Starting phenix.real_space_refine on Sat Mar 7 09:44:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sja_25160/03_2026/7sja_25160.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sja_25160/03_2026/7sja_25160.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/7sja_25160/03_2026/7sja_25160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sja_25160/03_2026/7sja_25160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sja_25160/03_2026/7sja_25160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sja_25160/03_2026/7sja_25160.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= -0.001 sd= 1.394 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 282 5.16 5 C 25698 2.51 5 N 6978 2.21 5 O 7914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 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: 40920 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 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: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 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: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 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: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Chain: "K" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Chain: "L" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 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: 9.58, per 1000 atoms: 0.23 Number of scatterers: 40920 At special positions: 0 Unit cell: (167.9, 103.5, 216.2, 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 282 16.00 P 36 15.00 Mg 12 11.99 O 7914 8.00 N 6978 7.00 C 25698 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 3.1 seconds 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9588 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 30 sheets defined 54.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.808A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.475A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.708A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (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 217 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.756A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.511A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.588A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 4.305A pdb=" N GLU A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.206A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.635A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.016A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.612A 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: 4.461A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.824A pdb=" N PHE B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.560A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.119A 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: 4.033A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.543A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (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: 3.514A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 4.039A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.070A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.404A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.795A 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 48 through 51 removed outlier: 3.808A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.474A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 111 through 128 removed outlier: 4.708A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (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 217 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.756A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.511A pdb=" N VAL C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.587A pdb=" N LYS C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 401 removed outlier: 4.305A pdb=" N GLU C 386 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.206A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.635A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.015A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.612A 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: 4.461A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.823A pdb=" N PHE D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 127 removed outlier: 3.560A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.119A 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: 4.032A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.543A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.514A pdb=" N VAL D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 4.039A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 373 through 391 removed outlier: 4.071A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 4.404A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.794A 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 48 through 51 removed outlier: 3.808A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.476A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 111 through 128 removed outlier: 4.708A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (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 217 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.757A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.511A pdb=" N VAL E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 298 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.588A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 401 removed outlier: 4.305A pdb=" N GLU E 386 " --> pdb=" O THR E 382 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.206A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.634A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 40 through 46 removed outlier: 4.014A pdb=" N LEU F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.611A 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: 4.462A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.824A pdb=" N PHE F 90 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 108 through 127 removed outlier: 3.559A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.118A 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: 4.033A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 214 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.542A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 241 " --> pdb=" O THR F 237 " (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 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.513A pdb=" N VAL F 326 " --> pdb=" O SER F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 removed outlier: 4.038A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 373 through 391 removed outlier: 4.070A pdb=" N LEU F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.404A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.795A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 40 through 46 removed outlier: 4.015A pdb=" N LEU G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.612A 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: 4.461A pdb=" N MET G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.824A pdb=" N PHE G 90 " --> pdb=" O PRO G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 108 through 127 removed outlier: 3.560A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.118A 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: 4.033A pdb=" N ASN G 184 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 214 Processing helix chain 'G' and resid 221 through 242 removed outlier: 3.543A pdb=" N LEU G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG G 241 " --> pdb=" O THR G 237 " (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 337 removed outlier: 3.514A pdb=" N VAL G 326 " --> pdb=" O SER G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 341 removed outlier: 4.039A pdb=" N PHE G 341 " --> pdb=" O SER G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 341' Processing helix chain 'G' and resid 373 through 391 removed outlier: 4.070A pdb=" N LEU G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 401 removed outlier: 4.404A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.795A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 40 through 46 removed outlier: 4.015A pdb=" N LEU H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.461A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.824A pdb=" N PHE H 90 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.559A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 Processing helix chain 'H' and resid 180 through 196 removed outlier: 4.033A pdb=" N ASN H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 214 Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.543A pdb=" N LEU H 225 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG H 241 " --> pdb=" O THR H 237 " (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 Processing helix chain 'H' and resid 304 through 308 Processing helix chain 'H' and resid 322 through 337 removed outlier: 3.514A pdb=" N VAL H 326 " --> pdb=" O SER H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 341 removed outlier: 4.039A pdb=" N PHE H 341 " --> pdb=" O SER H 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 338 through 341' Processing helix chain 'H' and resid 373 through 391 removed outlier: 4.071A pdb=" N LEU H 377 " --> pdb=" O ALA H 373 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 401 removed outlier: 4.405A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.795A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 40 through 46 removed outlier: 4.015A pdb=" N LEU I 44 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.612A 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: 4.462A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.823A pdb=" N PHE I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 127 removed outlier: 3.559A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 Processing helix chain 'I' and resid 180 through 196 removed outlier: 4.032A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 221 through 242 removed outlier: 3.543A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (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 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.514A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 removed outlier: 4.039A pdb=" N PHE I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 341' Processing helix chain 'I' and resid 373 through 391 removed outlier: 4.070A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG I 391 " --> pdb=" O ALA I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 401 removed outlier: 4.404A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.795A 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 48 through 51 removed outlier: 3.808A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 48 through 51' Processing helix chain 'J' and resid 71 through 81 removed outlier: 4.475A pdb=" N ILE J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 111 through 128 removed outlier: 4.708A pdb=" N ASP J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU J 117 " --> pdb=" O GLU J 113 " (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 217 Processing helix chain 'J' and resid 223 through 244 removed outlier: 3.757A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.511A pdb=" N VAL J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 281 Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 298 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 removed outlier: 3.587A pdb=" N LYS J 338 " --> pdb=" O THR J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 401 removed outlier: 4.305A pdb=" N GLU J 386 " --> pdb=" O THR J 382 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 4.205A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.635A 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 48 through 51 removed outlier: 3.807A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 71 through 81 removed outlier: 4.475A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 111 through 128 removed outlier: 4.708A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU K 117 " --> pdb=" O GLU K 113 " (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 217 Processing helix chain 'K' and resid 223 through 244 removed outlier: 3.758A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.511A pdb=" N VAL K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 281 Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 298 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 removed outlier: 3.588A pdb=" N LYS K 338 " --> pdb=" O THR K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 401 removed outlier: 4.305A pdb=" N GLU K 386 " --> pdb=" O THR K 382 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA K 389 " --> pdb=" O ALA K 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.206A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.635A 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 48 