-40) REVERT: B 331 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9253 (tp) REVERT: B 375 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8003 (pp30) REVERT: B 424 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.9009 (tm-30) REVERT: C 215 ARG cc_start: 0.8623 (mtm110) cc_final: 0.8353 (mtm-85) REVERT: C 218 ASP cc_start: 0.9150 (m-30) cc_final: 0.8636 (m-30) REVERT: C 256 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8720 (tt0) REVERT: C 280 LYS cc_start: 0.4633 (mmtt) cc_final: 0.3545 (mtmm) REVERT: C 300 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8637 (t0) REVERT: C 304 LYS cc_start: 0.9088 (tppt) cc_final: 0.8641 (tppt) REVERT: C 393 HIS cc_start: 0.8781 (t70) cc_final: 0.8412 (t70) REVERT: C 414 GLU cc_start: 0.8666 (mp0) cc_final: 0.8411 (mp0) REVERT: D 19 LYS cc_start: 0.8827 (tptt) cc_final: 0.8567 (mmmt) REVERT: D 41 ASP cc_start: 0.8691 (p0) cc_final: 0.8376 (p0) REVERT: D 124 CYS cc_start: 0.8899 (m) cc_final: 0.8632 (p) REVERT: D 164 MET cc_start: 0.7489 (ptp) cc_final: 0.7243 (pmm) REVERT: D 213 ARG cc_start: 0.8839 (ttm110) cc_final: 0.8616 (mtm110) REVERT: D 252 LYS cc_start: 0.9194 (mtpp) cc_final: 0.8830 (ttmm) REVERT: D 323 MET cc_start: 0.8420 (mmp) cc_final: 0.8135 (mmp) REVERT: D 327 ASP cc_start: 0.8966 (m-30) cc_final: 0.8673 (m-30) REVERT: D 375 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.6682 (pp30) REVERT: D 379 LYS cc_start: 0.9283 (mtmt) cc_final: 0.8919 (mtmt) REVERT: D 423 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8973 (mm-40) REVERT: E 22 GLU cc_start: 0.8719 (pt0) cc_final: 0.8388 (pt0) REVERT: E 88 HIS cc_start: 0.8670 (t70) cc_final: 0.8221 (t-170) REVERT: E 90 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8331 (mm-30) REVERT: E 214 ARG cc_start: 0.9118 (tmm-80) cc_final: 0.8568 (tmm-80) REVERT: E 230 LEU cc_start: 0.9610 (mp) cc_final: 0.9403 (mp) REVERT: E 326 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8977 (ttpt) REVERT: E 361 THR cc_start: 0.9213 (m) cc_final: 0.8908 (t) REVERT: E 377 MET cc_start: 0.9023 (ttp) cc_final: 0.8197 (tmm) REVERT: E 392 ASP cc_start: 0.8930 (m-30) cc_final: 0.8634 (m-30) REVERT: E 396 ASP cc_start: 0.8718 (m-30) cc_final: 0.8365 (m-30) REVERT: E 430 LYS cc_start: 0.9445 (ttpt) cc_final: 0.9242 (ttpp) REVERT: E 438 ASP cc_start: 0.8636 (t0) cc_final: 0.8161 (t0) REVERT: F 41 ASP cc_start: 0.8846 (p0) cc_final: 0.8517 (p0) REVERT: F 50 TYR cc_start: 0.8941 (m-10) cc_final: 0.8736 (m-10) REVERT: F 86 ARG cc_start: 0.5156 (mmt180) cc_final: 0.4240 (tpt170) REVERT: F 164 MET cc_start: 0.7714 (pmm) cc_final: 0.7456 (pmm) REVERT: F 168 SER cc_start: 0.9418 (p) cc_final: 0.9092 (p) REVERT: F 213 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7967 (ttp80) REVERT: F 252 LYS cc_start: 0.9299 (mtpp) cc_final: 0.9071 (ttmm) REVERT: F 257 MET cc_start: 0.8873 (mmp) cc_final: 0.8625 (mmt) REVERT: F 266 PHE cc_start: 0.8962 (m-10) cc_final: 0.8423 (m-10) REVERT: F 291 GLN cc_start: 0.8767 (pp30) cc_final: 0.8468 (pp30) REVERT: F 307 HIS cc_start: 0.9422 (m-70) cc_final: 0.9187 (m-70) REVERT: F 321 MET cc_start: 0.8311 (pmm) cc_final: 0.7872 (pmm) REVERT: F 323 MET cc_start: 0.8558 (mmt) cc_final: 0.7956 (mmt) REVERT: F 327 ASP cc_start: 0.8923 (m-30) cc_final: 0.8611 (m-30) REVERT: F 375 GLN cc_start: 0.7952 (pp30) cc_final: 0.7582 (pp30) REVERT: G 164 MET cc_start: 0.8533 (ttm) cc_final: 0.8000 (mtp) REVERT: G 180 VAL cc_start: 0.9504 (m) cc_final: 0.9237 (p) REVERT: G 197 ASP cc_start: 0.8757 (m-30) cc_final: 0.8499 (m-30) REVERT: G 203 ASP cc_start: 0.8009 (t70) cc_final: 0.7744 (t70) REVERT: G 284 LEU cc_start: 0.9099 (mt) cc_final: 0.8799 (mt) REVERT: G 293 MET cc_start: 0.8731 (tpp) cc_final: 0.8092 (mtt) REVERT: G 307 HIS cc_start: 0.9482 (m-70) cc_final: 0.9119 (m170) REVERT: H 45 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: H 50 TYR cc_start: 0.8926 (m-10) cc_final: 0.8708 (m-10) REVERT: H 164 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: H 213 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8421 (ttp80) REVERT: H 304 ASP cc_start: 0.9003 (t0) cc_final: 0.8600 (t0) REVERT: H 307 HIS cc_start: 0.9434 (m-70) cc_final: 0.9163 (m-70) REVERT: H 362 LYS cc_start: 0.8761 (pptt) cc_final: 0.8332 (pptt) REVERT: H 363 MET cc_start: 0.8891 (ptt) cc_final: 0.7919 (ptt) REVERT: H 375 GLN cc_start: 0.8805 (pt0) cc_final: 0.8260 (pp30) REVERT: H 423 GLN cc_start: 0.8759 (tp40) cc_final: 0.8149 (tp-100) REVERT: H 427 ASP cc_start: 0.7890 (p0) cc_final: 0.7608 (p0) REVERT: I 14 ASN cc_start: 0.9059 (m-40) cc_final: 0.8838 (m110) REVERT: I 203 ASP cc_start: 0.8279 (t0) cc_final: 0.7937 (t0) REVERT: I 213 ARG cc_start: 0.8881 (ttm110) cc_final: 0.8470 (ttp80) REVERT: I 293 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8302 (mtt) REVERT: I 299 MET cc_start: 0.9012 (tpp) cc_final: 0.8189 (mpp) REVERT: I 303 CYS cc_start: 0.8553 (p) cc_final: 0.8124 (p) REVERT: I 315 THR cc_start: 0.9710 (m) cc_final: 0.9227 (p) REVERT: I 329 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8643 (mm-40) REVERT: I 362 LYS cc_start: 0.8929 (tmmt) cc_final: 0.8503 (ttpp) REVERT: I 363 MET cc_start: 0.8931 (ptt) cc_final: 0.8667 (ptt) REVERT: I 406 MET cc_start: 0.8418 (tpt) cc_final: 0.7680 (tpp) REVERT: I 423 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8199 (tp-100) REVERT: I 427 ASP cc_start: 0.8017 (p0) cc_final: 0.7562 (p0) REVERT: J 67 PHE cc_start: 0.8667 (m-80) cc_final: 0.8453 (m-10) REVERT: J 88 HIS cc_start: 0.8878 (t70) cc_final: 0.8247 (t70) REVERT: J 90 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8780 (mm-30) REVERT: J 128 GLN cc_start: 0.8006 (pp30) cc_final: 0.7756 (pp30) REVERT: J 150 THR cc_start: 0.9309 (m) cc_final: 0.9063 (p) REVERT: J 155 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8994 (mt-10) REVERT: J 156 ARG cc_start: 0.8911 (mmp80) cc_final: 0.8675 (mmp80) REVERT: J 168 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8081 (mt-10) REVERT: J 205 ASP cc_start: 0.8175 (t0) cc_final: 0.7936 (t0) REVERT: J 207 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8875 (mm-30) REVERT: J 214 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8026 (ttp80) REVERT: J 290 GLU cc_start: 0.9290 (pt0) cc_final: 0.8879 (pp20) REVERT: J 293 ASN cc_start: 0.9629 (m-40) cc_final: 0.9310 (m-40) REVERT: J 313 MET cc_start: 0.8451 (mpp) cc_final: 0.7925 (mtm) REVERT: J 357 TYR cc_start: 0.9128 (m-80) cc_final: 0.8220 (m-80) REVERT: J 396 ASP cc_start: 0.8601 (m-30) cc_final: 0.8369 (m-30) REVERT: J 420 GLU cc_start: 0.8805 (pt0) cc_final: 0.8308 (pm20) REVERT: J 425 MET cc_start: 0.9079 (tpp) cc_final: 0.8633 (tpt) REVERT: K 108 TYR cc_start: 0.8729 (m-80) cc_final: 0.8479 (m-10) REVERT: K 150 THR cc_start: 0.9355 (m) cc_final: 0.9031 (p) REVERT: K 155 GLU cc_start: 0.9107 (pt0) cc_final: 0.8719 (pt0) REVERT: K 172 TYR cc_start: 0.8168 (t80) cc_final: 0.7556 (t80) REVERT: K 203 MET cc_start: 0.8883 (mmm) cc_final: 0.8365 (mmm) REVERT: K 205 ASP cc_start: 0.8111 (t0) cc_final: 0.7553 (t0) REVERT: K 218 ASP cc_start: 0.9438 (m-30) cc_final: 0.9203 (m-30) REVERT: K 280 LYS cc_start: 0.9061 (mttm) cc_final: 0.8409 (mmtt) REVERT: K 290 GLU cc_start: 0.9386 (pt0) cc_final: 0.9062 (pt0) REVERT: K 313 MET cc_start: 0.9135 (mtm) cc_final: 0.8765 (mtm) REVERT: K 336 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8914 (mmmm) REVERT: L 22 GLU cc_start: 0.9135 (pt0) cc_final: 0.8876 (pt0) REVERT: L 76 ASP cc_start: 0.9365 (m-30) cc_final: 0.9150 (m-30) REVERT: L 150 THR cc_start: 0.9483 (m) cc_final: 0.9202 (p) REVERT: L 155 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8805 (mt-10) REVERT: L 156 ARG cc_start: 0.9170 (mmp80) cc_final: 0.8929 (mmp80) REVERT: L 205 ASP cc_start: 0.8350 (t70) cc_final: 0.8107 (t0) REVERT: L 214 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8244 (ttp80) REVERT: L 218 ASP cc_start: 0.9398 (m-30) cc_final: 0.9118 (m-30) REVERT: L 286 LEU cc_start: 0.9281 (mt) cc_final: 0.9013 (pp) REVERT: L 290 GLU cc_start: 0.9386 (tt0) cc_final: 0.9158 (mt-10) REVERT: L 308 ARG cc_start: 0.9168 (mtm-85) cc_final: 0.8870 (mtm-85) REVERT: L 313 MET cc_start: 0.8595 (mpp) cc_final: 0.8308 (mtm) REVERT: L 361 THR cc_start: 0.8698 (m) cc_final: 0.8352 (p) REVERT: L 396 ASP cc_start: 0.8688 (m-30) cc_final: 0.8465 (m-30) REVERT: L 413 MET cc_start: 0.8423 (ttm) cc_final: 0.8042 (ttm) REVERT: L 425 MET cc_start: 0.9028 (tpp) cc_final: 0.8644 (tpt) REVERT: L 430 LYS cc_start: 0.9495 (ptmm) cc_final: 0.9277 (pttm) REVERT: M 14 ASN cc_start: 0.8094 (p0) cc_final: 0.7664 (p0) REVERT: M 20 MET cc_start: 0.9121 (mtt) cc_final: 0.8872 (mtp) REVERT: M 29 HIS cc_start: 0.9183 (t-90) cc_final: 0.8642 (t-90) REVERT: M 57 HIS cc_start: 0.7820 (t-170) cc_final: 0.6616 (t70) REVERT: M 60 LYS cc_start: 0.8397 (mmtm) cc_final: 0.7915 (mmtt) REVERT: M 84 LYS cc_start: 0.9385 (ttmt) cc_final: 0.9120 (ttpt) REVERT: M 118 ASN cc_start: 0.7821 (m-40) cc_final: 0.7503 (m110) REVERT: N 29 HIS cc_start: 0.9148 (t-90) cc_final: 0.8635 (t-90) REVERT: N 62 LYS cc_start: 0.8501 (mttp) cc_final: 0.8204 (mttp) REVERT: N 100 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7156 (mmtp) REVERT: N 104 ASN cc_start: 0.8304 (m-40) cc_final: 0.7981 (m110) REVERT: N 118 ASN cc_start: 0.7966 (m-40) cc_final: 0.7309 (m110) outliers start: 197 outliers final: 134 residues processed: 1489 average time/residue: 0.2745 time to fit residues: 662.6973 Evaluate side-chains 1500 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1354 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 222 TYR Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain I residue 83 HIS Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 223 optimal weight: 9.9990 chunk 418 optimal weight: 30.0000 chunk 476 optimal weight: 20.0000 chunk 474 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 419 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 276 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS B 35 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 227 HIS ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 307 HIS G 416 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 256 ASN I 291 GLN ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN K 300 ASN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 285 GLN M 109 GLN N 57 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.089251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069885 restraints weight = 104411.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072348 restraints weight = 56480.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074031 restraints weight = 36860.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075150 restraints weight = 27178.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075944 restraints weight = 21982.157| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 44232 Z= 0.204 Angle : 0.646 12.457 60052 Z= 0.331 Chirality : 0.045 0.179 6552 Planarity : 0.004 0.054 7788 Dihedral : 11.907 175.621 6071 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.76 % Favored : 97.20 % Rotamer: Outliers : 4.67 % Allowed : 20.48 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 5394 helix: 1.66 (0.11), residues: 2530 sheet: 0.64 (0.19), residues: 774 loop : -1.01 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 77 TYR 0.018 0.001 TYR H 200 PHE 0.025 0.002 PHE B 367 TRP 0.016 0.002 TRP A 21 HIS 0.011 0.001 HIS G 190 Details of bonding type rmsd covalent geometry : bond 0.00454 (44232) covalent geometry : angle 0.64595 (60052) hydrogen bonds : bond 0.04154 ( 2164) hydrogen bonds : angle 4.59150 ( 6381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 1376 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8800 (t70) cc_final: 0.8279 (t70) REVERT: A 215 ARG cc_start: 0.8537 (ttp-110) cc_final: 0.8227 (ttp80) REVERT: A 335 ILE cc_start: 0.9771 (tp) cc_final: 0.9513 (tp) REVERT: A 361 THR cc_start: 0.9244 (m) cc_final: 0.8838 (t) REVERT: A 377 MET cc_start: 0.9007 (tmm) cc_final: 0.8251 (tmm) REVERT: A 392 ASP cc_start: 0.8839 (m-30) cc_final: 0.8339 (t0) REVERT: B 41 ASP cc_start: 0.8619 (p0) cc_final: 0.8242 (p0) REVERT: B 161 ASP cc_start: 0.8999 (p0) cc_final: 0.8686 (p0) REVERT: B 164 MET cc_start: 0.7138 (pmm) cc_final: 0.6736 (pmm) REVERT: B 203 ASP cc_start: 0.8431 (t0) cc_final: 0.8109 (t0) REVERT: B 307 HIS cc_start: 0.9352 (m-70) cc_final: 0.9107 (m-70) REVERT: B 329 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8623 (mm-40) REVERT: B 375 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8071 (pp30) REVERT: C 163 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8260 (mmmt) REVERT: C 215 ARG cc_start: 0.8661 (mtm110) cc_final: 0.8455 (mtm-85) REVERT: C 218 ASP cc_start: 0.9151 (m-30) cc_final: 0.8842 (m-30) REVERT: C 256 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8739 (tt0) REVERT: C 280 LYS cc_start: 0.4873 (mmtt) cc_final: 0.3604 (mmmt) REVERT: C 293 ASN cc_start: 0.9312 (m110) cc_final: 0.9041 (p0) REVERT: C 319 TYR cc_start: 0.8876 (m-80) cc_final: 0.8353 (m-80) REVERT: C 377 MET cc_start: 0.8505 (ttp) cc_final: 0.7607 (ttp) REVERT: C 393 HIS cc_start: 0.8774 (t70) cc_final: 0.8423 (t70) REVERT: D 19 LYS cc_start: 0.8834 (tptt) cc_final: 0.8537 (tptp) REVERT: D 41 ASP cc_start: 0.8700 (p0) cc_final: 0.8378 (p0) REVERT: D 124 CYS cc_start: 0.8916 (m) cc_final: 0.8465 (p) REVERT: D 154 LYS cc_start: 0.9680 (mmmm) cc_final: 0.9431 (mmmm) REVERT: D 213 ARG cc_start: 0.8823 (ttm110) cc_final: 0.8564 (mtm110) REVERT: D 245 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: D 252 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8715 (ttmm) REVERT: D 324 LYS cc_start: 0.9283 (ptmm) cc_final: 0.9036 (ptmm) REVERT: D 327 ASP cc_start: 0.8981 (m-30) cc_final: 0.8681 (m-30) REVERT: D 375 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7078 (pp30) REVERT: D 379 LYS cc_start: 0.9282 (mtmt) cc_final: 0.9020 (mtmt) REVERT: D 423 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8574 (tm-30) REVERT: E 22 GLU cc_start: 0.8699 (pt0) cc_final: 0.8434 (pt0) REVERT: E 88 HIS cc_start: 0.8828 (t70) cc_final: 0.8460 (t70) REVERT: E 123 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8350 (ttp-110) REVERT: E 127 ASP cc_start: 0.8741 (m-30) cc_final: 0.8533 (m-30) REVERT: E 214 ARG cc_start: 0.9126 (tmm-80) cc_final: 0.8628 (tmm-80) REVERT: E 230 LEU cc_start: 0.9617 (mp) cc_final: 0.9397 (mp) REVERT: E 326 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9026 (ttpt) REVERT: E 361 THR cc_start: 0.9209 (m) cc_final: 0.8942 (t) REVERT: E 425 MET cc_start: 0.8999 (mmm) cc_final: 0.8764 (mmt) REVERT: E 430 LYS cc_start: 0.9443 (ttpt) cc_final: 0.9240 (ttpp) REVERT: E 438 ASP cc_start: 0.8651 (t0) cc_final: 0.8241 (t0) REVERT: F 41 ASP cc_start: 0.8848 (p0) cc_final: 0.8509 (p0) REVERT: F 86 ARG cc_start: 0.4842 (mmt180) cc_final: 0.3995 (tpt170) REVERT: F 161 ASP cc_start: 0.9127 (p0) cc_final: 0.8889 (p0) REVERT: F 164 MET cc_start: 0.7727 (pmm) cc_final: 0.7518 (pmm) REVERT: F 266 PHE cc_start: 0.8994 (m-10) cc_final: 0.8434 (m-10) REVERT: F 291 GLN cc_start: 0.8796 (pp30) cc_final: 0.8484 (pp30) REVERT: F 307 HIS cc_start: 0.9413 (m-70) cc_final: 0.9168 (m-70) REVERT: F 321 MET cc_start: 0.8260 (pmm) cc_final: 0.7782 (pmm) REVERT: F 323 MET cc_start: 0.8561 (mmt) cc_final: 0.7992 (mmt) REVERT: F 327 ASP cc_start: 0.8930 (m-30) cc_final: 0.8644 (m-30) REVERT: F 375 GLN cc_start: 0.8110 (pp30) cc_final: 0.7678 (pp30) REVERT: G 164 MET cc_start: 0.8506 (ttm) cc_final: 0.7971 (mtp) REVERT: G 197 ASP cc_start: 0.8736 (m-30) cc_final: 0.8491 (m-30) REVERT: G 203 ASP cc_start: 0.8131 (t70) cc_final: 0.7779 (t70) REVERT: G 213 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8460 (tmm-80) REVERT: G 293 MET cc_start: 0.8678 (tpp) cc_final: 0.8179 (mtt) REVERT: G 320 ARG cc_start: 0.8280 (mmm160) cc_final: 0.8043 (mmp80) REVERT: G 423 GLN cc_start: 0.8746 (tp40) cc_final: 0.8391 (tp40) REVERT: H 198 GLU cc_start: 0.8474 (pt0) cc_final: 0.8065 (pt0) REVERT: H 200 TYR cc_start: 0.9061 (m-10) cc_final: 0.8841 (m-10) REVERT: H 203 ASP cc_start: 0.8243 (t0) cc_final: 0.7769 (t0) REVERT: H 209 ASP cc_start: 0.8972 (t70) cc_final: 0.7874 (t70) REVERT: H 213 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8575 (ttp-110) REVERT: H 303 CYS cc_start: 0.8441 (p) cc_final: 0.8020 (p) REVERT: H 363 MET cc_start: 0.8923 (ptt) cc_final: 0.8349 (ptt) REVERT: H 375 GLN cc_start: 0.8823 (pt0) cc_final: 0.8306 (pp30) REVERT: H 423 GLN cc_start: 0.8710 (tp40) cc_final: 0.8144 (tp-100) REVERT: H 427 ASP cc_start: 0.7959 (p0) cc_final: 0.7662 (p0) REVERT: I 198 GLU cc_start: 0.8381 (pt0) cc_final: 0.8010 (pt0) REVERT: I 203 ASP cc_start: 0.8316 (t0) cc_final: 0.7896 (t0) REVERT: I 213 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8545 (ttp80) REVERT: I 293 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8283 (mtt) REVERT: I 299 MET cc_start: 0.9037 (tpp) cc_final: 0.8234 (mpp) REVERT: I 303 CYS cc_start: 0.8569 (p) cc_final: 0.8083 (p) REVERT: I 315 THR cc_start: 0.9718 (m) cc_final: 0.9248 (p) REVERT: I 329 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8642 (mm-40) REVERT: I 362 LYS cc_start: 0.8914 (tmmt) cc_final: 0.8389 (tttm) REVERT: I 363 MET cc_start: 0.8911 (ptt) cc_final: 0.8703 (ptt) REVERT: I 379 