through 51 removed outlier: 3.808A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'L' and resid 71 through 81 removed outlier: 4.476A pdb=" N ILE L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 111 through 128 removed outlier: 4.708A pdb=" N ASP L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU L 117 " --> pdb=" O GLU L 113 " (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 217 Processing helix chain 'L' and resid 223 through 244 removed outlier: 3.756A pdb=" N LEU L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 3.511A pdb=" N VAL L 260 " --> pdb=" O GLN L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 281 Processing helix chain 'L' and resid 287 through 297 Processing helix 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 removed outlier: 3.587A pdb=" N LYS L 338 " --> pdb=" O THR L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 401 removed outlier: 4.306A pdb=" N GLU L 386 " --> pdb=" O THR L 382 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA L 389 " --> pdb=" O ALA L 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 4.206A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.634A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.146A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 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 91 through 92 removed outlier: 8.324A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.147A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU C 3 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE C 135 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 5 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL C 137 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 7 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS C 139 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL C 9 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA9, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.325A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.147A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 273 Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 92 removed outlier: 8.324A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AB7, first strand: chain 'G' and resid 91 through 92 removed outlier: 8.324A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL G 169 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N HIS G 137 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AB9, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.324A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL H 169 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N HIS H 137 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AC2, first strand: chain 'I' and resid 91 through 92 removed outlier: 8.323A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AC4, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.146A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU J 3 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE J 135 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE J 5 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL J 137 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE J 7 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS J 139 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL J 9 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN J 133 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU J 167 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE J 135 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE J 169 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL J 137 " --> pdb=" O PHE J 169 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE J 171 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS J 139 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'J' and resid 269 through 273 Processing sheet with id=AC7, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.146A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU K 3 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE K 135 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE K 5 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL K 137 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE K 7 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS K 139 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 9 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN K 133 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU K 167 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE K 135 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE K 169 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL K 137 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE K 171 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS K 139 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AC9, first strand: chain 'K' and resid 269 through 273 Processing sheet with id=AD1, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.147A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU L 3 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE L 135 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE L 5 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL L 137 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE L 7 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS L 139 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL L 9 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN L 133 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU L 167 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE L 135 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE L 169 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL L 137 " --> pdb=" O PHE L 169 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE L 171 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS L 139 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'L' and resid 269 through 273 2028 hydrogen bonds defined for protein. 5850 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: 9.68 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13545 1.34 - 1.46: 7208 1.46 - 1.57: 20587 1.57 - 1.69: 60 1.69 - 1.81: 444 Bond restraints: 41844 Sorted by residual: bond pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.74e+00 bond pdb=" CA ARG B 359 " pdb=" C ARG B 359 " ideal model delta sigma weight residual 1.523 1.543 -0.020 1.34e-02 5.57e+03 2.18e+00 bond pdb=" N ARG B 359 " pdb=" CA ARG B 359 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.13e+00 bond pdb=" CA PHE L 169 " pdb=" CB PHE L 169 " ideal model delta sigma weight residual 1.539 1.475 0.065 4.88e-02 4.20e+02 1.75e+00 bond pdb=" CA PHE A 169 " pdb=" CB PHE A 169 " ideal model delta sigma weight residual 1.539 1.476 0.064 4.88e-02 4.20e+02 1.70e+00 ... (remaining 41839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 56639 3.23 - 6.46: 201 6.46 - 9.69: 2 9.69 - 12.92: 1 12.92 - 16.15: 1 Bond angle restraints: 56844 Sorted by residual: angle pdb=" N ARG D 359 " pdb=" CA ARG D 359 " pdb=" C ARG D 359 " ideal model delta sigma weight residual 110.80 126.95 -16.15 2.13e+00 2.20e-01 5.75e+01 angle pdb=" N PRO F 358 " pdb=" CA PRO F 358 " pdb=" C PRO F 358 " ideal model delta sigma weight residual 111.19 102.57 8.62 1.57e+00 4.06e-01 3.02e+01 angle pdb=" N ARG G 359 " pdb=" CA ARG G 359 " pdb=" C ARG G 359 " ideal model delta sigma weight residual 110.10 118.15 -8.05 1.49e+00 4.50e-01 2.92e+01 angle pdb=" N ARG B 359 " pdb=" CA ARG B 359 " pdb=" C ARG B 359 " ideal model delta sigma weight residual 110.80 122.25 -11.45 2.13e+00 2.20e-01 2.89e+01 angle pdb=" N GLY G 360 " pdb=" CA GLY G 360 " pdb=" C GLY G 360 " ideal model delta sigma weight residual 114.69 120.96 -6.27 1.19e+00 7.06e-01 2.78e+01 ... (remaining 56839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.04: 24424 33.04 - 66.08: 416 66.08 - 99.12: 24 99.12 - 132.15: 6 132.15 - 165.19: 18 Dihedral angle restraints: 24888 sinusoidal: 9948 harmonic: 14940 Sorted by residual: dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -60.60 165.19 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP K 501 " pdb=" C1' GTP K 501 " pdb=" N9 GTP K 501 " pdb=" O4' GTP K 501 " ideal model delta sinusoidal sigma weight residual 104.59 -60.58 165.17 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP J 501 " pdb=" C1' GTP J 501 " pdb=" N9 GTP J 501 " pdb=" O4' GTP J 501 " ideal model delta sinusoidal sigma weight residual 104.59 -60.56 165.16 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 24885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 5863 0.090 - 0.180: 355 0.180 - 0.270: 2 0.270 - 0.360: 1 0.360 - 0.450: 1 Chirality restraints: 6222 Sorted by residual: 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 2.06 0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA ARG B 359 " pdb=" N ARG B 359 " pdb=" C ARG B 359 " pdb=" CB ARG B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 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 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 6219 not shown) Planarity restraints: 7386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 357 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C PRO F 357 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO F 357 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO F 358 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 357 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C PRO D 357 " 0.038 2.00e-02 2.50e+03 pdb=" O PRO D 357 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO D 358 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 357 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C PRO B 357 " -0.037 2.00e-02 2.50e+03 pdb=" O PRO B 357 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 358 " 0.012 2.00e-02 2.50e+03 ... (remaining 7383 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 565 2.54 - 3.13: 34732 3.13 - 3.72: 66908 3.72 - 4.31: 89787 4.31 - 4.90: 150838 Nonbonded interactions: 342830 Sorted by model distance: nonbonded pdb=" O3B GTP J 501 " pdb="MG MG J 502 " model vdw 1.951 2.170 nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 1.951 2.170 nonbonded pdb=" O3B GTP K 501 " pdb="MG MG K 502 " model vdw 1.951 2.170 nonbonded pdb=" O3B GTP C 501 " pdb="MG MG C 502 " model vdw 1.951 2.170 nonbonded pdb=" O3B GTP L 501 " pdb="MG MG L 502 " model vdw 1.951 2.170 ... (remaining 342825 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: 0.08 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' } 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: 8.670 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: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 38.300 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.230 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:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.005 0.253 41862 Z= 0.255 Angle : 0.604 16.150 56844 Z= 0.347 Chirality : 0.043 0.450 6222 Planarity : 0.004 0.044 7386 Dihedral : 13.621 165.193 15300 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 5.93 % Allowed : 7.27 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.48 (0.12), residues: 5130 helix: 0.74 (0.10), residues: 2496 sheet: -0.17 (0.18), residues: 744 loop : -1.81 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 380 TYR 0.008 0.001 TYR L 83 PHE 0.010 0.001 PHE A 296 TRP 0.011 0.002 TRP F 21 HIS 0.005 0.001 HIS G 396 Details of bonding type rmsd covalent geometry : bond 0.00445 (41844) covalent geometry : angle 0.60413 (56844) hydrogen bonds : bond 0.12767 ( 2028) hydrogen bonds : angle 5.81026 ( 5850) Misc. bond : bond 0.06592 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1853 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 1592 time to evaluate : 1.584 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 CYS cc_start: 0.8223 (m) cc_final: 0.7867 (m) REVERT: A 33 ASP cc_start: 0.7798 (m-30) cc_final: 0.7449 (p0) REVERT: A 149 PHE cc_start: 0.8975 (t80) cc_final: 0.8743 (t80) REVERT: A 167 LEU cc_start: 0.8556 (mt) cc_final: 0.8117 (mt) REVERT: A 172 TYR cc_start: 0.7382 (t80) cc_final: 0.7010 (t80) REVERT: A 223 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7102 (p) REVERT: A 283 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6836 (m170) REVERT: A 317 LEU cc_start: 0.8933 (mt) cc_final: 0.8505 (mt) REVERT: A 396 ASP cc_start: 0.8145 (m-30) cc_final: 0.7738 (m-30) REVERT: A 402 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7616 (tpp80) REVERT: A 413 MET cc_start: 0.7489 (ttm) cc_final: 0.7073 (ttm) REVERT: A 430 LYS cc_start: 0.9304 (ttmt) cc_final: 0.8672 (tppt) REVERT: B 33 SER cc_start: 0.8660 (m) cc_final: 0.8132 (p) REVERT: B 184 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7421 (p0) REVERT: B 279 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: B 321 MET cc_start: 0.8275 (ptp) cc_final: 0.8074 (ptp) REVERT: B 324 LYS cc_start: 0.8881 (tmtp) cc_final: 0.8119 (tppt) REVERT: B 363 MET cc_start: 0.7312 (ptp) cc_final: 0.7065 (ptp) REVERT: B 395 LEU cc_start: 0.7994 (tp) cc_final: 0.7749 (tp) REVERT: B 415 MET cc_start: 0.7271 (ttm) cc_final: 0.6577 (ttp) REVERT: C 69 ASP cc_start: 0.7915 (t0) cc_final: 0.7218 (t70) REVERT: C 115 ILE cc_start: 0.9012 (tp) cc_final: 0.8677 (tp) REVERT: C 167 LEU cc_start: 0.8893 (mt) cc_final: 0.8426 (mt) REVERT: C 207 GLU cc_start: 0.8269 (tt0) cc_final: 0.8038 (mt-10) REVERT: C 223 THR cc_start: 0.7509 (OUTLIER) cc_final: 0.7248 (p) REVERT: C 257 THR cc_start: 0.9229 (m) cc_final: 0.9004 (p) REVERT: C 283 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5885 (m170) REVERT: C 301 GLN cc_start: 0.8138 (mt0) cc_final: 0.7573 (mm-40) REVERT: C 302 MET cc_start: 0.8225 (mtt) cc_final: 0.8005 (mtt) REVERT: C 430 LYS cc_start: 0.9381 (ttmt) cc_final: 0.9042 (pttm) REVERT: D 33 SER cc_start: 0.8885 (m) cc_final: 0.8520 (p) REVERT: D 94 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8238 (mm-40) REVERT: D 279 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: D 364 SER cc_start: 0.8500 (p) cc_final: 0.8163 (p) REVERT: D 395 LEU cc_start: 0.8181 (tp) cc_final: 0.7788 (tp) REVERT: E 20 CYS cc_start: 0.8606 (m) cc_final: 0.8254 (m) REVERT: E 49 PHE cc_start: 0.8373 (p90) cc_final: 0.7950 (p90) REVERT: E 69 ASP cc_start: 0.7902 (t0) cc_final: 0.7359 (t0) REVERT: E 84 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.8255 (ttp-110) REVERT: E 232 SER cc_start: 0.8829 (p) cc_final: 0.8423 (t) REVERT: E 257 THR cc_start: 0.9313 (m) cc_final: 0.8980 (p) REVERT: E 282 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: E 407 TRP cc_start: 0.8490 (m100) cc_final: 0.8194 (m100) REVERT: E 420 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8240 (pp20) REVERT: E 430 LYS cc_start: 0.9413 (ttmt) cc_final: 0.9062 (tppt) REVERT: F 3 GLU cc_start: 0.6393 (mp0) cc_final: 0.5762 (mp0) REVERT: F 33 SER cc_start: 0.8674 (m) cc_final: 0.8214 (p) REVERT: F 81 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6455 (m-10) REVERT: F 257 MET cc_start: 0.8488 (mmp) cc_final: 0.7969 (mmm) REVERT: F 279 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: F 281 TYR cc_start: 0.8075 (m-80) cc_final: 0.7592 (m-80) REVERT: F 297 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8148 (ptpt) REVERT: F 363 MET cc_start: 0.7448 (ptp) cc_final: 0.7190 (ptp) REVERT: G 2 ARG cc_start: 0.8816 (mtm180) cc_final: 0.8519 (mtm180) REVERT: G 6 HIS cc_start: 0.8069 (t70) cc_final: 0.7418 (t70) REVERT: G 11 GLN cc_start: 0.7972 (tt0) cc_final: 0.7767 (pt0) REVERT: G 27 GLU cc_start: 0.8817 (tt0) cc_final: 0.8604 (tt0) REVERT: G 41 ASP cc_start: 0.7579 (p0) cc_final: 0.6982 (p0) REVERT: G 58 LYS cc_start: 0.7175 (tttt) cc_final: 0.6957 (ttpt) REVERT: G 67 ASP cc_start: 0.8531 (t0) cc_final: 0.7312 (p0) REVERT: G 81 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: G 92 PHE cc_start: 0.8309 (p90) cc_final: 0.7133 (p90) REVERT: G 135 LEU cc_start: 0.8607 (tp) cc_final: 0.8401 (mp) REVERT: G 139 LEU cc_start: 0.7992 (mt) cc_final: 0.7777 (mt) REVERT: G 158 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8576 (tt0) REVERT: G 174 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8713 (mmmm) REVERT: G 208 TYR cc_start: 0.8910 (m-10) cc_final: 0.8661 (m-80) REVERT: G 216 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8409 (mmtp) REVERT: G 255 VAL cc_start: 0.8421 (t) cc_final: 0.8088 (p) REVERT: G 267 MET cc_start: 0.7996 (ptp) cc_final: 0.7672 (ptm) REVERT: G 289 LEU cc_start: 0.9204 (mp) cc_final: 0.8985 (mt) REVERT: G 292 GLN cc_start: 0.8034 (tt0) cc_final: 0.7796 (tt0) REVERT: G 322 SER cc_start: 0.8367 (m) cc_final: 0.8039 (p) REVERT: G 323 MET cc_start: 0.8162 (mmm) cc_final: 0.7927 (tpp) REVERT: G 367 PHE cc_start: 0.8581 (t80) cc_final: 0.8261 (t80) REVERT: G 376 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7959 (pt0) REVERT: G 379 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8902 (mttt) REVERT: G 397 TRP cc_start: 0.8634 (m100) cc_final: 0.8353 (m-10) REVERT: H 2 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8022 (ptm160) REVERT: H 6 HIS cc_start: 0.8241 (t70) cc_final: 0.7659 (t70) REVERT: H 41 ASP cc_start: 0.7205 (p0) cc_final: 0.6676 (p0) REVERT: H 118 ASP cc_start: 0.8650 (m-30) cc_final: 0.8285 (t0) REVERT: H 130 LEU cc_start: 0.8419 (tp) cc_final: 0.8156 (tp) REVERT: H 154 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8282 (mmmm) REVERT: H 159 TYR cc_start: 0.7866 (m-80) cc_final: 0.7328 (m-80) REVERT: H 216 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8470 (mmtp) REVERT: H 255 VAL cc_start: 0.7970 (t) cc_final: 0.7474 (p) REVERT: H 267 MET cc_start: 0.7685 (ptp) cc_final: 0.6822 (ptp) REVERT: H 293 MET cc_start: 0.8269 (mtm) cc_final: 0.8042 (mtp) REVERT: H 297 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8255 (mmtm) REVERT: H 321 MET cc_start: 0.8625 (ptp) cc_final: 0.8293 (ptp) REVERT: H 322 SER cc_start: 0.8127 (m) cc_final: 0.7633 (p) REVERT: H 339 SER cc_start: 0.7382 (p) cc_final: 0.7048 (t) REVERT: H 351 VAL cc_start: 0.9422 (t) cc_final: 0.9052 (m) REVERT: H 397 TRP cc_start: 0.8672 (m100) cc_final: 0.8338 (m-10) REVERT: I 2 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8246 (mtm-85) REVERT: I 6 HIS cc_start: 0.8050 (t70) cc_final: 0.7553 (t70) REVERT: I 33 SER cc_start: 0.9137 (m) cc_final: 0.8874 (p) REVERT: I 41 ASP cc_start: 0.8006 (p0) cc_final: 0.7190 (p0) REVERT: I 44 LEU cc_start: 0.9147 (mt) cc_final: 0.8913 (pp) REVERT: I 67 ASP cc_start: 0.8432 (t0) cc_final: 0.7418 (p0) REVERT: I 69 GLU cc_start: 0.7632 (pt0) cc_final: 0.7347 (pm20) REVERT: I 92 PHE cc_start: 0.8203 (p90) cc_final: 0.7409 (p90) REVERT: I 130 LEU cc_start: 0.8587 (tp) cc_final: 0.8266 (tp) REVERT: I 135 LEU cc_start: 0.8873 (tp) cc_final: 0.8592 (mp) REVERT: I 154 LYS cc_start: 0.9013 (mmtp) cc_final: 0.8806 (mmmm) REVERT: I 159 TYR cc_start: 0.7934 (m-80) cc_final: 0.7675 (m-80) REVERT: I 164 MET cc_start: 0.8469 (tpp) cc_final: 0.8248 (mmm) REVERT: I 184 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8798 (p0) REVERT: I 208 TYR cc_start: 0.9082 (m-10) cc_final: 0.8735 (m-80) REVERT: I 246 LEU cc_start: 0.8286 (tp) cc_final: 0.7964 (tt) REVERT: I 267 MET cc_start: 0.7782 (ptp) cc_final: 0.7233 (ptm) REVERT: I 297 LYS cc_start: 0.8787 (ptpt) cc_final: 0.8348 (mmtm) REVERT: I 321 MET cc_start: 0.8682 (ptp) cc_final: 0.8168 (ptp) REVERT: I 322 SER cc_start: 0.8365 (m) cc_final: 0.8015 (p) REVERT: I 339 SER cc_start: 0.7588 (p) cc_final: 0.7363 (t) REVERT: I 351 VAL cc_start: 0.9584 (t) cc_final: 0.9219 (p) REVERT: I 363 MET cc_start: 0.8092 (ptp) cc_final: 0.7776 (ptp) REVERT: I 367 PHE cc_start: 0.8512 (t80) cc_final: 0.8073 (t80) REVERT: I 376 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8053 (pt0) REVERT: J 33 ASP cc_start: 0.8303 (m-30) cc_final: 0.7997 (p0) REVERT: J 110 ILE cc_start: 0.9117 (mm) cc_final: 0.8896 (tp) REVERT: J 138 PHE cc_start: 0.8545 (m-10) cc_final: 0.8251 (m-10) REVERT: J 282 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: J 283 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7834 (m170) REVERT: J 375 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8580 (p) REVERT: J 377 MET cc_start: 0.8957 (ttp) cc_final: 0.8558 (ttp) REVERT: K 50 ASN cc_start: 0.8262 (t0) cc_final: 0.7958 (t0) REVERT: K 120 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8916 (t0) REVERT: K 160 ASP cc_start: 0.8648 (t70) cc_final: 0.8446 (t0) REVERT: K 172 TYR cc_start: 0.6950 (t80) cc_final: 0.6506 (t80) REVERT: K 219 ILE cc_start: 0.8353 (mt) cc_final: 0.7879 (mt) REVERT: K 282 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: K 345 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7393 (p0) REVERT: K 351 PHE cc_start: 0.8085 (m-80) cc_final: 0.7858 (m-10) REVERT: K 357 TYR cc_start: 0.7797 (m-80) cc_final: 0.7072 (m-80) REVERT: K 377 MET cc_start: 0.8823 (ttp) cc_final: 0.8500 (ttp) REVERT: K 388 TRP cc_start: 0.8557 (m100) cc_final: 0.8345 (m100) REVERT: L 20 CYS cc_start: 0.8136 (m) cc_final: 0.7668 (m) REVERT: L 31 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7869 (mt0) REVERT: L 50 ASN cc_start: 0.8477 (t0) cc_final: 0.8212 (t0) REVERT: L 133 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7964 (mm-40) REVERT: L 149 PHE cc_start: 0.9108 (t80) cc_final: 0.8868 (t80) REVERT: L 176 GLN cc_start: 0.8519 (mt0) cc_final: 0.8267 (mt0) REVERT: L 317 LEU cc_start: 0.9426 (mt) cc_final: 0.9108 (mt) REVERT: L 375 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8127 (p) REVERT: L 377 MET cc_start: 0.8961 (ttp) cc_final: 0.8642 (ttm) outliers start: 261 outliers final: 103 residues processed: 1776 average time/residue: 0.2441 time to fit residues: 706.4290 Evaluate side-chains 1138 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1015 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 283 HIS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 283 HIS Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 494 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 249 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS B 165 ASN B 307 HIS B 347 ASN B 423 GLN C 11 GLN C 128 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 249 ASN D 126 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS D 347 ASN E 11 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 249 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS F 307 HIS F 347 ASN F 423 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN G 298 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN ** H 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN H 247 ASN H 347 ASN ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 ASN I 245 GLN I 247 ASN I 396 HIS J 88 HIS ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN J 249 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 249 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.114436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.097097 restraints weight = 91436.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.100393 restraints weight = 46318.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.102619 restraints weight = 28512.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.104136 restraints weight = 19888.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.105206 restraints weight = 15193.288| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 41862 Z= 0.226 Angle : 0.685 10.912 56844 Z= 0.350 Chirality : 0.046 0.215 6222 Planarity : 0.005 0.059 7386 Dihedral : 13.075 167.025 5971 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 6.02 % Allowed : 16.62 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.17 (0.12), residues: 5130 helix: 0.88 (0.10), residues: 2586 sheet: -0.05 (0.18), residues: 756 loop : -1.59 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 229 TYR 0.025 0.002 TYR E 24 PHE 0.021 0.002 PHE C 49 TRP 0.023 0.002 TRP A 407 HIS 0.007 0.001 HIS H 137 Details of bonding type rmsd covalent geometry : bond 0.00505 (41844) covalent geometry : angle 0.68452 (56844) hydrogen bonds : bond 0.04823 ( 2028) hydrogen bonds : angle 4.85656 ( 5850) Misc. bond : bond 0.00208 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 1116 time to evaluate : 1.834 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8698 (tppt) REVERT: B 33 SER cc_start: 0.8784 (m) cc_final: 0.8322 (p) REVERT: B 213 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8016 (tmm-80) REVERT: B 279 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: B 363 MET cc_start: 0.7490 (ptp) cc_final: 0.7213 (ptp) REVERT: C 83 TYR cc_start: 0.7779 (m-80) cc_final: 0.7463 (m-80) REVERT: C 156 ARG cc_start: 0.9000 (mtp180) cc_final: 0.8723 (mmm-85) REVERT: C 223 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7519 (p) REVERT: C 257 THR cc_start: 0.9329 (m) cc_final: 0.9102 (p) REVERT: C 302 MET cc_start: 0.8220 (mtt) cc_final: 0.8015 (mtt) REVERT: C 430 LYS cc_start: 0.9310 (ttmt) cc_final: 0.9052 (pttm) REVERT: D 33 SER cc_start: 0.9073 (m) cc_final: 0.8705 (p) REVERT: D 94 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8136 (mm-40) REVERT: D 279 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: D 364 SER cc_start: 0.8696 (p) cc_final: 0.8156 (p) REVERT: D 421 GLU cc_start: 0.8358 (tp30) cc_final: 0.8030 (tp30) REVERT: E 49 PHE cc_start: 0.8278 (p90) cc_final: 0.7992 (p90) REVERT: E 69 ASP cc_start: 0.8133 (t0) cc_final: 0.7884 (t0) REVERT: E 84 ARG cc_start: 0.8445 (ttp-110) cc_final: 0.8190 (ttp-110) REVERT: E 88 HIS cc_start: 0.7354 (t-170) cc_final: 0.6618 (t70) REVERT: E 152 LEU cc_start: 0.8625 (tp) cc_final: 0.8305 (tt) REVERT: E 172 TYR cc_start: 0.7828 (t80) cc_final: 0.7509 (t80) REVERT: E 179 THR cc_start: 0.9277 (t) cc_final: 0.9070 (t) REVERT: E 232 SER cc_start: 0.8857 (p) cc_final: 0.8562 (t) REVERT: E 282 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: E 357 TYR cc_start: 0.7934 (m-80) cc_final: 0.7581 (m-80) REVERT: E 388 TRP cc_start: 0.8837 (m100) cc_final: 0.8623 (m100) REVERT: E 411 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8533 (tp30) REVERT: E 430 LYS cc_start: 0.9425 (ttmt) cc_final: 0.9053 (tppt) REVERT: F 33 SER cc_start: 0.8830 (m) cc_final: 0.8418 (p) REVERT: F 81 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7354 (m-10) REVERT: F 111 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: F 174 LYS cc_start: 0.8886 (ptpp) cc_final: 0.8581 (ptpp) REVERT: F 177 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8271 (t0) REVERT: F 200 TYR cc_start: 0.8970 (m-10) cc_final: 0.8642 (m-10) REVERT: F 257 MET cc_start: 0.8759 (mmp) cc_final: 0.8273 (mmm) REVERT: F 279 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: F 363 MET cc_start: 0.7622 (ptp) cc_final: 0.7236 (ptp) REVERT: F 370 ASN cc_start: 0.8509 (t0) cc_final: 0.8244 (t0) REVERT: F 422 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.7575 (t80) REVERT: G 6 HIS cc_start: 0.8044 (t70) cc_final: 0.7702 (t70) REVERT: G 7 ILE cc_start: 0.9196 (mt) cc_final: 0.8944 (mp) REVERT: G 41 ASP cc_start: 0.7690 (p0) cc_final: 0.7318 (p0) REVERT: G 101 TRP cc_start: 0.8713 (t60) cc_final: 0.8154 (t60) REVERT: G 136 THR cc_start: 0.8459 (m) cc_final: 0.7852 (p) REVERT: G 154 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8313 (mmmm) REVERT: G 164 MET cc_start: 0.8742 (mmm) cc_final: 0.8538 (mmm) REVERT: G 174 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8620 (mmmm) REVERT: G 207 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8730 (mm) REVERT: G 216 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8419 (mmtp) REVERT: G 267 MET cc_start: 0.7904 (ptp) cc_final: 0.7523 (ptm) REVERT: G 323 MET cc_start: 0.8008 (mmm) cc_final: 0.7805 (tpp) REVERT: G 351 VAL cc_start: 0.9420 (t) cc_final: 0.8989 (p) REVERT: G 367 PHE cc_start: 0.8548 (t80) cc_final: 0.8277 (t80) REVERT: G 422 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6306 (t80) REVERT: G 423 GLN cc_start: 0.8545 (tp40) cc_final: 0.8229 (tm-30) REVERT: H 6 HIS cc_start: 0.8176 (t70) cc_final: 0.7542 (t70) REVERT: H 12 CYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8785 (p) REVERT: H 41 ASP cc_start: 0.7222 (p0) cc_final: 0.6868 (p0) REVERT: H 130 LEU cc_start: 0.8352 (tp) cc_final: 0.8056 (tp) REVERT: H 136 THR cc_start: 0.8396 (m) cc_final: 0.7810 (p) REVERT: H 216 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8451 (mmtp) REVERT: H 267 MET cc_start: 0.7682 (ptp) cc_final: 0.7305 (ptm) REVERT: H 300 MET cc_start: 0.7902 (mtt) cc_final: 0.7620 (mtt) REVERT: H 322 SER cc_start: 0.8116 (m) cc_final: 0.7756 (p) REVERT: H 362 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8325 (mtmm) REVERT: H 379 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8728 (ptpt) REVERT: H 397 TRP cc_start: 0.8758 (m100) cc_final: 0.8496 (m-10) REVERT: I 6 HIS cc_start: 0.8070 (t70) cc_final: 0.7439 (t70) REVERT: I 35 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8443 (p0) REVERT: I 41 ASP cc_start: 0.7788 (p0) cc_final: 0.7152 (p0) REVERT: I 44 LEU cc_start: 0.9116 (mt) cc_final: 0.8896 (pp) REVERT: I 130 LEU cc_start: 0.8417 (tp) cc_final: 0.8088 (tp) REVERT: I 136 THR cc_start: 0.8250 (m) cc_final: 0.7567 (p) REVERT: I 184 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8373 (p0) REVERT: I 246 LEU cc_start: 0.8387 (tp) cc_final: 0.8124 (tt) REVERT: I 267 MET cc_start: 0.7924 (ptp) cc_final: 0.7522 (ptm) REVERT: I 289 LEU cc_start: 0.9111 (mt) cc_final: 0.8870 (mt) REVERT: I 322 SER cc_start: 0.8270 (m) cc_final: 0.7968 (p) REVERT: I 363 MET cc_start: 0.8318 (ptp) cc_final: 0.8049 (ptp) REVERT: I 367 PHE cc_start: 0.8531 (t80) cc_final: 0.8133 (t80) REVERT: I 379 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8686 (ptpt) REVERT: I 388 MET cc_start: 0.7221 (mmt) cc_final: 0.7012 (mmt) REVERT: J 84 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7847 (ttp-110) REVERT: J 138 PHE cc_start: 0.8636 (m-10) cc_final: 0.8327 (m-10) REVERT: J 207 GLU cc_start: 0.8303 (tp30) cc_final: 0.8084 (tp30) REVERT: J 229 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8255 (mmm160) REVERT: J 282 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: J 388 TRP cc_start: 0.8583 (m100) cc_final: 0.8239 (m100) REVERT: K 31 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8125 (mt0) REVERT: K 50 ASN cc_start: 0.8250 (t0) cc_final: 0.8044 (t0) REVERT: K 127 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7777 (p0) REVERT: K 156 ARG cc_start: 0.9071 (mmm-85) cc_final: 0.8851 (mmm-85) REVERT: K 172 TYR cc_start: 0.7350 (t80) cc_final: 0.6776 (t80) REVERT: K 282 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: K 283 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7632 (m170) REVERT: K 388 TRP cc_start: 0.8753 (m100) cc_final: 0.8222 (m100) REVERT: L 84 ARG cc_start: 0.8192 (ttp-110) cc_final: 0.7222 (ttm-80) REVERT: L 183 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8359 (mm-30) REVERT: L 302 MET cc_start: 0.8375 (mtt) cc_final: 0.8130 (mtt) outliers start: 265 outliers final: 177 residues processed: 1288 average time/residue: 0.2573 time to fit residues: 548.3768 Evaluate side-chains 1116 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 921 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 320 ARG Chi-restraints excluded: chain H residue 367 PHE Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 283 HIS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 283 HIS Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 428 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 332 ILE Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 255 optimal weight: 9.9990 chunk 442 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 448 optimal weight: 0.1980 chunk 154 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 458 optimal weight: 3.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN D 165 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS F 256 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 396 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 245 GLN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN ** L 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.114214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.096983 restraints weight = 92046.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.100205 restraints weight = 46696.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.102398 restraints weight = 28812.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.103885 restraints weight = 20179.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.104931 restraints weight = 15455.779| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 41862 Z= 0.195 Angle : 0.663 9.001 56844 Z= 0.339 Chirality : 0.046 0.208 6222 Planarity : 0.004 0.074 7386 Dihedral : 12.948 168.269 5917 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.04 % Allowed : 18.07 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.02 (0.12), residues: 5130 helix: 1.07 (0.10), residues: 2490 sheet: 0.13 (0.18), residues: 756 loop : -1.46 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 380 TYR 0.023 0.002 TYR I 159 PHE 0.025 0.002 PHE K 49 TRP 0.041 0.002 TRP A 407 HIS 0.013 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00440 (41844) covalent geometry : angle 0.66257 (56844) hydrogen bonds : bond 0.04453 ( 2028) hydrogen bonds : angle 4.74865 ( 5850) Misc. bond : bond 0.00203 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 1022 time to evaluate : 1.733 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8317 (p90) cc_final: 0.8086 (p90) REVERT: A 149 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8676 (t80) REVERT: A 262 TYR cc_start: 0.9055 (m-80) cc_final: 0.8814 (m-80) REVERT: A 430 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8724 (tppt) REVERT: B 33 SER cc_start: 0.8773 (m) cc_final: 0.8343 (p) REVERT: B 111 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: B 147 MET cc_start: 0.8795 (mmm) cc_final: 0.8428 (ttm) REVERT: B 184 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7602 (p0) REVERT: B 279 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: B 395 LEU cc_start: 0.7932 (tp) cc_final: 0.7719 (tp) REVERT: B 403 MET cc_start: 0.7985 (mmm) cc_final: 0.7619 (mmm) REVERT: B 422 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7585 (t80) REVERT: C 156 ARG cc_start: 0.8892 (mtp180) cc_final: 0.8550 (mmm-85) REVERT: C 203 MET cc_start: 0.8501 (mmm) cc_final: 0.7874 (mmm) REVERT: C 223 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7651 (p) REVERT: C 257 THR cc_start: 0.9349 (m) cc_final: 0.9129 (p) REVERT: C 358 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8561 (mm110) REVERT: C 370 LYS cc_start: 0.8124 (tttp) cc_final: 0.7527 (tptp) REVERT: C 430 LYS cc_start: 0.9280 (ttmt) cc_final: 0.9053 (pttm) REVERT: C 432 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7233 (t80) REVERT: D 33 SER cc_start: 0.9087 (m) cc_final: 0.8718 (p) REVERT: D 125 GLU cc_start: 0.8228 (tp30) cc_final: 0.8005 (tp30) REVERT: D 364 SER cc_start: 0.8349 (p) cc_final: 0.7920 (p) REVERT: D 421 GLU cc_start: 0.8368 (tp30) cc_final: 0.8124 (tp30) REVERT: E 49 PHE cc_start: 0.8204 (p90) cc_final: 0.7908 (p90) REVERT: E 156 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8516 (mmm-85) REVERT: E 172 TYR cc_start: 0.7850 (t80) cc_final: 0.7576 (t80) REVERT: E 232 SER cc_start: 0.8893 (p) cc_final: 0.8623 (t) REVERT: E 284 GLU cc_start: 0.6820 (tp30) cc_final: 0.6603 (tp30) REVERT: E 357 TYR cc_start: 0.8006 (m-80) cc_final: 0.7687 (m-80) REVERT: E 388 TRP cc_start: 0.8867 (m100) cc_final: 0.8618 (m100) REVERT: E 398 MET cc_start: 0.9255 (mmm) cc_final: 0.8955 (mmm) REVERT: E 411 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8437 (tp30) REVERT: E 430 LYS cc_start: 0.9405 (ttmt) cc_final: 0.9047 (tppt) REVERT: F 33 SER cc_start: 0.8787 (m) cc_final: 0.8399 (p) REVERT: F 81 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.5793 (m-10) REVERT: F 111 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: F 177 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8365 (t0) REVERT: F 200 TYR cc_start: 0.8896 (m-10) cc_final: 0.8671 (m-10) REVERT: F 279 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: F 363 MET cc_start: 0.7434 (ptp) cc_final: 0.7026 (ptp) REVERT: F 364 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8179 (p) REVERT: F 370 ASN cc_start: 0.8575 (t0) cc_final: 0.8342 (t0) REVERT: G 6 HIS cc_start: 0.8050 (t70) cc_final: 0.7696 (t70) REVERT: G 7 ILE cc_start: 0.9270 (mt) cc_final: 0.9039 (mp) REVERT: G 41 ASP cc_start: 0.7753 (p0) cc_final: 0.7506 (p0) REVERT: G 81 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.5165 (m-10) REVERT: G 101 TRP cc_start: 0.8743 (t60) cc_final: 0.8189 (t60) REVERT: G 136 THR cc_start: 0.8637 (m) cc_final: 0.8205 (p) REVERT: G 174 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8607 (mmmm) REVERT: G 216 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8387 (mmtp) REVERT: G 267 MET cc_start: 0.7844 (ptp) cc_final: 0.7000 (ptm) REVERT: G 323 MET cc_start: 0.8056 (mmm) cc_final: 0.7757 (tpp) REVERT: G 351 VAL cc_start: 0.9435 (t) cc_final: 0.9048 (p) REVERT: G 362 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8949 (mtmm) REVERT: G 422 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6374 (t80) REVERT: H 6 HIS cc_start: 0.7933 (t70) cc_final: 0.7435 (t70) REVERT: H 41 ASP cc_start: 0.7296 (p0) cc_final: 0.7090 (p0) REVERT: H 53 GLU cc_start: 0.7487 (tp30) cc_final: 0.7181 (tp30) REVERT: H 130 LEU cc_start: 0.8394 (tp) cc_final: 0.8042 (tp) REVERT: H 136 THR cc_start: 0.8696 (m) cc_final: 0.8171 (p) REVERT: H 216 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8402 (mmtp) REVERT: H 267 MET cc_start: 0.7660 (ptp) cc_final: 0.7394 (ptp) REVERT: H 322 SER cc_start: 0.8076 (m) cc_final: 0.7430 (p) REVERT: H 362 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8353 (mtmm) REVERT: I 6 HIS cc_start: 0.8035 (t70) cc_final: 0.7603 (t70) REVERT: I 19 LYS cc_start: 0.8962 (tptt) cc_final: 0.8715 (tptt) REVERT: I 41 ASP cc_start: 0.7926 (p0) cc_final: 0.7321 (p0) REVERT: I 58 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7420 (ttpt) REVERT: I 67 ASP cc_start: 0.8175 (t0) cc_final: 0.7791 (t0) REVERT: I 92 PHE cc_start: 0.8595 (p90) cc_final: 0.8380 (p90) REVERT: I 101 TRP cc_start: 0.8593 (t60) cc_final: 0.8195 (t60) REVERT: I 130 LEU cc_start: 0.8305 (tp) cc_final: 0.8072 (tp) REVERT: I 136 THR cc_start: 0.8443 (m) cc_final: 0.7855 (p) REVERT: I 184 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8456 (p0) REVERT: I 216 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7558 (pptt) REVERT: I 246 LEU cc_start: 0.8442 (tp) cc_final: 0.8136 (tt) REVERT: I 267 MET cc_start: 0.7872 (ptp) cc_final: 0.7628 (ptm) REVERT: I 322 SER cc_start: 0.8272 (m) cc_final: 0.7831 (p) REVERT: I 363 MET cc_start: 0.8151 (ptp) cc_final: 0.7935 (ptp) REVERT: J 84 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7887 (ttp-110) REVERT: J 110 ILE cc_start: 0.9204 (mm) cc_final: 0.8869 (tp) REVERT: J 138 PHE cc_start: 0.8686 (m-10) cc_final: 0.8372 (m-10) REVERT: J 230 LEU cc_start: 0.9324 (mp) cc_final: 0.8889 (tt) REVERT: J 251 ASP cc_start: 0.7401 (t0) cc_final: 0.6937 (t70) REVERT: J 322 ASP cc_start: 0.7428 (p0) cc_final: 0.7050 (p0) REVERT: J 388 TRP cc_start: 0.8575 (m100) cc_final: 0.8275 (m100) REVERT: J 398 MET cc_start: 0.8125 (mtm) cc_final: 0.7914 (mtm) REVERT: J 432 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7222 (t80) REVERT: K 33 ASP cc_start: 0.8282 (p0) cc_final: 0.8064 (p0) REVERT: K 49 PHE cc_start: 0.8395 (p90) cc_final: 0.8138 (p90) REVERT: K 127 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7569 (p0) REVERT: K 149 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8077 (t80) REVERT: K 157 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9198 (mm) REVERT: K 282 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: K 283 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7514 (m170) REVERT: K 397 LEU cc_start: 0.8968 (mt) cc_final: 0.8743 (mp) REVERT: L 84 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.6962 (ttm-80) REVERT: L 149 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8884 (t80) REVERT: L 269 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8614 (pp) outliers start: 266 outliers final: 180 residues processed: 1205 average time/residue: 0.2494 time to fit residues: 497.6020 Evaluate side-chains 1104 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 899 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 283 HIS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 283 HIS Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 428 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 138 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 443 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 325 optimal weight: 2.9990 chunk 308 optimal weight: 10.0000 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 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 28 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS C 301 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 ASN F 131 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 396 HIS I 245 GLN I 292 GLN J 101 ASN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 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 = 0.4185 r_free = 0.4185 target = 0.114627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.097477 restraints weight = 91006.