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8833 (mtmt) REVERT: I 406 MET cc_start: 0.8402 (tpt) cc_final: 0.7827 (tpp) REVERT: I 423 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8202 (tp-100) REVERT: I 427 ASP cc_start: 0.8009 (p0) cc_final: 0.7598 (p0) REVERT: J 88 HIS cc_start: 0.8877 (t70) cc_final: 0.8253 (t70) REVERT: J 90 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8824 (mm-30) REVERT: J 150 THR cc_start: 0.9383 (m) cc_final: 0.9172 (p) REVERT: J 155 GLU cc_start: 0.9407 (mt-10) cc_final: 0.8968 (mt-10) REVERT: J 156 ARG cc_start: 0.8965 (mmp80) cc_final: 0.8754 (mmp80) REVERT: J 168 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8027 (mt-10) REVERT: J 205 ASP cc_start: 0.8154 (t0) cc_final: 0.7913 (t0) REVERT: J 214 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8108 (ttp80) REVERT: J 293 ASN cc_start: 0.9617 (m-40) cc_final: 0.9292 (m-40) REVERT: J 313 MET cc_start: 0.8389 (mpp) cc_final: 0.7885 (mtm) REVERT: J 357 TYR cc_start: 0.9126 (m-80) cc_final: 0.8216 (m-80) REVERT: J 420 GLU cc_start: 0.8841 (pt0) cc_final: 0.8400 (pm20) REVERT: K 155 GLU cc_start: 0.9117 (pt0) cc_final: 0.8678 (pt0) REVERT: K 163 LYS cc_start: 0.7200 (mmpt) cc_final: 0.6959 (mmpt) REVERT: K 172 TYR cc_start: 0.8131 (t80) cc_final: 0.7768 (t80) REVERT: K 176 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7438 (tm-30) REVERT: K 203 MET cc_start: 0.8855 (mmm) cc_final: 0.8644 (mmp) REVERT: K 205 ASP cc_start: 0.8105 (t0) cc_final: 0.7375 (t0) REVERT: K 214 ARG cc_start: 0.8615 (ttp80) cc_final: 0.7960 (ttp80) REVERT: K 218 ASP cc_start: 0.9432 (m-30) cc_final: 0.9189 (m-30) REVERT: K 290 GLU cc_start: 0.9360 (pt0) cc_final: 0.9006 (pt0) REVERT: K 300 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8531 (t0) REVERT: K 304 LYS cc_start: 0.9412 (tppt) cc_final: 0.8979 (tppt) REVERT: K 308 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8858 (mtm-85) REVERT: K 313 MET cc_start: 0.9103 (mtm) cc_final: 0.8792 (mtm) REVERT: L 22 GLU cc_start: 0.9132 (pt0) cc_final: 0.8877 (pt0) REVERT: L 76 ASP cc_start: 0.9357 (m-30) cc_final: 0.9145 (m-30) REVERT: L 90 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8747 (mm-30) REVERT: L 155 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8832 (mt-10) REVERT: L 156 ARG cc_start: 0.9173 (mmp80) cc_final: 0.8950 (mmp80) REVERT: L 205 ASP cc_start: 0.8317 (t70) cc_final: 0.7679 (t0) REVERT: L 214 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8270 (ttp80) REVERT: L 218 ASP cc_start: 0.9395 (m-30) cc_final: 0.9148 (m-30) REVERT: L 286 LEU cc_start: 0.9332 (mt) cc_final: 0.9030 (pp) REVERT: L 290 GLU cc_start: 0.9390 (tt0) cc_final: 0.9137 (mt-10) REVERT: L 304 LYS cc_start: 0.9330 (tppt) cc_final: 0.8997 (tppt) REVERT: L 308 ARG cc_start: 0.9172 (mtm-85) cc_final: 0.8860 (mtm-85) REVERT: L 313 MET cc_start: 0.8544 (mpp) cc_final: 0.8296 (mtm) REVERT: L 396 ASP cc_start: 0.8706 (m-30) cc_final: 0.8482 (m-30) REVERT: L 413 MET cc_start: 0.8455 (ttm) cc_final: 0.8090 (ttm) REVERT: L 430 LYS cc_start: 0.9506 (ptmm) cc_final: 0.9285 (pttm) REVERT: M 14 ASN cc_start: 0.8117 (p0) cc_final: 0.7763 (p0) REVERT: M 29 HIS cc_start: 0.9146 (t-90) cc_final: 0.8558 (t-90) REVERT: M 57 HIS cc_start: 0.7796 (t-170) cc_final: 0.6503 (t70) REVERT: M 60 LYS cc_start: 0.8402 (mmtm) cc_final: 0.7854 (mmtt) REVERT: M 84 LYS cc_start: 0.9403 (ttmt) cc_final: 0.9144 (ttpt) REVERT: M 118 ASN cc_start: 0.7972 (m-40) cc_final: 0.7585 (m110) REVERT: N 29 HIS cc_start: 0.9126 (t-90) cc_final: 0.8422 (t-90) REVERT: N 100 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7499 (mmtp) REVERT: N 103 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7726 (t70) REVERT: N 118 ASN cc_start: 0.8000 (m-40) cc_final: 0.7373 (m110) outliers start: 217 outliers final: 152 residues processed: 1474 average time/residue: 0.2739 time to fit residues: 654.9656 Evaluate side-chains 1478 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1317 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 336 LYS Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 334 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 109 GLN Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 500 optimal weight: 6.9990 chunk 343 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 445 optimal weight: 8.9990 chunk 356 optimal weight: 5.9990 chunk 511 optimal weight: 8.9990 chunk 365 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN G 227 HIS ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 307 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** I 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 HIS ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN L 41 HIS ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 73 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.089508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071377 restraints weight = 104210.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073785 restraints weight = 56088.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075419 restraints weight = 36274.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076522 restraints weight = 26501.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077276 restraints weight = 21158.733| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 44232 Z= 0.194 Angle : 0.656 12.636 60052 Z= 0.335 Chirality : 0.045 0.186 6552 Planarity : 0.004 0.052 7788 Dihedral : 11.901 175.803 6071 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Rotamer: Outliers : 4.24 % Allowed : 21.34 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.12), residues: 5394 helix: 1.68 (0.11), residues: 2512 sheet: 0.62 (0.19), residues: 774 loop : -0.97 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 77 TYR 0.028 0.001 TYR D 222 PHE 0.028 0.002 PHE D 367 TRP 0.016 0.002 TRP I 344 HIS 0.014 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00433 (44232) covalent geometry : angle 0.65618 (60052) hydrogen bonds : bond 0.04146 ( 2164) hydrogen bonds : angle 4.61729 ( 6381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 1368 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8796 (t70) cc_final: 0.8252 (t70) REVERT: A 215 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.8234 (ttp80) REVERT: A 317 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.8925 (mt) REVERT: A 361 THR cc_start: 0.9219 (m) cc_final: 0.8841 (t) REVERT: A 377 MET cc_start: 0.8951 (tmm) cc_final: 0.8363 (tmm) REVERT: B 41 ASP cc_start: 0.8625 (p0) cc_final: 0.8253 (p0) REVERT: B 161 ASP cc_start: 0.8991 (p0) cc_final: 0.8645 (p0) REVERT: B 164 MET cc_start: 0.7210 (pmm) cc_final: 0.6798 (pmm) REVERT: B 203 ASP cc_start: 0.8452 (t0) cc_final: 0.8095 (t0) REVERT: B 213 ARG cc_start: 0.8569 (ttm170) cc_final: 0.7933 (mtm110) REVERT: B 299 MET cc_start: 0.8778 (mmm) cc_final: 0.8230 (mmm) REVERT: B 307 HIS cc_start: 0.9326 (m-70) cc_final: 0.9065 (m-70) REVERT: B 329 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8667 (mm-40) REVERT: C 1 MET cc_start: 0.7640 (pmm) cc_final: 0.7318 (pmm) REVERT: C 215 ARG cc_start: 0.8671 (mtm110) cc_final: 0.8462 (mtm-85) REVERT: C 245 ASP cc_start: 0.8606 (t0) cc_final: 0.8345 (t0) REVERT: C 256 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8725 (tt0) REVERT: C 280 LYS cc_start: 0.4780 (mmtt) cc_final: 0.3577 (mmmt) REVERT: C 293 ASN cc_start: 0.9286 (m110) cc_final: 0.9033 (p0) REVERT: C 304 LYS cc_start: 0.9135 (tppt) cc_final: 0.8624 (tppt) REVERT: C 319 TYR cc_start: 0.8886 (m-80) cc_final: 0.8304 (m-80) REVERT: C 377 MET cc_start: 0.8451 (ttp) cc_final: 0.7535 (ttp) REVERT: C 393 HIS cc_start: 0.8781 (t70) cc_final: 0.8441 (t70) REVERT: D 19 LYS cc_start: 0.8839 (tptt) cc_final: 0.8558 (mmmt) REVERT: D 41 ASP cc_start: 0.8659 (p0) cc_final: 0.8335 (p0) REVERT: D 124 CYS cc_start: 0.8967 (m) cc_final: 0.8711 (m) REVERT: D 213 ARG cc_start: 0.8797 (ttm110) cc_final: 0.8565 (mtm110) REVERT: D 252 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8783 (ttmm) REVERT: D 324 LYS cc_start: 0.9274 (ptmm) cc_final: 0.9005 (ptmm) REVERT: D 327 ASP cc_start: 0.8966 (m-30) cc_final: 0.8694 (m-30) REVERT: D 375 GLN cc_start: 0.8476 (pp30) cc_final: 0.6307 (pp30) REVERT: D 379 LYS cc_start: 0.9245 (mtmt) cc_final: 0.8936 (mtmt) REVERT: D 424 GLN cc_start: 0.9411 (OUTLIER) cc_final: 0.9190 (tm-30) REVERT: E 123 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8324 (ttp-110) REVERT: E 214 ARG cc_start: 0.9131 (tmm-80) cc_final: 0.8637 (tmm-80) REVERT: E 230 LEU cc_start: 0.9603 (mp) cc_final: 0.9392 (mp) REVERT: E 326 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8981 (ttpt) REVERT: E 361 THR cc_start: 0.9203 (m) cc_final: 0.8943 (t) REVERT: E 425 MET cc_start: 0.8987 (mmm) cc_final: 0.8768 (mmt) REVERT: E 430 LYS cc_start: 0.9438 (ttpt) cc_final: 0.9227 (ttpp) REVERT: E 438 ASP cc_start: 0.8639 (t0) cc_final: 0.8264 (t0) REVERT: F 41 ASP cc_start: 0.8823 (p0) cc_final: 0.8482 (p0) REVERT: F 50 TYR cc_start: 0.8971 (m-10) cc_final: 0.8744 (m-80) REVERT: F 86 ARG cc_start: 0.4953 (mmt180) cc_final: 0.4054 (tpt170) REVERT: F 161 ASP cc_start: 0.9165 (p0) cc_final: 0.8914 (p0) REVERT: F 168 SER cc_start: 0.9408 (p) cc_final: 0.9130 (p) REVERT: F 252 LYS cc_start: 0.9292 (ttmm) cc_final: 0.9020 (mttm) REVERT: F 266 PHE cc_start: 0.8961 (m-10) cc_final: 0.8432 (m-10) REVERT: F 291 GLN cc_start: 0.8769 (pp30) cc_final: 0.8477 (pp30) REVERT: F 307 HIS cc_start: 0.9387 (m-70) cc_final: 0.9172 (m-70) REVERT: F 321 MET cc_start: 0.8216 (pmm) cc_final: 0.7756 (pmm) REVERT: F 323 MET cc_start: 0.8530 (mmt) cc_final: 0.7950 (mmt) REVERT: F 324 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8995 (ptmm) REVERT: F 327 ASP cc_start: 0.8917 (m-30) cc_final: 0.8625 (m-30) REVERT: F 375 GLN cc_start: 0.8128 (pp30) cc_final: 0.7630 (pp30) REVERT: G 164 MET cc_start: 0.8491 (ttm) cc_final: 0.7940 (mtp) REVERT: G 197 ASP cc_start: 0.8771 (m-30) cc_final: 0.8480 (m-30) REVERT: G 203 ASP cc_start: 0.8185 (t70) cc_final: 0.7811 (t70) REVERT: G 213 ARG cc_start: 0.8900 (ttp80) cc_final: 0.8436 (tmm-80) REVERT: G 293 MET cc_start: 0.8714 (tpp) cc_final: 0.8182 (mtt) REVERT: G 403 MET cc_start: 0.7877 (ttp) cc_final: 0.6918 (ttm) REVERT: G 423 GLN cc_start: 0.8717 (tp40) cc_final: 0.8360 (tp40) REVERT: H 45 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: H 143 THR cc_start: 0.8845 (m) cc_final: 0.8591 (p) REVERT: H 198 GLU cc_start: 0.8429 (pt0) cc_final: 0.7984 (pt0) REVERT: H 200 TYR cc_start: 0.9054 (m-10) cc_final: 0.8795 (m-10) REVERT: H 209 ASP cc_start: 0.8925 (t70) cc_final: 0.7765 (t70) REVERT: H 213 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8544 (ttp-110) REVERT: H 282 ARG cc_start: 0.7893 (ptm-80) cc_final: 0.7610 (ptm-80) REVERT: H 303 CYS cc_start: 0.8271 (p) cc_final: 0.7935 (p) REVERT: H 363 MET cc_start: 0.8973 (ptt) cc_final: 0.8703 (ptt) REVERT: H 375 GLN cc_start: 0.8858 (pt0) cc_final: 0.8312 (pp30) REVERT: H 423 GLN cc_start: 0.8705 (tp40) cc_final: 0.8155 (tp-100) REVERT: H 427 ASP cc_start: 0.7898 (p0) cc_final: 0.7607 (p0) REVERT: I 198 GLU cc_start: 0.8402 (pt0) cc_final: 0.8017 (pt0) REVERT: I 203 ASP cc_start: 0.8343 (t0) cc_final: 0.7889 (t0) REVERT: I 213 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8536 (ttp80) REVERT: I 293 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8274 (mtt) REVERT: I 299 MET cc_start: 0.9045 (tpp) cc_final: 0.8265 (mpp) REVERT: I 303 CYS cc_start: 0.8559 (p) cc_final: 0.8040 (p) REVERT: I 315 THR cc_start: 0.9728 (m) cc_final: 0.9230 (p) REVERT: I 329 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8586 (mm-40) REVERT: I 362 LYS cc_start: 0.8896 (tmmt) cc_final: 0.8302 (tttm) REVERT: I 363 MET cc_start: 0.8909 (ptt) cc_final: 0.8697 (ptt) REVERT: I 379 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8827 (mtmt) REVERT: I 406 MET cc_start: 0.8413 (tpt) cc_final: 0.7854 (tpp) REVERT: I 423 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8171 (tp-100) REVERT: I 427 ASP cc_start: 0.8000 (p0) cc_final: 0.7729 (p0) REVERT: J 88 HIS cc_start: 0.8883 (t70) cc_final: 0.8412 (t70) REVERT: J 150 THR cc_start: 0.9410 (m) cc_final: 0.9188 (p) REVERT: J 155 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8968 (mt-10) REVERT: J 168 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7999 (mt-10) REVERT: J 205 ASP cc_start: 0.8074 (t0) cc_final: 0.7840 (t0) REVERT: J 214 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8121 (ttp80) REVERT: J 290 GLU cc_start: 0.9252 (pt0) cc_final: 0.8834 (pp20) REVERT: J 293 ASN cc_start: 0.9598 (m-40) cc_final: 0.9267 (m-40) REVERT: J 313 MET cc_start: 0.8442 (mpp) cc_final: 0.7933 (mtm) REVERT: J 357 TYR cc_start: 0.9106 (m-80) cc_final: 0.8232 (m-80) REVERT: J 396 ASP cc_start: 0.8555 (m-30) cc_final: 0.8328 (m-30) REVERT: J 420 GLU cc_start: 0.8848 (pt0) cc_final: 0.8455 (pm20) REVERT: K 155 GLU cc_start: 0.9059 (pt0) cc_final: 0.8548 (pt0) REVERT: K 156 ARG cc_start: 0.8607 (mmp80) cc_final: 0.8264 (mmp80) REVERT: K 172 TYR cc_start: 0.8094 (t80) cc_final: 0.7800 (t80) REVERT: K 205 ASP cc_start: 0.8072 (t0) cc_final: 0.7469 (t0) REVERT: K 214 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8064 (ttp80) REVERT: K 218 ASP cc_start: 0.9401 (m-30) cc_final: 0.9151 (m-30) REVERT: K 290 GLU cc_start: 0.9432 (pt0) cc_final: 0.8996 (pt0) REVERT: K 300 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8462 (t0) REVERT: K 313 MET cc_start: 0.9083 (mtm) cc_final: 0.8839 (mtm) REVERT: L 22 GLU cc_start: 0.9100 (pt0) cc_final: 0.8850 (pt0) REVERT: L 76 ASP cc_start: 0.9329 (m-30) cc_final: 0.9127 (m-30) REVERT: L 150 THR cc_start: 0.9406 (m) cc_final: 0.9125 (p) REVERT: L 155 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8822 (mt-10) REVERT: L 156 ARG cc_start: 0.9160 (mmp80) cc_final: 0.8954 (mmp80) REVERT: L 205 ASP cc_start: 0.8255 (t70) cc_final: 0.7529 (t70) REVERT: L 214 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8248 (ttp80) REVERT: L 218 ASP cc_start: 0.9376 (m-30) cc_final: 0.9132 (m-30) REVERT: L 286 LEU cc_start: 0.9322 (mt) cc_final: 0.9013 (pp) REVERT: L 290 GLU cc_start: 0.9365 (tt0) cc_final: 0.9080 (mt-10) REVERT: L 293 ASN cc_start: 0.9428 (m110) cc_final: 0.9164 (p0) REVERT: L 304 LYS cc_start: 0.9308 (tppt) cc_final: 0.8986 (tppt) REVERT: L 396 ASP cc_start: 0.8662 (m-30) cc_final: 0.8454 (m-30) REVERT: L 413 MET cc_start: 0.8406 (ttm) cc_final: 0.8056 (ttm) REVERT: L 430 LYS cc_start: 0.9517 (ptmm) cc_final: 0.9300 (pttm) REVERT: M 14 ASN cc_start: 0.8086 (p0) cc_final: 0.7723 (p0) REVERT: M 20 MET cc_start: 0.9079 (mtt) cc_final: 0.8786 (mtp) REVERT: M 29 HIS cc_start: 0.9061 (t-90) cc_final: 0.8479 (t-90) REVERT: M 57 HIS cc_start: 0.7770 (t-170) cc_final: 0.7489 (t70) REVERT: M 84 LYS cc_start: 0.9417 (ttmt) cc_final: 0.9155 (ttpt) REVERT: M 100 LYS cc_start: 0.8181 (tppt) cc_final: 0.7740 (mmtp) REVERT: M 103 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7862 (t70) REVERT: M 104 ASN cc_start: 0.8619 (m-40) cc_final: 0.8359 (m110) REVERT: M 118 ASN cc_start: 0.8064 (m-40) cc_final: 0.7719 (m110) REVERT: N 29 HIS cc_start: 0.8975 (t-90) cc_final: 0.8463 (t-90) REVERT: N 103 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7704 (t70) REVERT: N 118 ASN cc_start: 0.8073 (m-40) cc_final: 0.7384 (m110) outliers start: 197 outliers final: 157 residues processed: 1457 average time/residue: 0.2707 time to fit residues: 639.8814 Evaluate side-chains 1484 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1317 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 304 ASP Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 114 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 336 LYS Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 172 optimal weight: 8.9990 chunk 377 optimal weight: 7.9990 chunk 403 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 417 optimal weight: 30.0000 chunk 402 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 392 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN C 101 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS G 245 GLN ** G 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN G 298 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 126 ASN I 57 HIS I 165 ASN I 256 ASN ** I 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.087728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069264 restraints weight = 105318.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071651 restraints weight = 56316.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073349 restraints weight = 36004.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074493 restraints weight = 26084.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075261 restraints weight = 20659.583| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 44232 Z= 0.236 Angle : 0.687 13.109 60052 Z= 0.352 Chirality : 0.046 0.211 6552 Planarity : 0.004 0.055 7788 Dihedral : 11.957 176.475 6068 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 4.39 % Allowed : 22.12 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 5394 helix: 1.61 (0.11), residues: 2518 sheet: 0.58 (0.19), residues: 774 loop : -0.98 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 77 TYR 0.028 0.002 TYR D 222 PHE 0.029 0.002 PHE D 367 TRP 0.015 0.002 TRP A 21 HIS 0.029 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00525 (44232) covalent geometry : angle 0.68710 (60052) hydrogen bonds : bond 0.04299 ( 2164) hydrogen bonds : angle 4.71582 ( 6381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 1333 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8566 (pt0) cc_final: 0.8354 (pt0) REVERT: A 211 ASP cc_start: 0.8788 (t70) cc_final: 0.8485 (t70) REVERT: A 361 THR cc_start: 0.9263 (m) cc_final: 0.8971 (t) REVERT: A 377 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8425 (tmm) REVERT: B 41 ASP cc_start: 0.8607 (p0) cc_final: 0.8228 (p0) REVERT: B 66 VAL cc_start: 0.9586 (t) cc_final: 0.9329 (p) REVERT: B 161 ASP cc_start: 0.9041 (p0) cc_final: 0.8697 (p0) REVERT: B 164 MET cc_start: 0.7334 (pmm) cc_final: 0.6956 (pmm) REVERT: B 203 ASP cc_start: 0.8508 (t0) cc_final: 0.8284 (t0) REVERT: B 307 HIS cc_start: 0.9343 (m-70) cc_final: 0.9053 (m-70) REVERT: B 329 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8897 (mm-40) REVERT: B 367 PHE cc_start: 0.9353 (t80) cc_final: 0.9117 (t80) REVERT: B 375 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: B 376 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7849 (mt-10) REVERT: C 245 ASP cc_start: 0.8628 (t0) cc_final: 0.8346 (t0) REVERT: C 256 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: C 280 LYS cc_start: 0.4487 (mmtt) cc_final: 0.3169 (mmmt) REVERT: C 304 LYS cc_start: 0.9131 (tppt) cc_final: 0.8617 (tppt) REVERT: C 308 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8388 (mtm110) REVERT: C 377 MET cc_start: 0.8455 (ttp) cc_final: 0.7635 (ttp) REVERT: D 19 LYS cc_start: 0.8877 (tptt) cc_final: 0.8589 (mmmt) REVERT: D 41 ASP cc_start: 0.8674 (p0) cc_final: 0.8324 (p0) REVERT: D 124 CYS cc_start: 0.8982 (m) cc_final: 0.8756 (m) REVERT: D 252 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8774 (ttmm) REVERT: D 327 ASP cc_start: 0.8965 (m-30) cc_final: 0.8702 (m-30) REVERT: D 341 PHE cc_start: 0.8855 (m-80) cc_final: 0.8640 (m-80) REVERT: D 375 GLN cc_start: 0.7966 (pp30) cc_final: 0.6161 (pp30) REVERT: D 379 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8850 (mtmt) REVERT: D 424 GLN cc_start: 0.9437 (OUTLIER) cc_final: 0.9201 (tm-30) REVERT: D 425 TYR cc_start: 0.8729 (m-10) cc_final: 0.8395 (m-10) REVERT: E 15 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: E 36 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8104 (ttt) REVERT: E 214 ARG cc_start: 0.9148 (tmm-80) cc_final: 0.8643 (tmm-80) REVERT: E 230 LEU cc_start: 0.9603 (mp) cc_final: 0.9390 (mp) REVERT: E 326 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9051 (ttpt) REVERT: E 361 THR cc_start: 0.9223 (m) cc_final: 0.8954 (t) REVERT: E 392 ASP cc_start: 0.8874 (m-30) cc_final: 0.8573 (m-30) REVERT: E 396 ASP cc_start: 0.8608 (m-30) cc_final: 0.8301 (m-30) REVERT: E 425 MET cc_start: 0.8928 (mmm) cc_final: 0.8659 (mmt) REVERT: E 430 LYS cc_start: 0.9420 (ttpt) cc_final: 0.9194 (ttpp) REVERT: E 438 ASP cc_start: 0.8721 (t0) cc_final: 0.8372 (t0) REVERT: F 41 ASP cc_start: 0.8747 (p0) cc_final: 0.8371 (p0) REVERT: F 50 TYR cc_start: 0.9018 (m-10) cc_final: 0.8752 (m-80) REVERT: F 86 ARG cc_start: 0.5165 (mmt180) cc_final: 0.3969 (tpt170) REVERT: F 161 ASP cc_start: 0.9166 (p0) cc_final: 0.8947 (p0) REVERT: F 266 PHE cc_start: 0.8894 (m-10) cc_final: 0.8254 (m-10) REVERT: F 291 GLN cc_start: 0.8801 (pp30) cc_final: 0.8512 (pp30) REVERT: F 307 HIS cc_start: 0.9410 (m-70) cc_final: 0.9194 (m-70) REVERT: F 321 MET cc_start: 0.8217 (pmm) cc_final: 0.7812 (pmm) REVERT: F 324 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8948 (ptmm) REVERT: F 327 ASP cc_start: 0.8922 (m-30) cc_final: 0.8643 (m-30) REVERT: F 375 GLN cc_start: 0.8156 (pp30) cc_final: 0.7637 (pp30) REVERT: G 164 MET cc_start: 0.8480 (ttm) cc_final: 0.7903 (mtp) REVERT: G 197 ASP cc_start: 0.8748 (m-30) cc_final: 0.8546 (m-30) REVERT: G 203 ASP cc_start: 0.8182 (t70) cc_final: 0.7836 (t70) REVERT: G 213 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8418 (tmm-80) REVERT: G 293 MET cc_start: 0.8716 (tpp) cc_final: 0.8329 (mtt) REVERT: G 423 GLN cc_start: 0.8689 (tp40) cc_final: 0.8209 (tp-100) REVERT: H 45 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: H 200 TYR cc_start: 0.9046 (m-10) cc_final: 0.8779 (m-10) REVERT: H 209 ASP cc_start: 0.8899 (t70) cc_final: 0.7703 (t70) REVERT: H 282 ARG cc_start: 0.7996 (ptm-80) cc_final: 0.7690 (ptm-80) REVERT: H 288 GLU cc_start: 0.8492 (tt0) cc_final: 0.7730 (tt0) REVERT: H 303 CYS cc_start: 0.8290 (p) cc_final: 0.7960 (p) REVERT: H 375 GLN cc_start: 0.8858 (pt0) cc_final: 0.8339 (pp30) REVERT: H 423 GLN cc_start: 0.8704 (tp40) cc_final: 0.8166 (tp-100) REVERT: H 427 ASP cc_start: 0.7959 (p0) cc_final: 0.7680 (p0) REVERT: I 51 TYR cc_start: 0.9068 (m-80) cc_final: 0.8701 (m-80) REVERT: I 198 GLU cc_start: 0.8510 (pt0) cc_final: 0.8147 (pt0) REVERT: I 203 ASP cc_start: 0.8361 (t0) cc_final: 0.7905 (t0) REVERT: I 213 ARG cc_start: 0.8828 (ttm110) cc_final: 0.8473 (tmm-80) REVERT: I 293 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8318 (mtt) REVERT: I 299 MET cc_start: 0.9058 (tpp) cc_final: 0.8289 (mpp) REVERT: I 303 CYS cc_start: 0.8521 (p) cc_final: 0.8064 (p) REVERT: I 315 THR cc_start: 0.9723 (m) cc_final: 0.9221 (p) REVERT: I 329 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8585 (mm-40) REVERT: I 362 LYS cc_start: 0.8919 (tmmt) cc_final: 0.8537 (tmmt) REVERT: I 363 MET cc_start: 0.8907 (ptt) cc_final: 0.8550 (ptt) REVERT: I 379 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8822 (mtmt) REVERT: I 406 MET cc_start: 0.8408 (tpt) cc_final: 0.7849 (tpp) REVERT: I 423 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8228 (tp-100) REVERT: I 427 ASP cc_start: 0.8021 (p0) cc_final: 0.7754 (p0) REVERT: J 88 HIS cc_start: 0.8853 (t70) cc_final: 0.8442 (t70) REVERT: J 150 THR cc_start: 0.9398 (m) cc_final: 0.9091 (p) REVERT: J 154 MET cc_start: 0.9160 (mmp) cc_final: 0.8808 (mmp) REVERT: J 155 GLU cc_start: 0.9378 (mt-10) cc_final: 0.8929 (mt-10) REVERT: J 168 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7658 (mt-10) REVERT: J 203 MET cc_start: 0.8894 (mmm) cc_final: 0.8481 (mmm) REVERT: J 205 ASP cc_start: 0.8109 (t0) cc_final: 0.7770 (t0) REVERT: J 214 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8144 (ttp80) REVERT: J 290 GLU cc_start: 0.9257 (pt0) cc_final: 0.8833 (pp20) REVERT: J 293 ASN cc_start: 0.9588 (m-40) cc_final: 0.9261 (m-40) REVERT: J 304 LYS cc_start: 0.9476 (tppt) cc_final: 0.9169 (tppt) REVERT: J 313 MET cc_start: 0.8459 (mpp) cc_final: 0.7986 (mtm) REVERT: J 357 TYR cc_start: 0.9083 (m-80) cc_final: 0.8231 (m-80) REVERT: J 396 ASP cc_start: 0.8534 (m-30) cc_final: 0.8299 (m-30) REVERT: J 413 MET cc_start: 0.8879 (mtp) cc_final: 0.8545 (ttm) REVERT: J 420 GLU cc_start: 0.8846 (pt0) cc_final: 0.8455 (pm20) REVERT: K 121 ARG cc_start: 0.9409 (mmm160) cc_final: 0.9183 (mmm160) REVERT: K 205 ASP cc_start: 0.7984 (t0) cc_final: 0.7231 (t0) REVERT: K 214 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8085 (ttp80) REVERT: K 218 ASP cc_start: 0.9387 (m-30) cc_final: 0.9165 (m-30) REVERT: K 290 GLU cc_start: 0.9445 (pt0) cc_final: 0.9076 (pt0) REVERT: K 300 ASN cc_start: 0.9125 (t0) cc_final: 0.8621 (t0) REVERT: K 304 LYS cc_start: 0.9466 (tppt) cc_final: 0.8996 (tppt) REVERT: K 313 MET cc_start: 0.9098 (mtm) cc_final: 0.8897 (mtm) REVERT: L 21 TRP cc_start: 0.9426 (m100) cc_final: 0.9033 (m100) REVERT: L 22 GLU cc_start: 0.9090 (pt0) cc_final: 0.8849 (pt0) REVERT: L 76 ASP cc_start: 0.9333 (m-30) cc_final: 0.9130 (m-30) REVERT: L 150 THR cc_start: 0.9422 (m) cc_final: 0.9136 (p) REVERT: L 155 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8782 (mt-10) REVERT: L 205 ASP cc_start: 0.8289 (t70) cc_final: 0.7517 (t70) REVERT: L 214 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8136 (ttp80) REVERT: L 218 ASP cc_start: 0.9387 (m-30) cc_final: 0.9161 (m-30) REVERT: L 286 LEU cc_start: 0.9331 (mt) cc_final: 0.9036 (pp) REVERT: L 290 GLU cc_start: 0.9375 (tt0) cc_final: 0.9102 (mt-10) REVERT: L 293 ASN cc_start: 0.9445 (m110) cc_final: 0.9188 (p0) REVERT: L 304 LYS cc_start: 0.9322 (tppt) cc_final: 0.8997 (tppt) REVERT: L 308 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8814 (mtm-85) REVERT: L 313 MET cc_start: 0.9045 (mtm) cc_final: 0.8213 (mtm) REVERT: L 413 MET cc_start: 0.8397 (ttm) cc_final: 0.8027 (ttm) REVERT: L 430 LYS cc_start: 0.9529 (ptmm) cc_final: 0.9320 (pttm) REVERT: M 14 ASN cc_start: 0.8056 (p0) cc_final: 0.7664 (p0) REVERT: M 20 MET cc_start: 0.9091 (mtt) cc_final: 0.8851 (mtp) REVERT: M 29 HIS cc_start: 0.9066 (t-90) cc_final: 0.8459 (t-90) REVERT: M 84 LYS cc_start: 0.9414 (ttmt) cc_final: 