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.100719 restraints weight = 46143.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.102924 restraints weight = 28438.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.104420 restraints weight = 19855.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.105445 restraints weight = 15197.778| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 41862 Z= 0.155 Angle : 0.633 9.472 56844 Z= 0.319 Chirality : 0.045 0.212 6222 Planarity : 0.004 0.046 7386 Dihedral : 12.818 167.343 5902 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.93 % Allowed : 19.05 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.15 (0.12), residues: 5130 helix: 1.09 (0.10), residues: 2496 sheet: 0.30 (0.18), residues: 756 loop : -1.33 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 156 TYR 0.020 0.001 TYR L 24 PHE 0.026 0.001 PHE G 20 TRP 0.044 0.002 TRP A 407 HIS 0.012 0.001 HIS G 307 Details of bonding type rmsd covalent geometry : bond 0.00353 (41844) covalent geometry : angle 0.63272 (56844) hydrogen bonds : bond 0.04101 ( 2028) hydrogen bonds : angle 4.60398 ( 5850) Misc. bond : bond 0.00175 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 995 time to evaluate : 1.542 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 49 PHE cc_start: 0.8350 (p90) cc_final: 0.8015 (p90) REVERT: A 149 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8719 (t80) REVERT: A 166 LYS cc_start: 0.8243 (mtpt) cc_final: 0.8018 (mttt) REVERT: A 262 TYR cc_start: 0.8996 (m-80) cc_final: 0.8775 (m-80) REVERT: A 377 MET cc_start: 0.8781 (tmt) cc_final: 0.8520 (tmm) REVERT: A 379 SER cc_start: 0.8846 (t) cc_final: 0.8569 (t) REVERT: A 430 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8729 (tppt) REVERT: B 33 SER cc_start: 0.8755 (m) cc_final: 0.8342 (p) REVERT: B 111 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: B 131 GLN cc_start: 0.8129 (tp40) cc_final: 0.7470 (tp40) REVERT: B 184 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7558 (p0) REVERT: C 119 LEU cc_start: 0.8839 (mp) cc_final: 0.8438 (mp) REVERT: C 154 MET cc_start: 0.9328 (mmp) cc_final: 0.9072 (mmm) REVERT: C 223 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7788 (p) REVERT: C 257 THR cc_start: 0.9297 (m) cc_final: 0.9081 (p) REVERT: C 326 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8582 (ttpt) REVERT: C 358 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8597 (mm110) REVERT: C 370 LYS cc_start: 0.8158 (tttp) cc_final: 0.7567 (tptp) REVERT: C 430 LYS cc_start: 0.9267 (ttmt) cc_final: 0.9053 (pttm) REVERT: C 432 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7307 (t80) REVERT: D 22 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7332 (tp30) REVERT: D 26 ASP cc_start: 0.7921 (m-30) cc_final: 0.7617 (m-30) REVERT: D 33 SER cc_start: 0.9091 (m) cc_final: 0.8746 (p) REVERT: D 136 THR cc_start: 0.8119 (m) cc_final: 0.6610 (t) REVERT: D 297 LYS cc_start: 0.8894 (tttt) cc_final: 0.8618 (ttpt) REVERT: D 315 THR cc_start: 0.9280 (m) cc_final: 0.9079 (p) REVERT: D 364 SER cc_start: 0.8433 (p) cc_final: 0.8051 (p) REVERT: E 49 PHE cc_start: 0.8206 (p90) cc_final: 0.7898 (p90) REVERT: E 115 ILE cc_start: 0.9251 (tp) cc_final: 0.8946 (tp) REVERT: E 172 TYR cc_start: 0.7901 (t80) cc_final: 0.7614 (t80) REVERT: E 232 SER cc_start: 0.8928 (p) cc_final: 0.8616 (t) REVERT: E 357 TYR cc_start: 0.8037 (m-80) cc_final: 0.7709 (m-80) REVERT: E 370 LYS cc_start: 0.8172 (tttp) cc_final: 0.7677 (tptp) REVERT: E 388 TRP cc_start: 0.8820 (m100) cc_final: 0.8597 (m100) REVERT: E 398 MET cc_start: 0.9243 (mmm) cc_final: 0.8872 (mmt) REVERT: E 411 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8453 (tp30) REVERT: E 430 LYS cc_start: 0.9415 (ttmt) cc_final: 0.9038 (tppt) REVERT: F 33 SER cc_start: 0.8860 (m) cc_final: 0.8503 (p) REVERT: F 69 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: F 111 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: F 136 THR cc_start: 0.8102 (m) cc_final: 0.7782 (m) REVERT: F 174 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8695 (ptpp) REVERT: F 177 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8355 (t0) REVERT: F 257 MET cc_start: 0.8441 (mmm) cc_final: 0.7865 (mmm) REVERT: F 279 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: F 292 GLN cc_start: 0.8104 (tt0) cc_final: 0.7843 (tt0) REVERT: F 363 MET cc_start: 0.7414 (ptp) cc_final: 0.7004 (ptp) REVERT: F 364 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8250 (p) REVERT: F 370 ASN cc_start: 0.8604 (t0) cc_final: 0.8342 (t0) REVERT: F 422 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.7591 (t80) REVERT: G 7 ILE cc_start: 0.9288 (mt) cc_final: 0.9005 (mp) REVERT: G 12 CYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8846 (p) REVERT: G 22 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8334 (tp30) REVERT: G 26 ASP cc_start: 0.8259 (m-30) cc_final: 0.7742 (m-30) REVERT: G 41 ASP cc_start: 0.7846 (p0) cc_final: 0.7642 (p0) REVERT: G 81 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5367 (m-10) REVERT: G 101 TRP cc_start: 0.8769 (t60) cc_final: 0.8350 (t60) REVERT: G 135 LEU cc_start: 0.8908 (tp) cc_final: 0.8704 (tt) REVERT: G 136 THR cc_start: 0.8619 (m) cc_final: 0.8400 (p) REVERT: G 174 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8570 (mmmm) REVERT: G 216 LYS cc_start: 0.8587 (mmtp) cc_final: 0.8353 (mmtp) REVERT: G 323 MET cc_start: 0.8041 (mmm) cc_final: 0.7782 (tpp) REVERT: G 351 VAL cc_start: 0.9414 (t) cc_final: 0.9040 (p) REVERT: G 362 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8774 (mtmm) REVERT: G 367 PHE cc_start: 0.8674 (t80) cc_final: 0.8250 (t80) REVERT: G 422 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.6524 (t80) REVERT: H 6 HIS cc_start: 0.7915 (t70) cc_final: 0.7461 (t70) REVERT: H 41 ASP cc_start: 0.7513 (p0) cc_final: 0.7259 (p0) REVERT: H 53 GLU cc_start: 0.7444 (tp30) cc_final: 0.7147 (tp30) REVERT: H 81 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.6202 (m-10) REVERT: H 101 TRP cc_start: 0.8513 (t60) cc_final: 0.8184 (t60) REVERT: H 130 LEU cc_start: 0.8384 (tp) cc_final: 0.8048 (tp) REVERT: H 136 THR cc_start: 0.8710 (m) cc_final: 0.8421 (p) REVERT: H 216 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8393 (mmtp) REVERT: H 257 MET cc_start: 0.8318 (mmm) cc_final: 0.8019 (mmm) REVERT: H 322 SER cc_start: 0.7911 (m) cc_final: 0.7579 (p) REVERT: H 362 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8370 (mtmm) REVERT: I 6 HIS cc_start: 0.8070 (t70) cc_final: 0.7665 (t70) REVERT: I 41 ASP cc_start: 0.7916 (p0) cc_final: 0.7610 (p0) REVERT: I 53 GLU cc_start: 0.7529 (tp30) cc_final: 0.7183 (tp30) REVERT: I 67 ASP cc_start: 0.8135 (t0) cc_final: 0.7676 (t70) REVERT: I 92 PHE cc_start: 0.8650 (p90) cc_final: 0.8400 (p90) REVERT: I 101 TRP cc_start: 0.8635 (t60) cc_final: 0.8286 (t60) REVERT: I 130 LEU cc_start: 0.8360 (tp) cc_final: 0.8024 (tp) REVERT: I 134 GLN cc_start: 0.8407 (pt0) cc_final: 0.8067 (pp30) REVERT: I 136 THR cc_start: 0.8616 (m) cc_final: 0.8203 (p) REVERT: I 216 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7570 (pptt) REVERT: I 246 LEU cc_start: 0.8429 (tp) cc_final: 0.8109 (tt) REVERT: I 322 SER cc_start: 0.8099 (m) cc_final: 0.7890 (p) REVERT: I 343 GLU cc_start: 0.8507 (tp30) cc_final: 0.8262 (tp30) REVERT: I 363 MET cc_start: 0.8118 (ptp) cc_final: 0.7764 (ptp) REVERT: J 84 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7855 (ttp-110) REVERT: J 138 PHE cc_start: 0.8746 (m-10) cc_final: 0.8439 (m-10) REVERT: J 203 MET cc_start: 0.8723 (mmp) cc_final: 0.7964 (mmm) REVERT: J 230 LEU cc_start: 0.9303 (mp) cc_final: 0.8927 (tt) REVERT: J 251 ASP cc_start: 0.7224 (t0) cc_final: 0.6928 (t70) REVERT: J 332 ILE cc_start: 0.9539 (mm) cc_final: 0.9183 (tp) REVERT: J 358 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8453 (tp40) REVERT: J 432 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7172 (t80) REVERT: K 127 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7563 (p0) REVERT: K 149 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8015 (t80) REVERT: K 157 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9054 (mm) REVERT: K 203 MET cc_start: 0.8528 (mmp) cc_final: 0.7767 (mmm) REVERT: K 282 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: K 388 TRP cc_start: 0.8712 (m100) cc_final: 0.8027 (m100) REVERT: L 84 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.6996 (ttm-80) REVERT: L 149 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8835 (t80) outliers start: 261 outliers final: 185 residues processed: 1181 average time/residue: 0.2451 time to fit residues: 480.5780 Evaluate side-chains 1106 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 898 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 283 HIS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 428 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 233 optimal weight: 0.9990 chunk 307 optimal weight: 8.9990 chunk 351 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 420 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 292 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.113259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.096279 restraints weight = 91737.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.099449 restraints weight = 46587.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.101603 restraints weight = 28825.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.103034 restraints weight = 20230.