0.9058 (ttpt) REVERT: M 103 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7881 (t70) REVERT: M 104 ASN cc_start: 0.8624 (m-40) cc_final: 0.8321 (m110) REVERT: M 118 ASN cc_start: 0.8051 (m-40) cc_final: 0.7710 (m110) REVERT: N 29 HIS cc_start: 0.9027 (t-90) cc_final: 0.8456 (t-90) REVERT: N 100 LYS cc_start: 0.8317 (mmmm) cc_final: 0.7632 (mmtp) REVERT: N 103 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7765 (t70) REVERT: N 114 PHE cc_start: 0.9100 (t80) cc_final: 0.8842 (t80) REVERT: N 118 ASN cc_start: 0.8039 (m-40) cc_final: 0.7299 (m110) outliers start: 204 outliers final: 162 residues processed: 1431 average time/residue: 0.2690 time to fit residues: 623.2417 Evaluate side-chains 1462 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 1288 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 304 ASP Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 336 LYS Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain I residue 114 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 336 LYS Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain M residue 122 LYS Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 347 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 494 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 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 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN C 50 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 165 ASN ** I 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN L 42 HIS ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.090759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072079 restraints weight = 102964.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074459 restraints weight = 56902.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.076148 restraints weight = 37283.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077284 restraints weight = 27376.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.078055 restraints weight = 21930.802| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 44232 Z= 0.152 Angle : 0.687 14.232 60052 Z= 0.348 Chirality : 0.045 0.188 6552 Planarity : 0.004 0.083 7788 Dihedral : 11.841 177.263 6068 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 3.66 % Allowed : 23.02 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.12), residues: 5394 helix: 1.62 (0.11), residues: 2494 sheet: 0.56 (0.19), residues: 786 loop : -0.91 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 308 TYR 0.026 0.001 TYR B 281 PHE 0.029 0.001 PHE D 367 TRP 0.021 0.002 TRP I 344 HIS 0.011 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00349 (44232) covalent geometry : angle 0.68743 (60052) hydrogen bonds : bond 0.04111 ( 2164) hydrogen bonds : angle 4.69973 ( 6381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1380 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8566 (pt0) cc_final: 0.8364 (pt0) REVERT: A 211 ASP cc_start: 0.8736 (t70) cc_final: 0.8382 (t70) REVERT: A 215 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8419 (ttp-170) REVERT: A 313 MET cc_start: 0.9085 (mtm) cc_final: 0.8846 (mtm) REVERT: A 361 THR cc_start: 0.9200 (m) cc_final: 0.8917 (t) REVERT: A 377 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8405 (tmm) REVERT: A 425 MET cc_start: 0.8633 (mpp) cc_final: 0.8324 (mpp) REVERT: B 41 ASP cc_start: 0.8610 (p0) cc_final: 0.8244 (p0) REVERT: B 161 ASP cc_start: 0.9012 (p0) cc_final: 0.8676 (p0) REVERT: B 164 MET cc_start: 0.7409 (pmm) cc_final: 0.6994 (pmm) REVERT: B 203 ASP cc_start: 0.8420 (t0) cc_final: 0.8197 (t0) REVERT: B 307 HIS cc_start: 0.9368 (m-70) cc_final: 0.9068 (m-70) REVERT: B 329 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8883 (mm-40) REVERT: B 367 PHE cc_start: 0.9343 (t80) cc_final: 0.9047 (t80) REVERT: B 379 LYS cc_start: 0.9221 (mtmt) cc_final: 0.8988 (mtmt) REVERT: C 245 ASP cc_start: 0.8595 (t0) cc_final: 0.8274 (t0) REVERT: C 280 LYS cc_start: 0.4741 (mmtt) cc_final: 0.3442 (mmmt) REVERT: C 293 ASN cc_start: 0.9292 (m110) cc_final: 0.9054 (p0) REVERT: C 304 LYS cc_start: 0.9089 (tppt) cc_final: 0.8593 (tppt) REVERT: C 308 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8249 (mtm110) REVERT: C 319 TYR cc_start: 0.8868 (m-80) cc_final: 0.8318 (m-80) REVERT: C 377 MET cc_start: 0.8369 (ttp) cc_final: 0.7600 (ttp) REVERT: C 433 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8641 (mm-30) REVERT: D 19 LYS cc_start: 0.8837 (tptt) cc_final: 0.8539 (mmmt) REVERT: D 41 ASP cc_start: 0.8724 (p0) cc_final: 0.8373 (p0) REVERT: D 198 GLU cc_start: 0.8343 (pt0) cc_final: 0.7869 (pt0) REVERT: D 252 LYS cc_start: 0.9124 (mtpp) cc_final: 0.8664 (ttmm) REVERT: D 266 PHE cc_start: 0.8674 (m-10) cc_final: 0.8417 (m-10) REVERT: D 291 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8510 (pp30) REVERT: D 327 ASP cc_start: 0.8979 (m-30) cc_final: 0.8705 (m-30) REVERT: D 424 GLN cc_start: 0.9495 (OUTLIER) cc_final: 0.9210 (tm-30) REVERT: D 425 TYR cc_start: 0.8713 (m-10) cc_final: 0.8307 (m-10) REVERT: E 15 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: E 36 MET cc_start: 0.8462 (mtp) cc_final: 0.8120 (ttt) REVERT: E 214 ARG cc_start: 0.9134 (tmm-80) cc_final: 0.8663 (tmm-80) REVERT: E 280 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8498 (mtmm) REVERT: E 326 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9027 (ttpt) REVERT: E 361 THR cc_start: 0.9192 (m) cc_final: 0.8925 (t) REVERT: E 425 MET cc_start: 0.8873 (mmm) cc_final: 0.8657 (mmt) REVERT: E 430 LYS cc_start: 0.9406 (ttpt) cc_final: 0.9160 (ttpp) REVERT: E 433 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8630 (mm-30) REVERT: E 438 ASP cc_start: 0.8687 (t0) cc_final: 0.8304 (t0) REVERT: F 41 ASP cc_start: 0.8782 (p0) cc_final: 0.8408 (p0) REVERT: F 50 TYR cc_start: 0.8943 (m-10) cc_final: 0.8703 (m-80) REVERT: F 86 ARG cc_start: 0.5053 (mmt180) cc_final: 0.3885 (tpt170) REVERT: F 161 ASP cc_start: 0.9142 (p0) cc_final: 0.8864 (p0) REVERT: F 252 LYS cc_start: 0.9284 (tttp) cc_final: 0.8968 (mttm) REVERT: F 266 PHE cc_start: 0.8782 (m-10) cc_final: 0.8271 (m-10) REVERT: F 291 GLN cc_start: 0.8768 (pp30) cc_final: 0.8465 (pp30) REVERT: F 321 MET cc_start: 0.8066 (pmm) cc_final: 0.7644 (pmm) REVERT: F 327 ASP cc_start: 0.8958 (m-30) cc_final: 0.8661 (m-30) REVERT: G 19 LYS cc_start: 0.8916 (tptt) cc_final: 0.8644 (tptt) REVERT: G 164 MET cc_start: 0.8447 (ttm) cc_final: 0.7886 (mtp) REVERT: G 197 ASP cc_start: 0.8552 (m-30) cc_final: 0.8319 (m-30) REVERT: G 203 ASP cc_start: 0.8187 (t70) cc_final: 0.7759 (t70) REVERT: G 213 ARG cc_start: 0.8891 (ttp80) cc_final: 0.8428 (tmm-80) REVERT: G 293 MET cc_start: 0.8631 (tpp) cc_final: 0.8348 (mtt) REVERT: G 307 HIS cc_start: 0.9441 (m170) cc_final: 0.9232 (m-70) REVERT: G 362 LYS cc_start: 0.8577 (tmmt) cc_final: 0.8343 (tmmt) REVERT: G 423 GLN cc_start: 0.8644 (tp40) cc_final: 0.8175 (tp-100) REVERT: H 19 LYS cc_start: 0.8783 (tptm) cc_final: 0.8549 (tptt) REVERT: H 143 THR cc_start: 0.8827 (m) cc_final: 0.8587 (p) REVERT: H 198 GLU cc_start: 0.8287 (pt0) cc_final: 0.7867 (pt0) REVERT: H 245 GLN cc_start: 0.8809 (mt0) cc_final: 0.8345 (mt0) REVERT: H 282 ARG cc_start: 0.7976 (ptm-80) cc_final: 0.7746 (ptm-80) REVERT: H 303 CYS cc_start: 0.8300 (p) cc_final: 0.7872 (p) REVERT: H 320 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8229 (tpp80) REVERT: H 375 GLN cc_start: 0.8822 (pt0) cc_final: 0.8312 (pp30) REVERT: H 423 GLN cc_start: 0.8662 (tp40) cc_final: 0.8096 (tp-100) REVERT: H 427 ASP cc_start: 0.7901 (p0) cc_final: 0.7577 (p0) REVERT: I 198 GLU cc_start: 0.8441 (pt0) cc_final: 0.8094 (pt0) REVERT: I 203 ASP cc_start: 0.8360 (t0) cc_final: 0.7851 (t0) REVERT: I 293 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: I 299 MET cc_start: 0.9065 (tpp) cc_final: 0.8266 (mpp) REVERT: I 303 CYS cc_start: 0.8551 (p) cc_final: 0.8035 (p) REVERT: I 315 THR cc_start: 0.9717 (m) cc_final: 0.9227 (p) REVERT: I 362 LYS cc_start: 0.8922 (tmmt) cc_final: 0.8536 (tmmt) REVERT: I 363 MET cc_start: 0.8871 (ptt) cc_final: 0.8539 (ptt) REVERT: I 379 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8815 (mtmt) REVERT: I 406 MET cc_start: 0.8395 (tpt) cc_final: 0.7818 (tpp) REVERT: I 423 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8148 (tp-100) REVERT: I 427 ASP cc_start: 0.7981 (p0) cc_final: 0.7592 (p0) REVERT: J 150 THR cc_start: 0.9409 (m) cc_final: 0.9103 (p) REVERT: J 154 MET cc_start: 0.9174 (mmp) cc_final: 0.8810 (mmp) REVERT: J 155 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8945 (mt-10) REVERT: J 168 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7661 (mt-10) REVERT: J 205 ASP