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.104120 restraints weight = 15558.375| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 41862 Z= 0.198 Angle : 0.663 8.700 56844 Z= 0.335 Chirality : 0.046 0.227 6222 Planarity : 0.004 0.047 7386 Dihedral : 12.783 168.204 5887 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.18 % Allowed : 20.19 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 5130 helix: 1.02 (0.10), residues: 2496 sheet: 0.30 (0.19), residues: 756 loop : -1.29 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 156 TYR 0.033 0.002 TYR E 24 PHE 0.024 0.002 PHE C 49 TRP 0.027 0.002 TRP A 407 HIS 0.011 0.001 HIS G 307 Details of bonding type rmsd covalent geometry : bond 0.00450 (41844) covalent geometry : angle 0.66265 (56844) hydrogen bonds : bond 0.04207 ( 2028) hydrogen bonds : angle 4.66898 ( 5850) Misc. bond : bond 0.00194 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 930 time to evaluate : 1.655 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 49 PHE cc_start: 0.8332 (p90) cc_final: 0.7991 (p90) REVERT: A 149 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8702 (t80) REVERT: A 166 LYS cc_start: 0.8277 (mtpt) cc_final: 0.8074 (mttt) REVERT: A 377 MET cc_start: 0.8802 (tmt) cc_final: 0.8479 (tmm) REVERT: A 430 LYS cc_start: 0.9213 (ttmt) cc_final: 0.8756 (tppt) REVERT: B 33 SER cc_start: 0.8778 (m) cc_final: 0.8400 (p) REVERT: B 111 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: B 184 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7657 (p0) REVERT: B 279 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: C 156 ARG cc_start: 0.8939 (mtp85) cc_final: 0.8630 (mmm-85) REVERT: C 203 MET cc_start: 0.8577 (mmm) cc_final: 0.7973 (mmm) REVERT: C 358 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8635 (mm-40) REVERT: C 370 LYS cc_start: 0.8113 (tttp) cc_final: 0.7606 (tmtt) REVERT: C 393 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8614 (t-90) REVERT: C 398 MET cc_start: 0.8990 (mmt) cc_final: 0.8533 (mmt) REVERT: C 430 LYS cc_start: 0.9376 (ttmt) cc_final: 0.9143 (pttm) REVERT: C 432 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7340 (t80) REVERT: D 22 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7591 (tp30) REVERT: D 33 SER cc_start: 0.9070 (m) cc_final: 0.8727 (p) REVERT: D 257 MET cc_start: 0.8134 (mmm) cc_final: 0.7568 (mmt) REVERT: D 315 THR cc_start: 0.9313 (m) cc_final: 0.9079 (p) REVERT: D 364 SER cc_start: 0.8525 (p) cc_final: 0.8140 (p) REVERT: E 49 PHE cc_start: 0.8264 (p90) cc_final: 0.7939 (p90) REVERT: E 232 SER cc_start: 0.8939 (p) cc_final: 0.8656 (t) REVERT: E 370 LYS cc_start: 0.8264 (tttp) cc_final: 0.7663 (tptp) REVERT: E 388 TRP cc_start: 0.8829 (m100) cc_final: 0.8627 (m100) REVERT: E 398 MET cc_start: 0.9212 (mmm) cc_final: 0.8878 (mmt) REVERT: E 430 LYS cc_start: 0.9419 (ttmt) cc_final: 0.9065 (tppt) REVERT: F 19 LYS cc_start: 0.8598 (tptt) cc_final: 0.8250 (tptt) REVERT: F 33 SER cc_start: 0.8857 (m) cc_final: 0.8539 (p) REVERT: F 67 ASP cc_start: 0.7581 (t0) cc_final: 0.7312 (t70) REVERT: F 69 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7822 (pp20) REVERT: F 111 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: F 136 THR cc_start: 0.7997 (m) cc_final: 0.7684 (m) REVERT: F 177 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8371 (t0) REVERT: F 257 MET cc_start: 0.8504 (mmm) cc_final: 0.7882 (mmm) REVERT: F 292 GLN cc_start: 0.7992 (tt0) cc_final: 0.7580 (tt0) REVERT: F 363 MET cc_start: 0.7499 (ptp) cc_final: 0.7195 (ptp) REVERT: F 364 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8099 (p) REVERT: F 370 ASN cc_start: 0.8613 (t0) cc_final: 0.8365 (t0) REVERT: F 422 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.7590 (t80) REVERT: G 12 CYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8793 (p) REVERT: G 22 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8255 (tp30) REVERT: G 26 ASP cc_start: 0.8294 (m-30) cc_final: 0.7693 (m-30) REVERT: G 81 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5338 (m-10) REVERT: G 136 THR cc_start: 0.8738 (m) cc_final: 0.8323 (p) REVERT: G 174 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8615 (mmmm) REVERT: G 216 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8427 (mmtp) REVERT: G 267 MET cc_start: 0.7841 (ptm) cc_final: 0.6711 (ttp) REVERT: G 292 GLN cc_start: 0.8030 (tt0) cc_final: 0.7777 (tt0) REVERT: G 299 MET cc_start: 0.7351 (mmp) cc_final: 0.6826 (mmp) REVERT: G 323 MET cc_start: 0.8102 (mmm) cc_final: 0.7749 (tpp) REVERT: G 351 VAL cc_start: 0.9412 (t) cc_final: 0.9064 (p) REVERT: G 367 PHE cc_start: 0.8641 (t80) cc_final: 0.8293 (t80) REVERT: G 422 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6393 (t80) REVERT: H 6 HIS cc_start: 0.7721 (t70) cc_final: 0.7440 (t70) REVERT: H 41 ASP cc_start: 0.7639 (p0) cc_final: 0.7422 (p0) REVERT: H 53 GLU cc_start: 0.7448 (tp30) cc_final: 0.7077 (tp30) REVERT: H 73 MET cc_start: 0.8950 (mpp) cc_final: 0.8605 (mpp) REVERT: H 81 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.6288 (m-10) REVERT: H 101 TRP cc_start: 0.8645 (t60) cc_final: 0.8243 (t60) REVERT: H 130 LEU cc_start: 0.8389 (tp) cc_final: 0.8117 (tp) REVERT: H 134 GLN cc_start: 0.8521 (pp30) cc_final: 0.8300 (pp30) REVERT: H 136 THR cc_start: 0.8733 (m) cc_final: 0.8380 (p) REVERT: H 267 MET cc_start: 0.7778 (ptm) cc_final: 0.7458 (ptm) REVERT: H 300 MET cc_start: 0.8392 (mmm) cc_final: 0.8080 (mmt) REVERT: H 322 SER cc_start: 0.7995 (m) cc_final: 0.7703 (p) REVERT: H 362 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8368 (mtmm) REVERT: I 6 HIS cc_start: 0.8071 (t70) cc_final: 0.7518 (t70) REVERT: I 41 ASP cc_start: 0.7889 (p0) cc_final: 0.7662 (p0) REVERT: I 53 GLU cc_start: 0.7523 (tp30) cc_final: 0.7160 (tp30) REVERT: I 67 ASP cc_start: 0.8288 (t0) cc_final: 0.6947 (p0) REVERT: I 92 PHE cc_start: 0.8644 (p90) cc_final: 0.8246 (p90) REVERT: I 101 TRP cc_start: 0.8801 (t60) cc_final: 0.8406 (t60) REVERT: I 130 LEU cc_start: 0.8402 (tp) cc_final: 0.8063 (tp) REVERT: I 134 GLN cc_start: 0.8469 (pt0) cc_final: 0.8148 (pp30) REVERT: I 136 THR cc_start: 0.8691 (m) cc_final: 0.8275 (p) REVERT: I 216 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7603 (pptt) REVERT: I 246 LEU cc_start: 0.8449 (tp) cc_final: 0.8106 (tt) REVERT: I 300 MET cc_start: 0.8209 (mtt) cc_final: 0.7953 (mtt) REVERT: I 322 SER cc_start: 0.8151 (m) cc_final: 0.7925 (p) REVERT: I 327 ASP cc_start: 0.9197 (m-30) cc_final: 0.8507 (m-30) REVERT: I 343 GLU cc_start: 0.8500 (tp30) cc_final: 0.8259 (tp30) REVERT: I 363 MET cc_start: 0.8104 (ptp) cc_final: 0.7817 (ptp) REVERT: J 84 ARG cc_start: 0.8069 (ttp-110) cc_final: 0.7868 (ttp-110) REVERT: J 138 PHE cc_start: 0.8787 (m-10) cc_final: 0.8424 (m-10) REVERT: J 230 LEU cc_start: 0.9317 (mp) cc_final: 0.8926 (tt) REVERT: J 251 ASP cc_start: 0.7288 (t0) cc_final: 0.6994 (t70) REVERT: J 332 ILE cc_start: 0.9558 (mm) cc_final: 0.9242 (tp) REVERT: J 358 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8455 (tp40) REVERT: J 388 TRP cc_start: 0.8588 (m100) cc_final: 0.8282 (m100) REVERT: J 432 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7294 (t80) REVERT: K 90 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7278 (tm-30) REVERT: K 127 ASP cc_start: 0.7741 (p0) cc_final: 0.7445 (p0) REVERT: K 149 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.7998 (t80) REVERT: K 157 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9075 (mm) REVERT: K 203 MET cc_start: 0.8606 (mmp) cc_final: 0.7835 (mmm) REVERT: K 388 TRP cc_start: 0.8765 (m100) cc_final: 0.8004 (m100) REVERT: L 149 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8845 (t80) outliers start: 272 outliers final: 214 residues processed: 1121 average time/residue: 0.2392 time to fit residues: 448.1844 Evaluate side-chains 1102 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 868 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 367 PHE Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 283 HIS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 428 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 339 optimal weight: 6.9990 chunk 397 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 351 optimal weight: 6.9990 chunk 347 optimal weight: 9.9990 chunk 457 optimal weight: 5.9990 chunk 499 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 356 optimal weight: 5.9990 chunk 281 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 423 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN I 292 GLN I 347 ASN ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.113207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.095771 restraints weight = 91777.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.098984 restraints weight = 46885.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.101151 restraints weight = 29133.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.102654 restraints weight = 20590.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.103718 restraints weight = 15861.731| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 41862 Z= 0.182 Angle : 0.660 9.546 56844 Z= 0.332 Chirality : 0.045 0.193 6222 Planarity : 0.004 0.058 7386 Dihedral : 12.699 167.993 5876 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.31 % Allowed : 21.37 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.17 (0.12), residues: 5130 helix: 1.08 (0.10), residues: 2460 sheet: 0.30 (0.19), residues: 756 loop : -1.20 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 214 TYR 0.034 0.001 TYR E 24 PHE 0.027 0.002 PHE G 20 TRP 0.017 0.002 TRP B 21 HIS 0.011 0.001 HIS G 307 Details of bonding type rmsd covalent geometry : bond 0.00416 (41844) covalent geometry : angle 0.66048 (56844) hydrogen bonds : bond 0.04128 ( 2028) hydrogen bonds : angle 4.64261 ( 5850) Misc. bond : bond 0.00186 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 917 time to evaluate : 1.605 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 49 PHE cc_start: 0.8344 (p90) cc_final: 0.7988 (p90) REVERT: A 123 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8132 (ttm-80) REVERT: A 149 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8712 (t80) REVERT: A 370 LYS cc_start: 0.7926 (tttp) cc_final: 0.7268 (tptp) REVERT: A 377 MET cc_start: 0.8778 (tmt) cc_final: 0.8430 (tmm) REVERT: A 430 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8741 (tppt) REVERT: B 33 SER cc_start: 0.8792 (m) cc_final: 0.8432 (p) REVERT: B 125 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 184 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.7594 (p0) REVERT: B 279 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: B 424 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8059 (tm-30) REVERT: C 326 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8632 (ttpt) REVERT: C 358 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8635 (mm-40) REVERT: C 393 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8643 (t-90) REVERT: C 398 MET cc_start: 0.8988 (mmt) cc_final: 0.8571 (mmt) REVERT: C 430 LYS cc_start: 0.9371 (ttmt) cc_final: 0.9127 (pttm) REVERT: C 432 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7365 (t80) REVERT: D 22 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7553 (tp30) REVERT: D 33 SER cc_start: 0.9075 (m) cc_final: 0.8731 (p) REVERT: D 136 THR cc_start: 0.8171 (m) cc_final: 0.6772 (t) REVERT: D 257 MET cc_start: 0.8043 (mmm) cc_final: 0.7263 (mmt) REVERT: D 312 THR cc_start: 0.8850 (p) cc_final: 0.8617 (p) REVERT: D 364 SER cc_start: 0.8543 (p) cc_final: 0.8143 (p) REVERT: D 388 MET cc_start: 0.8765 (mmt) cc_final: 0.8488 (mmt) REVERT: E 49 PHE cc_start: 0.8185 (p90) cc_final: 0.7864 (p90) REVERT: E 84 ARG cc_start: 0.8373 (ttp-110) cc_final: 0.8048 (ttm-80) REVERT: E 232 SER cc_start: 0.8933 (p) cc_final: 0.8652 (t) REVERT: E 370 LYS cc_start: 0.8215 (tttp) cc_final: 0.7651 (tptp) REVERT: E 388 TRP cc_start: 0.8841 (m100) cc_final: 0.8593 (m100) REVERT: E 398 MET cc_start: 0.9188 (mmm) cc_final: 0.8866 (mmt) REVERT: E 430 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9058 (tppt) REVERT: F 33 SER cc_start: 0.8882 (m) cc_final: 0.8555 (p) REVERT: F 67 ASP cc_start: 0.7718 (t0) cc_final: 0.7331 (t70) REVERT: F 69 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7795 (pp20) REVERT: F 111 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: F 136 THR cc_start: 0.7993 (m) cc_final: 0.7634 (m) REVERT: F 177 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8354 (t0) REVERT: F 257 MET cc_start: 0.8468 (mmm) cc_final: 0.7831 (mmm) REVERT: F 363 MET cc_start: 0.7558 (ptp) cc_final: 0.7186 (ptp) REVERT: F 364 SER cc_start: 0.8429 (OUTLIER) cc_final: 0.8149 (p) REVERT: F 370 ASN cc_start: 0.8620 (t0) cc_final: 0.8416 (t0) REVERT: F 422 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7629 (t80) REVERT: G 12 CYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8843 (p) REVERT: G 22 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8294 (tp30) REVERT: G 26 ASP cc_start: 0.8170 (m-30) cc_final: 0.7545 (m-30) REVERT: G 81 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: G 101 TRP cc_start: 0.8688 (t60) cc_final: 0.8209 (t60) REVERT: G 136 THR cc_start: 0.8666 (m) cc_final: 0.8340 (p) REVERT: G 174 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8674 (mmmm) REVERT: G 216 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8406 (mmtp) REVERT: G 267 MET cc_start: 0.7895 (ptm) cc_final: 0.7303 (ttp) REVERT: G 292 GLN cc_start: 0.7983 (tt0) cc_final: 0.7734 (tt0) REVERT: G 298 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8486 (t0) REVERT: G 323 MET cc_start: 0.8113 (mmm) cc_final: 0.7761 (tpp) REVERT: G 351 VAL cc_start: 0.9324 (t) cc_final: 0.9050 (m) REVERT: G 367 PHE cc_start: 0.8639 (t80) cc_final: 0.8233 (t80) REVERT: G 422 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.6434 (t80) REVERT: H 6 HIS cc_start: 0.7703 (t70) cc_final: 0.7414 (t70) REVERT: H 41 ASP cc_start: 0.7690 (p0) cc_final: 0.7479 (p0) REVERT: H 53 GLU cc_start: 0.7600 (tp30) cc_final: 0.7264 (tp30) REVERT: H 101 TRP cc_start: 0.8556 (t60) cc_final: 0.8181 (t60) REVERT: H 130 LEU cc_start: 0.8425 (tp) cc_final: 0.8104 (tp) REVERT: H 136 THR cc_start: 0.8698 (m) cc_final: 0.8284 (p) REVERT: H 205 GLU cc_start: 0.7869 (pp20) cc_final: 0.7578 (pp20) REVERT: H 216 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7723 (pptt) REVERT: H 267 MET cc_start: 0.7751 (ptm) cc_final: 0.7518 (ptm) REVERT: H 300 MET cc_start: 0.8295 (mmm) cc_final: 0.7859 (mmt) REVERT: H 322 SER cc_start: 0.7952 (m) cc_final: 0.7697 (p) REVERT: H 362 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8373 (mtmm) REVERT: I 6 HIS cc_start: 0.8004 (t70) cc_final: 0.7624 (t70) REVERT: I 19 LYS cc_start: 0.8879 (tptt) cc_final: 0.8601 (tptt) REVERT: I 41 ASP cc_start: 0.7945 (p0) cc_final: 0.7733 (p0) REVERT: I 53 GLU cc_start: 0.7512 (tp30) cc_final: 0.7156 (tp30) REVERT: I 67 ASP cc_start: 0.8170 (t0) cc_final: 0.7835 (t70) REVERT: I 92 PHE cc_start: 0.8712 (p90) cc_final: 0.8443 (p90) REVERT: I 101 TRP cc_start: 0.8767 (t60) cc_final: 0.8384 (t60) REVERT: I 130 LEU cc_start: 0.8346 (tp) cc_final: 0.8043 (tp) REVERT: I 134 GLN cc_start: 0.8543 (pt0) cc_final: 0.8164 (pp30) REVERT: I 136 THR cc_start: 0.8687 (m) cc_final: 0.8284 (p) REVERT: I 216 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7606 (pptt) REVERT: I 246 LEU cc_start: 0.8416 (tp) cc_final: 0.8089 (tt) REVERT: I 267 MET cc_start: 0.8449 (ptm) cc_final: 0.8134 (ptm) REVERT: I 300 MET cc_start: 0.8100 (mtt) cc_final: 0.7822 (mtt) REVERT: I 322 SER cc_start: 0.8039 (m) cc_final: 0.7762 (p) REVERT: I 343 GLU cc_start: 0.8497 (tp30) cc_final: 0.8253 (tp30) REVERT: I 363 MET cc_start: 0.8139 (ptp) cc_final: 0.7919 (ptp) REVERT: J 138 PHE cc_start: 0.8805 (m-80) cc_final: 0.8432 (m-10) REVERT: J 203 MET cc_start: 0.8763 (mmp) cc_final: 0.8000 (mmm) REVERT: J 230 LEU cc_start: 0.9311 (mp) cc_final: 0.8933 (tt) REVERT: J 251 ASP cc_start: 0.7371 (t0) cc_final: 0.7107 (t70) REVERT: J 332 ILE cc_start: 0.9556 (mm) cc_final: 0.9250 (tp) REVERT: J 358 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8468 (tp40) REVERT: J 432 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7326 (t80) REVERT: K 127 ASP cc_start: 0.7883 (p0) cc_final: 0.7594 (p0) REVERT: K 149 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7984 (t80) REVERT: K 157 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9060 (mm) REVERT: K 203 MET cc_start: 0.8645 (mmp) cc_final: 0.7955 (mmm) REVERT: K 309 HIS cc_start: 0.8338 (m-70) cc_final: 0.7917 (m-70) REVERT: K 380 ASN cc_start: 0.8528 (t0) cc_final: 0.8156 (t0) REVERT: L 149 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8826 (t80) outliers start: 278 outliers final: 216 residues processed: 1116 average time/residue: 0.2360 time to fit residues: 441.0342 Evaluate side-chains 1108 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 872 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 367 PHE Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 237 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 283 HIS Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 428 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 384 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 0.0070 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 432 optimal weight: 0.7980 chunk 391 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 502 optimal weight: 0.0050 chunk 20 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 overall best weight: 0.5014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 134 GLN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 HIS I 292 GLN J 139 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN K 28 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.117297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.099765 restraints weight = 89759.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.103071 restraints weight = 46325.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.105321 restraints weight = 28804.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.106837 restraints weight = 20243.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.107864 restraints weight = 15561.672| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 41862 Z= 0.124 Angle : 0.644 11.155 56844 Z= 0.320 Chirality : 0.044 0.212 6222 Planarity : 0.004 0.072 7386 Dihedral : 12.497 165.704 5873 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.41 % Allowed : 23.14 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.33 (0.12), residues: 5130 helix: 1.14 (0.10), residues: 2496 sheet: 0.55 (0.19), residues: 756 loop : -1.15 (0.15), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 422 TYR 0.030 0.001 TYR C 24 PHE 0.025 0.001 PHE C 49 TRP 0.016 0.002 TRP G 21 HIS 0.008 0.001 HIS G 307 Details of bonding type rmsd covalent geometry : bond 0.00273 (41844) covalent geometry : angle 0.64380 (56844) hydrogen bonds : bond 0.03733 ( 2028) hydrogen bonds : angle 4.51690 ( 5850) Misc. bond : bond 0.00143 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1039 time to evaluate : 1.597 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 129 CYS cc_start: 0.6966 (m) cc_final: 0.6743 (m) REVERT: A 149 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8646 (t80) REVERT: A 203 MET cc_start: 0.8463 (mmm) cc_final: 0.8237 (mmm) REVERT: A 377 MET cc_start: 0.8700 (tmt) cc_final: 0.8385 (tmm) REVERT: A 398 MET cc_start: 0.8945 (mmt) cc_final: 0.8211 (mmt) REVERT: A 430 LYS cc_start: 0.9204 (ttmt) cc_final: 0.8741 (tppt) REVERT: A 432 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7142 (t80) REVERT: B 33 SER cc_start: 0.8728 (m) cc_final: 0.8463 (p) REVERT: B 125 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7767 (tm-30) REVERT: B 136 THR cc_start: 0.8171 (m) cc_final: 0.7951 (m) REVERT: B 184 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7296 (p0) REVERT: B 279 GLN cc_start: 0.8492 (pt0) cc_final: 0.8186 (pt0) REVERT: C 97 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7089 (mm-30) REVERT: C 232 SER cc_start: 0.8801 (t) cc_final: 0.8512 (t) REVERT: C 257 THR cc_start: 0.9225 (m) cc_final: 0.9001 (p) REVERT: C 282 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: C 326 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8695 (ttpt) REVERT: C 358 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8575 (mm-40) REVERT: C 370 LYS cc_start: 0.7971 (tttp) cc_final: 0.7427 (tptp) REVERT: C 430 LYS cc_start: 0.9363 (ttmt) cc_final: 0.9108 (pttm) REVERT: C 432 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7374 (t80) REVERT: D 22 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7392 (tp30) REVERT: D 26 ASP cc_start: 0.7925 (m-30) cc_final: 0.7695 (p0) REVERT: D 33 SER cc_start: 0.9041 (m) cc_final: 0.8718 (p) REVERT: D 101 TRP cc_start: 0.8282 (t60) cc_final: 0.7701 (t60) REVERT: D 213 ARG cc_start: 0.8197 (tmm-80) cc_final: 0.7559 (tmm160) REVERT: D 297 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.7617 (tttp) REVERT: D 364 SER cc_start: 0.8507 (p) cc_final: 0.8138 (p) REVERT: D 388 MET cc_start: 0.8683 (mmt) cc_final: 0.8397 (mmt) REVERT: E 49 PHE cc_start: 0.8127 (p90) cc_final: 0.7860 (p90) REVERT: E 84 ARG cc_start: 0.8259 (ttp-110) cc_final: 0.7884 (mtm-85) REVERT: E 232 SER cc_start: 0.8943 (p) cc_final: 0.8641 (t) REVERT: E 357 TYR cc_start: 0.8042 (m-80) cc_final: 0.7781 (m-80) REVERT: E 370 LYS cc_start: 0.8114 (tttp) cc_final: 0.7575 (tptp) REVERT: E 388 TRP cc_start: 0.8718 (m100) cc_final: 0.8473 (m100) REVERT: E 391 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8990 (mt) REVERT: E 398 MET cc_start: 0.9065 (mmm) cc_final: 0.8799 (mmt) REVERT: E 430 LYS cc_start: 0.9432 (ttmt) cc_final: 0.9071 (tppt) REVERT: F 33 SER cc_start: 0.8827 (m) cc_final: 0.8475 (p) REVERT: F 111 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: F 136 THR cc_start: 0.8004 (m) cc_final: 0.6479 (t) REVERT: F 177 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8342 (t0) REVERT: F 257 MET cc_start: 0.8221 (mmm) cc_final: 0.7826 (mmm) REVERT: F 279 GLN cc_start: 0.8367 (pt0) cc_final: 0.8157 (mt0) REVERT: F 364 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7956 (p) REVERT: F 370 ASN cc_start: 0.8624 (t0) cc_final: 0.8390 (t0) REVERT: F 422 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7712 (t80) REVERT: G 22 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8268 (tp30) REVERT: G 26 ASP cc_start: 0.8209 (m-30) cc_final: 0.7671 (m-30) REVERT: G 81 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.5079 (m-10) REVERT: G 101 TRP cc_start: 0.8740 (t60) cc_final: 0.8416 (t60) REVERT: G 134 GLN cc_start: 0.8151 (pp30) cc_final: 0.7949 (pp30) REVERT: G 174 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8644 (mmmt) REVERT: G 181 GLU cc_start: 0.8529 (pt0) cc_final: 0.8239 (pm20) REVERT: G 216 LYS cc_start: 0.8598 (mmtp) cc_final: 0.7985 (pptt) REVERT: G 257 MET cc_start: 0.8421 (mmm) cc_final: 0.7911 (mmm) REVERT: G 292 GLN cc_start: 0.7751 (tt0) cc_final: 0.7514 (tt0) REVERT: G 297 LYS cc_start: 0.8623 (mmtm) cc_final: 0.8407 (mmtm) REVERT: G 300 MET cc_start: 0.8131 (tpp) cc_final: 0.7761 (mmt) REVERT: G 323 MET cc_start: 0.7819 (mmm) cc_final: 0.7604 (tpp) REVERT: G 351 VAL cc_start: 0.9312 (t) cc_final: 0.9059 (m) REVERT: G 367 PHE cc_start: 0.8639 (t80) cc_final: 0.8337 (t80) REVERT: G 422 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6531 (t80) REVERT: H 41 ASP cc_start: 0.7602 (p0) cc_final: 0.7393 (p0) REVERT: H 53 GLU cc_start: 0.7530 (tp30) cc_final: 0.7131 (tp30) REVERT: H 101 TRP cc_start: 0.8600 (t60) cc_final: 0.8283 (t60) REVERT: H 130 LEU cc_start: 0.8319 (tp) cc_final: 0.8066 (tp) REVERT: H 136 THR cc_start: 0.8612 (m) cc_final: 0.8390 (p) REVERT: H 216 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7685 (pptt) REVERT: H 286 VAL cc_start: 0.8086 (t) cc_final: 0.7705 (t) REVERT: H 300 MET cc_start: 0.8213 (mmm) cc_final: 0.7831 (mmt) REVERT: H 304 ASP cc_start: 0.7157 (t0) cc_final: 0.6906 (t0) REVERT: H 307 HIS cc_start: 0.8775 (m-70) cc_final: 0.8407 (m-70) REVERT: H 322 SER cc_start: 0.7772 (m) cc_final: 0.7484 (p) REVERT: I 6 HIS cc_start: 0.7999 (t70) cc_final: 0.7548 (t70) REVERT: I 26 ASP cc_start: 0.8311 (m-30) cc_final: 0.8007 (p0) REVERT: I 41 ASP cc_start: 0.7885 (p0) cc_final: 0.7590 (p0) REVERT: I 67 ASP cc_start: 0.7949 (t0) cc_final: 0.7118 (p0) REVERT: I 73 MET cc_start: 0.8203 (mmt) cc_final: 0.7970 (mmm) REVERT: I 92 PHE cc_start: 0.8658 (p90) cc_final: 0.8293 (p90) REVERT: I 101 TRP cc_start: 0.8771 (t60) cc_final: 0.8455 (t60) REVERT: I 130 LEU cc_start: 0.8317 (tp) cc_final: 0.7948 (tp) REVERT: I 134 GLN cc_start: 0.8455 (pt0) cc_final: 0.8237 (pp30) REVERT: I 136 THR cc_start: 0.8609 (m) cc_final: 0.8313 (p) REVERT: I 216 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7540 (pptt) REVERT: I 246 LEU cc_start: 0.8395 (tp) cc_final: 0.7985 (tt) REVERT: I 267 MET cc_start: 0.8414 (ptm) cc_final: 0.7564 (ptm) REVERT: I 300 MET cc_start: 0.7933 (mtt) cc_final: 0.7628 (mtt) REVERT: I 322 SER cc_start: 0.8013 (m) cc_final: 0.7782 (p) REVERT: I 343 GLU cc_start: 0.8390 (tp30) cc_final: 0.8166 (tp30) REVERT: I 363 MET cc_start: 0.7932 (ptp) cc_final: 0.7357 (ptt) REVERT: I 406 MET cc_start: 0.7168 (ppp) cc_final: 0.6903 (ppp) REVERT: J 138 PHE cc_start: 0.8816 (m-80) cc_final: 0.8437 (m-10) REVERT: J 251 ASP cc_start: 0.7094 (t0) cc_final: 0.6864 (t70) REVERT: J 332 ILE cc_start: 0.9562 (mm) cc_final: 0.9220 (tp) REVERT: J 380 ASN cc_start: 0.8437 (t0) cc_final: 0.8131 (t0) REVERT: J 432 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7338 (t80) REVERT: K 127 ASP cc_start: 0.7822 (p0) cc_final: 0.7554 (p0) REVERT: K 149 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7902 (t80) REVERT: K 203 MET cc_start: 0.8549 (mmp) cc_final: 0.7956 (mmm) REVERT: K 282 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: K 309 HIS cc_start: 0.8225 (m-70) cc_final: 0.7824 (m-70) REVERT: K 380 ASN cc_start: 0.8491 (t0) cc_final: 0.7911 (t0) REVERT: K 391 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8318 (mt) REVERT: K 422 ARG cc_start: 0.7116 (tpt90) cc_final: 0.6906 (tpt90) REVERT: L 149 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8778 (t80) outliers start: 194 outliers final: 135 residues processed: 1173 average time/residue: 0.2423 time to fit residues: 473.1773 Evaluate side-chains 1069 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 915 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 237 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 98 optimal weight: 4.9990 chunk 254 optimal weight: 0.7980 chunk 304 optimal weight: 6.9990 chunk 422 optimal weight: 2.9990 chunk 427 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 379 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 101 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN J 228 ASN J 293 ASN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 228 ASN L 393 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.117174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.099392 restraints weight = 89707.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.102654 restraints weight = 45980.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.104856 restraints weight = 28547.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.106329 restraints weight = 20072.