cc_start: 0.8091 (t0) cc_final: 0.7703 (t0) REVERT: J 214 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8133 (ttp80) REVERT: J 290 GLU cc_start: 0.9237 (pt0) cc_final: 0.8834 (pp20) REVERT: J 293 ASN cc_start: 0.9587 (m-40) cc_final: 0.9259 (m-40) REVERT: J 304 LYS cc_start: 0.9484 (tppt) cc_final: 0.9169 (tppt) REVERT: J 313 MET cc_start: 0.8422 (mpp) cc_final: 0.7963 (mtm) REVERT: J 357 TYR cc_start: 0.9101 (m-80) cc_final: 0.8235 (m-80) REVERT: J 396 ASP cc_start: 0.8547 (m-30) cc_final: 0.8315 (m-30) REVERT: J 413 MET cc_start: 0.8812 (mtp) cc_final: 0.8472 (ttm) REVERT: J 420 GLU cc_start: 0.8858 (pt0) cc_final: 0.8466 (pm20) REVERT: J 425 MET cc_start: 0.8949 (tpp) cc_final: 0.8526 (tpt) REVERT: K 172 TYR cc_start: 0.8145 (t80) cc_final: 0.7821 (t80) REVERT: K 205 ASP cc_start: 0.8022 (t0) cc_final: 0.7156 (t0) REVERT: K 207 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8515 (mm-30) REVERT: K 214 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8125 (ttp80) REVERT: K 218 ASP cc_start: 0.9380 (m-30) cc_final: 0.9171 (m-30) REVERT: K 290 GLU cc_start: 0.9437 (pt0) cc_final: 0.9065 (pt0) REVERT: K 300 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8495 (t0) REVERT: K 304 LYS cc_start: 0.9469 (tppt) cc_final: 0.8951 (tppt) REVERT: K 329 ASN cc_start: 0.9499 (m110) cc_final: 0.9295 (m110) REVERT: L 21 TRP cc_start: 0.9367 (m100) cc_final: 0.8956 (m100) REVERT: L 22 GLU cc_start: 0.9084 (pt0) cc_final: 0.8850 (pt0) REVERT: L 76 ASP cc_start: 0.9328 (m-30) cc_final: 0.9119 (m-30) REVERT: L 150 THR cc_start: 0.9383 (m) cc_final: 0.9101 (p) REVERT: L 155 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8934 (mt-10) REVERT: L 156 ARG cc_start: 0.9100 (mmp80) cc_final: 0.8885 (mmp80) REVERT: L 205 ASP cc_start: 0.8323 (t70) cc_final: 0.7304 (t0) REVERT: L 214 ARG cc_start: 0.8596 (ttp80) cc_final: 0.8183 (ttp80) REVERT: L 218 ASP cc_start: 0.9370 (m-30) cc_final: 0.9137 (m-30) REVERT: L 286 LEU cc_start: 0.9332 (mt) cc_final: 0.9033 (pp) REVERT: L 290 GLU cc_start: 0.9363 (tt0) cc_final: 0.9080 (mt-10) REVERT: L 293 ASN cc_start: 0.9443 (m110) cc_final: 0.9170 (p0) REVERT: L 304 LYS cc_start: 0.9331 (tppt) cc_final: 0.8990 (tppt) REVERT: L 308 ARG cc_start: 0.9100 (mtm-85) cc_final: 0.8780 (mtm-85) REVERT: L 313 MET cc_start: 0.9001 (mtm) cc_final: 0.8132 (mtm) REVERT: L 413 MET cc_start: 0.8338 (ttm) cc_final: 0.7939 (ttm) REVERT: L 430 LYS cc_start: 0.9522 (ptmm) cc_final: 0.9313 (pttm) REVERT: M 14 ASN cc_start: 0.8023 (p0) cc_final: 0.7644 (p0) REVERT: M 20 MET cc_start: 0.9063 (mtt) cc_final: 0.8789 (mtp) REVERT: M 29 HIS cc_start: 0.9051 (t-90) cc_final: 0.8433 (t-90) REVERT: M 57 HIS cc_start: 0.7368 (t-170) cc_final: 0.7158 (t70) REVERT: M 84 LYS cc_start: 0.9415 (ttmt) cc_final: 0.9056 (ttpt) REVERT: M 103 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7847 (t70) REVERT: M 118 ASN cc_start: 0.8062 (m-40) cc_final: 0.7728 (m110) REVERT: N 29 HIS cc_start: 0.9062 (t-90) cc_final: 0.8452 (t-90) REVERT: N 103 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7695 (t70) REVERT: N 114 PHE cc_start: 0.9070 (t80) cc_final: 0.8825 (t80) REVERT: N 118 ASN cc_start: 0.7938 (m-40) cc_final: 0.7029 (m110) REVERT: N 122 LYS cc_start: 0.8472 (ptpp) cc_final: 0.8097 (pttt) outliers start: 170 outliers final: 137 residues processed: 1454 average time/residue: 0.2807 time to fit residues: 662.1565 Evaluate side-chains 1474 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1328 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 304 ASP Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 336 LYS Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 163 LYS Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 182 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 318 optimal weight: 5.9990 chunk 490 optimal weight: 9.9990 chunk 371 optimal weight: 7.9990 chunk 361 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 511 optimal weight: 0.6980 chunk 355 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 293 ASN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 ASN ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 227 HIS H 334 GLN H 347 ASN I 57 HIS I 165 ASN ** I 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN J 8 HIS ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.090157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.071160 restraints weight = 104038.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073584 restraints weight = 56537.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075315 restraints weight = 36568.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076519 restraints weight = 26701.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077244 restraints weight = 21228.054| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 44232 Z= 0.174 Angle : 0.704 14.618 60052 Z= 0.358 Chirality : 0.046 0.210 6552 Planarity : 0.005 0.121 7788 Dihedral : 11.816 177.756 6068 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Rotamer: Outliers : 3.40 % Allowed : 23.71 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 5394 helix: 1.56 (0.11), residues: 2494 sheet: 0.61 (0.19), residues: 774 loop : -0.87 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 282 TYR 0.029 0.001 TYR F 222 PHE 0.028 0.002 PHE D 367 TRP 0.027 0.002 TRP H 344 HIS 0.010 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00400 (44232) covalent geometry : angle 0.70450 (60052) hydrogen bonds : bond 0.04145 ( 2164) hydrogen bonds : angle 4.72966 ( 6381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1363 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8575 (pt0) cc_final: 0.8374 (pt0) REVERT: A 211 ASP cc_start: 0.8761 (t70) cc_final: 0.8298 (t70) REVERT: A 300 ASN cc_start: 0.8740 (t0) cc_final: 0.8539 (t0) REVERT: A 361 THR cc_start: 0.9246 (m) cc_final: 0.8948 (t) REVERT: A 377 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8374 (tmm) REVERT: A 425 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8367 (mpp) REVERT: B 41 ASP cc_start: 0.8640 (p0) cc_final: 0.8276 (p0) REVERT: B 111 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 161 ASP cc_start: 0.9073 (p0) cc_final: 0.8720 (p0) REVERT: B 164 MET cc_start: 0.7411 (pmm) cc_final: 0.7024 (pmm) REVERT: B 203 ASP cc_start: 0.8406 (t0) cc_final: 0.8202 (t0) REVERT: B 307 HIS cc_start: 0.9390 (m-70) cc_final: 0.9101 (m-70) REVERT: B 329 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8929 (mm-40) REVERT: B 375 GLN cc_start: 0.8411 (pt0) cc_final: 0.7972 (pp30) REVERT: C 245 ASP cc_start: 0.8628 (t0) cc_final: 0.8300 (t0) REVERT: C 279 GLU cc_start: 0.8899 (pm20) cc_final: 0.8600 (pm20) REVERT: C 280 LYS cc_start: 0.4565 (mmtt) cc_final: 0.3219 (mmmt) REVERT: C 293 ASN cc_start: 0.9294 (m110) cc_final: 0.9042 (p0) REVERT: C 304 LYS cc_start: 0.9158 (tppt) cc_final: 0.8625 (tppt) REVERT: C 308 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8331 (mtm110) REVERT: C 319 TYR cc_start: 0.8899 (m-80) cc_final: 0.8352 (m-80) REVERT: C 377 MET cc_start: 0.8438 (ttp) cc_final: 0.7697 (ttp) REVERT: C 393 HIS cc_start: 0.8823 (t70) cc_final: 0.8602 (t70) REVERT: C 420 GLU cc_start: 0.8582 (pt0) cc_final: 0.8236 (pm20) REVERT: C 433 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8711 (mm-30) REVERT: D 19 LYS cc_start: 0.8833 (tptt) cc_final: 0.8531 (mmmt) REVERT: D 41 ASP cc_start: 0.8748 (p0) cc_final: 0.8389 (p0) REVERT: D 124 CYS cc_start: 0.8922 (m) cc_final: 0.8588 (p) REVERT: D 198 GLU cc_start: 0.8392 (pt0) cc_final: 0.7861 (pt0) REVERT: D 252 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8670 (ttmm) REVERT: D 266 PHE cc_start: 0.8752 (m-10) cc_final: 0.8453 (m-10) REVERT: D 291 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8537 (pp30) REVERT: D 307 HIS cc_start: 0.9397 (m-70) cc_final: 0.9083 (m-70) REVERT: D 327 ASP cc_start: 0.9002 (m-30) cc_final: 0.8727 (m-30) REVERT: D 341 PHE cc_start: 0.8855 (m-80) cc_final: 0.8602 (m-80) REVERT: D 379 LYS cc_start: 0.9175 (mtmt) cc_final: 0.8941 (mtmt) REVERT: E 15 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: E 36 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8145 (ttt) REVERT: E 214 ARG cc_start: 0.9179 (tmm-80) cc_final: 0.8686 (tmm-80) REVERT: E 280 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8542 (mtmm) REVERT: E 326 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9014 (ttpt) REVERT: E 361 THR cc_start: 0.9210 (m) cc_final: 0.8940 (t) REVERT: E 392 ASP cc_start: 0.8883 (m-30) cc_final: 0.8514 (m-30) REVERT: E 396 ASP cc_start: 0.8602 (m-30) cc_final: 0.8276 (m-30) REVERT: E 433 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8677 (mm-30) REVERT: E 438 ASP cc_start: 0.8728 (t0) cc_final: 0.8385 (t0) REVERT: F 41 ASP cc_start: 0.8817 (p0) cc_final: 0.8431 (p0) REVERT: F 50 TYR cc_start: 0.8974 (m-10) cc_final: 0.8754 (m-80) REVERT: F 86 ARG cc_start: 0.5040 (mmt180) cc_final: 0.3890 (tpt170) REVERT: F 161 ASP cc_start: 0.9205 (p0) cc_final: 0.8971 (p0) REVERT: F 252 LYS cc_start: 0.9282 (tttp) cc_final: 0.9013 (mttm) REVERT: F 266 PHE cc_start: 0.8858 (m-10) cc_final: 0.8128 (m-10) REVERT: F 291 GLN cc_start: 0.8791 (pp30) cc_final: 0.8484 (pp30) REVERT: F 323 MET cc_start: 0.8530 (mmt) cc_final: 0.7986 (mmt) REVERT: F 324 LYS cc_start: 0.9259 (ptmm) cc_final: 0.9041 (ptmm) REVERT: F 327 ASP cc_start: 0.8977 (m-30) cc_final: 0.8678 (m-30) REVERT: F 337 ASN cc_start: 0.8527 (t0) cc_final: 0.8315 (t0) REVERT: F 375 GLN cc_start: 0.8011 (pp30) cc_final: 0.6043 (pp30) REVERT: F 379 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8540 (mtmt) REVERT: F 416 ASN cc_start: 0.9365 (m-40) cc_final: 0.9107 (m-40) REVERT: G 19 LYS cc_start: 0.8954 (tptt) cc_final: 0.8214 (tptt) REVERT: G 164 MET cc_start: 0.8386 (ttm) cc_final: 0.7649 (mtp) REVERT: G 197 ASP cc_start: 0.8595 (m-30) cc_final: 0.8335 (m-30) REVERT: G 203 ASP cc_start: 0.8221 (t70) cc_final: 0.7769 (t70) REVERT: G 213 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8484 (tmm-80) REVERT: G 293 MET cc_start: 0.8666 (tpp) cc_final: 0.8363 (mtt) REVERT: G 307 HIS cc_start: 0.9467 (m170) cc_final: 0.9148 (m90) REVERT: G 350 LYS cc_start: 0.9139 (tptp) cc_final: 0.8552 (tppt) REVERT: G 423 GLN cc_start: 0.8649 (tp40) cc_final: 0.7844 (tp-100) REVERT: G 427 ASP cc_start: 0.8199 (p0) cc_final: 0.7338 (p0) REVERT: H 143 THR cc_start: 0.8798 (m) cc_final: 0.8557 (p) REVERT: H 209 ASP cc_start: 0.8901 (t70) cc_final: 0.8696 (t70) REVERT: H 245 GLN cc_start: 0.8848 (mt0) cc_final: 0.8367 (mt0) REVERT: H 303 CYS cc_start: 0.8296 (p) cc_final: 0.7897 (p) REVERT: H 375 GLN cc_start: 0.8843 (pt0) cc_final: 0.8348 (pp30) REVERT: H 423 GLN cc_start: 0.8683 (tp40) cc_final: 0.8126 (tp-100) REVERT: H 427 ASP cc_start: 0.7953 (p0) cc_final: 0.7608 (p0) REVERT: I 203 ASP cc_start: 0.8345 (t0) cc_final: 0.7836 (t0) REVERT: I 293 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8326 (mtt) REVERT: I 299 MET cc_start: 0.9188 (tpp) cc_final: 0.8341 (mpp) REVERT: I 303 CYS cc_start: 0.8513 (p) cc_final: 0.7990 (p) REVERT: I 315 THR cc_start: 0.9734 (m) cc_final: 0.9265 (p) REVERT: I 336 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8262 (ptmm) REVERT: I 362 LYS cc_start: 0.8909 (tmmt) cc_final: 0.8524 (tmmt) REVERT: I 363 MET cc_start: 0.8850 (ptt) cc_final: 0.8529 (ptt) REVERT: I 379 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8815 (mtmt) REVERT: I 383 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8586 (tm-30) REVERT: I 406 MET cc_start: 0.8449 (tpt) cc_final: 0.7315 (tpp) REVERT: I 423 GLN cc_start: 0.8820 (tp40) cc_final: 0.8316 (tp40) REVERT: J 67 PHE cc_start: 0.8734 (m-80) cc_final: 0.8479 (m-10) REVERT: J 90 GLU cc_start: 0.8944 (mp0) cc_final: 0.8730 (mp0) REVERT: J 154 MET cc_start: 0.9216 (mmp) cc_final: 0.8809 (mmp) REVERT: J 155 GLU cc_start: 0.9372 (mt-10) cc_final: 0.8988 (mt-10) REVERT: J 168 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7684 (mt-10) REVERT: J 203 MET cc_start: 0.8927 (mmm) cc_final: 0.8527 (mmm) REVERT: J 205 ASP cc_start: 0.8107 (t0) cc_final: 0.7774 (t0) REVERT: J 214 ARG cc_start: 0.8625 (ttp80) cc_final: 0.8163 (ttp80) REVERT: J 290 GLU cc_start: 0.9268 (pt0) cc_final: 0.8877 (pp20) REVERT: J 293 ASN cc_start: 0.9594 (m-40) cc_final: 0.9275 (m-40) REVERT: J 313 MET cc_start: 0.8394 (mpp) cc_final: 0.7949 (mtm) REVERT: J 357 TYR cc_start: 0.9127 (m-80) cc_final: 0.8251 (m-80) REVERT: J 377 MET cc_start: 0.8761 (ttm) cc_final: 0.8556 (ttm) REVERT: J 396 ASP cc_start: 0.8586 (m-30) cc_final: 0.8332 (m-30) REVERT: J 413 MET cc_start: 0.8842 (mtp) cc_final: 0.8513 (ttm) REVERT: J 420 GLU cc_start: 0.8885 (pt0) cc_final: 0.8482 (pm20) REVERT: J 425 MET cc_start: 0.9029 (tpp) cc_final: 0.8589 (tpt) REVERT: K 205 ASP cc_start: 0.7965 (t0) cc_final: 0.7246 (t0) REVERT: K 207 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8942 (mm-30) REVERT: K 214 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8144 (ttp80) REVERT: K 218 ASP cc_start: 0.9400 (m-30) cc_final: 0.9192 (m-30) REVERT: K 290 GLU cc_start: 0.9450 (pt0) cc_final: 0.9086 (pt0) REVERT: K 300 ASN cc_start: 0.9083 (t0) cc_final: 0.8825 (t0) REVERT: L 21 TRP cc_start: 0.9348 (m100) cc_final: 0.8904 (m100) REVERT: L 22 GLU cc_start: 0.9103 (pt0) cc_final: 0.8871 (pt0) REVERT: L 76 ASP cc_start: 0.9338 (m-30) cc_final: 0.9127 (m-30) REVERT: L 150 THR cc_start: 0.9388 (m) cc_final: 0.9110 (p) REVERT: L 155 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8974 (mt-10) REVERT: L 205 ASP cc_start: 0.8348 (t70) cc_final: 0.7244 (t0) REVERT: L 214 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8192 (ttp80) REVERT: L 218 ASP cc_start: 0.9390 (m-30) cc_final: 0.9149 (m-30) REVERT: L 286 LEU cc_start: 0.9346 (mt) cc_final: 0.9048 (pp) REVERT: L 290 GLU cc_start: 0.9396 (tt0) cc_final: 0.9101 (mt-10) REVERT: L 293 ASN cc_start: 0.9456 (m110) cc_final: 0.9185 (p0) REVERT: L 304 LYS cc_start: 0.9344 (tppt) cc_final: 0.8967 (tppt) REVERT: L 308 ARG cc_start: 0.9122 (mtm-85) cc_final: 0.8766 (mtm-85) REVERT: L 313 MET cc_start: 0.9009 (mtm) cc_final: 0.8123 (mtm) REVERT: L 413 MET cc_start: 0.8358 (ttm) cc_final: 0.7876 (ttm) REVERT: L 430 LYS cc_start: 0.9521 (ptmm) cc_final: 0.9318 (pttm) REVERT: M 14 ASN cc_start: 0.8055 (p0) cc_final: 0.7689 (p0) REVERT: M 20 MET cc_start: 0.9095 (mtt) cc_final: 0.8850 (mtp) REVERT: M 29 HIS cc_start: 0.9159 (t-90) cc_final: 0.8497 (t-90) REVERT: M 57 HIS cc_start: 0.7490 (t-170) cc_final: 0.7237 (t70) REVERT: M 84 LYS cc_start: 0.9390 (ttmt) cc_final: 0.9036 (ttpt) REVERT: M 103 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7810 (t70) REVERT: M 104 ASN cc_start: 0.8572 (m-40) cc_final: 0.8286 (m110) REVERT: M 118 ASN cc_start: 0.7990 (m-40) cc_final: 0.7677 (m110) REVERT: N 29 HIS cc_start: 0.9162 (t-90) cc_final: 0.8499 (t-90) REVERT: N 100 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7776 (mmtp) REVERT: N 103 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7701 (t70) REVERT: N 114 PHE cc_start: 0.8965 (t80) cc_final: 0.8747 (t80) REVERT: N 118 ASN cc_start: 0.7868 (m-40) cc_final: 0.6960 (m110) REVERT: N 122 LYS cc_start: 0.8503 (ptpp) cc_final: 0.8139 (pttt) outliers start: 158 outliers final: 138 residues processed: 1432 average time/residue: 0.2691 time to fit residues: 625.3464 Evaluate side-chains 1457 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1309 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 304 ASP Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 336 LYS Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 336 LYS Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 40 optimal weight: 7.9990 chunk 396 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 306 optimal weight: 8.9990 chunk 419 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 317 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 462 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 227 HIS I 57 HIS ** I 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.090417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071277 restraints weight = 104775.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.073736 restraints weight = 57288.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075480 restraints weight = 36990.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076654 restraints weight = 27035.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077474 restraints weight = 21594.432| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 44232 Z= 0.168 Angle : 0.713 14.564 60052 Z= 0.362 Chirality : 0.046 0.214 6552 Planarity : 0.005 0.088 7788 Dihedral : 11.782 178.633 6068 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 3.49 % Allowed : 24.16 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 5394 helix: 1.55 (0.11), residues: 2488 sheet: 0.57 (0.19), residues: 786 loop : -0.79 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 282 TYR 0.023 0.001 TYR B 281 PHE 0.028 0.002 PHE D 367 TRP 0.028 0.002 TRP G 344 HIS 0.013 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00386 (44232) covalent geometry : angle 0.71258 (60052) hydrogen bonds : bond 0.04146 ( 2164) hydrogen bonds : angle 4.73613 ( 6381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12582.43 seconds wall clock time: 217 minutes 18.56 seconds (13038.56 seconds total)