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.107382 restraints weight = 15449.594| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 41862 Z= 0.133 Angle : 0.677 11.558 56844 Z= 0.333 Chirality : 0.045 0.237 6222 Planarity : 0.004 0.099 7386 Dihedral : 12.385 165.149 5857 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.95 % Allowed : 24.27 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.40 (0.12), residues: 5130 helix: 1.16 (0.10), residues: 2460 sheet: 0.61 (0.19), residues: 756 loop : -1.01 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 282 TYR 0.038 0.001 TYR G 159 PHE 0.019 0.001 PHE E 138 TRP 0.020 0.002 TRP J 388 HIS 0.011 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00306 (41844) covalent geometry : angle 0.67652 (56844) hydrogen bonds : bond 0.03768 ( 2028) hydrogen bonds : angle 4.52184 ( 5850) Misc. bond : bond 0.00172 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 943 time to evaluate : 1.481 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 49 PHE cc_start: 0.8162 (p90) cc_final: 0.7832 (p90) REVERT: A 129 CYS cc_start: 0.7072 (m) cc_final: 0.6851 (m) REVERT: A 149 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8735 (t80) REVERT: A 377 MET cc_start: 0.8691 (tmt) cc_final: 0.8285 (tmm) REVERT: A 430 LYS cc_start: 0.9261 (ttmt) cc_final: 0.8772 (tppt) REVERT: A 432 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7175 (t80) REVERT: B 33 SER cc_start: 0.8826 (m) cc_final: 0.8495 (p) REVERT: B 125 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 136 THR cc_start: 0.8008 (m) cc_final: 0.7760 (m) REVERT: B 184 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7462 (p0) REVERT: B 279 GLN cc_start: 0.8634 (pt0) cc_final: 0.8330 (pt0) REVERT: B 403 MET cc_start: 0.8154 (tpp) cc_final: 0.7852 (mmp) REVERT: B 416 ASN cc_start: 0.8717 (m-40) cc_final: 0.8456 (p0) REVERT: B 422 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7630 (t80) REVERT: C 97 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7042 (mm-30) REVERT: C 232 SER cc_start: 0.8782 (t) cc_final: 0.8508 (t) REVERT: C 282 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: C 326 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8723 (ttpt) REVERT: C 358 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8583 (mm-40) REVERT: C 370 LYS cc_start: 0.7967 (tttp) cc_final: 0.7419 (tptp) REVERT: C 377 MET cc_start: 0.8539 (tmm) cc_final: 0.7713 (tmm) REVERT: C 379 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8594 (m) REVERT: C 430 LYS cc_start: 0.9368 (ttmt) cc_final: 0.9108 (pttm) REVERT: C 432 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7365 (t80) REVERT: D 22 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7461 (tp30) REVERT: D 26 ASP cc_start: 0.7930 (m-30) cc_final: 0.7616 (p0) REVERT: D 33 SER cc_start: 0.9107 (m) cc_final: 0.8735 (p) REVERT: D 101 TRP cc_start: 0.8243 (t60) cc_final: 0.7687 (t60) REVERT: D 213 ARG cc_start: 0.8199 (tmm-80) cc_final: 0.7531 (tmm160) REVERT: D 257 MET cc_start: 0.7818 (mmm) cc_final: 0.7423 (mmm) REVERT: D 297 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.7666 (tttp) REVERT: D 312 THR cc_start: 0.9087 (t) cc_final: 0.8886 (p) REVERT: D 364 SER cc_start: 0.8554 (p) cc_final: 0.8143 (p) REVERT: D 388 MET cc_start: 0.8805 (mmt) cc_final: 0.8416 (mmt) REVERT: E 49 PHE cc_start: 0.8279 (p90) cc_final: 0.7992 (p90) REVERT: E 84 ARG cc_start: 0.8318 (ttp-110) cc_final: 0.7893 (mtm-85) REVERT: E 167 LEU cc_start: 0.8884 (mt) cc_final: 0.8634 (mp) REVERT: E 232 SER cc_start: 0.8947 (p) cc_final: 0.8660 (t) REVERT: E 282 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: E 357 TYR cc_start: 0.8138 (m-80) cc_final: 0.7835 (m-80) REVERT: E 370 LYS cc_start: 0.8139 (tttp) cc_final: 0.7598 (tptp) REVERT: E 388 TRP cc_start: 0.8731 (m100) cc_final: 0.8499 (m100) REVERT: E 398 MET cc_start: 0.9087 (mmm) cc_final: 0.8805 (mmt) REVERT: E 430 LYS cc_start: 0.9432 (ttmt) cc_final: 0.9064 (tppt) REVERT: F 33 SER cc_start: 0.8903 (m) cc_final: 0.8536 (p) REVERT: F 69 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7519 (pp20) REVERT: F 111 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: F 136 THR cc_start: 0.7849 (m) cc_final: 0.6359 (t) REVERT: F 177 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8334 (t0) REVERT: F 257 MET cc_start: 0.8221 (mmm) cc_final: 0.7722 (mmm) REVERT: F 279 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: F 364 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7976 (p) REVERT: F 422 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.7665 (t80) REVERT: G 12 CYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8784 (p) REVERT: G 22 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8309 (tp30) REVERT: G 26 ASP cc_start: 0.8211 (m-30) cc_final: 0.7715 (m-30) REVERT: G 81 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5057 (m-10) REVERT: G 101 TRP cc_start: 0.8718 (t60) cc_final: 0.8401 (t60) REVERT: G 134 GLN cc_start: 0.8212 (pp30) cc_final: 0.7780 (pp30) REVERT: G 174 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8676 (mmmt) REVERT: G 181 GLU cc_start: 0.8549 (pt0) cc_final: 0.8254 (pm20) REVERT: G 216 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8373 (mmtp) REVERT: G 323 MET cc_start: 0.7926 (mmm) cc_final: 0.7672 (tpp) REVERT: G 351 VAL cc_start: 0.9320 (t) cc_final: 0.9091 (m) REVERT: G 363 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7814 (ptp) REVERT: G 422 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.6573 (t80) REVERT: H 53 GLU cc_start: 0.7556 (tp30) cc_final: 0.7110 (tp30) REVERT: H 101 TRP cc_start: 0.8606 (t60) cc_final: 0.8282 (t60) REVERT: H 130 LEU cc_start: 0.8315 (tp) cc_final: 0.8042 (tp) REVERT: H 136 THR cc_start: 0.8627 (m) cc_final: 0.8369 (p) REVERT: H 216 LYS cc_start: 0.8227 (mmtp) cc_final: 0.7692 (pptt) REVERT: H 300 MET cc_start: 0.8116 (mmm) cc_final: 0.7715 (mmt) REVERT: H 362 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8364 (mtmm) REVERT: I 6 HIS cc_start: 0.7920 (t70) cc_final: 0.7285 (t70) REVERT: I 41 ASP cc_start: 0.7951 (p0) cc_final: 0.7683 (p0) REVERT: I 67 ASP cc_start: 0.8031 (t0) cc_final: 0.7207 (p0) REVERT: I 92 PHE cc_start: 0.8660 (p90) cc_final: 0.8281 (p90) REVERT: I 101 TRP cc_start: 0.8771 (t60) cc_final: 0.8488 (t60) REVERT: I 130 LEU cc_start: 0.8313 (tp) cc_final: 0.7964 (tp) REVERT: I 136 THR cc_start: 0.8699 (m) cc_final: 0.8386 (p) REVERT: I 181 GLU cc_start: 0.8594 (pt0) cc_final: 0.8367 (pt0) REVERT: I 216 LYS cc_start: 0.8188 (mmtp) cc_final: 0.7577 (pptt) REVERT: I 246 LEU cc_start: 0.8403 (tp) cc_final: 0.8038 (tt) REVERT: I 267 MET cc_start: 0.8511 (ptm) cc_final: 0.7656 (ptm) REVERT: I 292 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6703 (pp30) REVERT: I 300 MET cc_start: 0.8029 (mtt) cc_final: 0.7800 (mtt) REVERT: I 330 MET cc_start: 0.8443 (mmm) cc_final: 0.8144 (tmm) REVERT: I 343 GLU cc_start: 0.8438 (tp30) cc_final: 0.8221 (tp30) REVERT: I 362 LYS cc_start: 0.8358 (pptt) cc_final: 0.8151 (pptt) REVERT: I 363 MET cc_start: 0.7742 (ptp) cc_final: 0.6997 (ptt) REVERT: J 49 PHE cc_start: 0.8653 (p90) cc_final: 0.8243 (p90) REVERT: J 55 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7148 (tm-30) REVERT: J 138 PHE cc_start: 0.8837 (m-80) cc_final: 0.8449 (m-10) REVERT: J 230 LEU cc_start: 0.9268 (mp) cc_final: 0.8858 (tt) REVERT: J 332 ILE cc_start: 0.9573 (mm) cc_final: 0.9191 (tp) REVERT: J 377 MET cc_start: 0.8371 (ttp) cc_final: 0.8170 (ttp) REVERT: J 380 ASN cc_start: 0.8544 (t0) cc_final: 0.8177 (t0) REVERT: J 432 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7433 (t80) REVERT: K 127 ASP cc_start: 0.7801 (p0) cc_final: 0.7534 (p0) REVERT: K 149 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.7869 (t80) REVERT: K 203 MET cc_start: 0.8713 (mmp) cc_final: 0.8086 (mmm) REVERT: K 282 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: K 309 HIS cc_start: 0.8394 (m-70) cc_final: 0.7838 (m90) REVERT: K 432 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7718 (t80) REVERT: L 138 PHE cc_start: 0.8832 (m-80) cc_final: 0.8307 (m-10) REVERT: L 149 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8803 (t80) REVERT: L 322 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7432 (p0) REVERT: L 339 ARG cc_start: 0.7590 (tpm170) cc_final: 0.7362 (tpm170) outliers start: 174 outliers final: 132 residues processed: 1060 average time/residue: 0.2369 time to fit residues: 419.0805 Evaluate side-chains 1056 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 897 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 83 HIS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 237 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 322 ASP Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 309 optimal weight: 9.9990 chunk 362 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 451 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 471 optimal weight: 5.9990 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 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 216 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN I 292 GLN ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS J 293 ASN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS K 128 GLN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.115107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.097467 restraints weight = 91705.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.100619 restraints weight = 47259.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.102769 restraints weight = 29585.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.104248 restraints weight = 20949.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.105310 restraints weight = 16147.081| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 41862 Z= 0.182 Angle : 0.713 12.967 56844 Z= 0.353 Chirality : 0.046 0.254 6222 Planarity : 0.004 0.076 7386 Dihedral : 12.404 167.013 5849 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.43 % Allowed : 24.52 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.28 (0.12), residues: 5130 helix: 1.07 (0.10), residues: 2460 sheet: 0.73 (0.20), residues: 678 loop : -1.10 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 214 TYR 0.038 0.001 TYR E 24 PHE 0.037 0.002 PHE D 167 TRP 0.014 0.002 TRP J 388 HIS 0.011 0.001 HIS H 6 Details of bonding type rmsd covalent geometry : bond 0.00420 (41844) covalent geometry : angle 0.71346 (56844) hydrogen bonds : bond 0.03978 ( 2028) hydrogen bonds : angle 4.59701 ( 5850) Misc. bond : bond 0.00186 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 912 time to evaluate : 1.560 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: A 49 PHE cc_start: 0.8173 (p90) cc_final: 0.7868 (p90) REVERT: A 149 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8722 (t80) REVERT: A 377 MET cc_start: 0.8778 (tmt) cc_final: 0.8332 (tmm) REVERT: A 430 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8736 (tppt) REVERT: A 432 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7228 (t80) REVERT: B 33 SER cc_start: 0.8834 (m) cc_final: 0.8510 (p) REVERT: B 125 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 184 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7570 (p0) REVERT: B 279 GLN cc_start: 0.8569 (pt0) cc_final: 0.8276 (pt0) REVERT: B 350 LYS cc_start: 0.8668 (tppt) cc_final: 0.8067 (tppt) REVERT: B 404 ASP cc_start: 0.7651 (p0) cc_final: 0.7416 (p0) REVERT: B 416 ASN cc_start: 0.8710 (m-40) cc_final: 0.8464 (p0) REVERT: C 97 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7102 (mm-30) REVERT: C 232 SER cc_start: 0.8828 (t) cc_final: 0.8591 (t) REVERT: C 282 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: C 326 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8679 (ttpt) REVERT: C 358 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8591 (mm-40) REVERT: C 370 LYS cc_start: 0.7934 (tttp) cc_final: 0.7356 (tptp) REVERT: C 430 LYS cc_start: 0.9364 (ttmt) cc_final: 0.9134 (pttm) REVERT: C 432 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7487 (t80) REVERT: D 22 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7542 (tp30) REVERT: D 33 SER cc_start: 0.9141 (m) cc_final: 0.8807 (p) REVERT: D 203 ASP cc_start: 0.8134 (t0) cc_final: 0.7734 (t70) REVERT: D 213 ARG cc_start: 0.8199 (tmm-80) cc_final: 0.7685 (ttm170) REVERT: D 233 MET cc_start: 0.8847 (mmt) cc_final: 0.8405 (mmt) REVERT: D 257 MET cc_start: 0.7954 (mmm) cc_final: 0.7463 (mmm) REVERT: D 364 SER cc_start: 0.8573 (p) cc_final: 0.8175 (p) REVERT: D 388 MET cc_start: 0.8845 (mmt) cc_final: 0.8444 (mmt) REVERT: E 49 PHE cc_start: 0.8301 (p90) cc_final: 0.7993 (p90) REVERT: E 84 ARG cc_start: 0.8359 (ttp-110) cc_final: 0.8074 (ttm-80) REVERT: E 172 TYR cc_start: 0.7338 (t80) cc_final: 0.6863 (t80) REVERT: E 232 SER cc_start: 0.8992 (p) cc_final: 0.8699 (t) REVERT: E 370 LYS cc_start: 0.8149 (tttp) cc_final: 0.7605 (tptp) REVERT: E 388 TRP cc_start: 0.8725 (m100) cc_final: 0.8416 (m100) REVERT: E 398 MET cc_start: 0.9144 (mmm) cc_final: 0.8800 (mmt) REVERT: E 430 LYS cc_start: 0.9418 (ttmt) cc_final: 0.9048 (tppt) REVERT: F 33 SER cc_start: 0.8815 (m) cc_final: 0.8462 (p) REVERT: F 111 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8598 (mp0) REVERT: F 136 THR cc_start: 0.7998 (m) cc_final: 0.7646 (m) REVERT: F 177 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8396 (t0) REVERT: F 279 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: F 364 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.8016 (p) REVERT: F 422 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7667 (t80) REVERT: G 12 CYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8793 (p) REVERT: G 22 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8274 (tp30) REVERT: G 26 ASP cc_start: 0.8196 (m-30) cc_final: 0.7682 (m-30) REVERT: G 101 TRP cc_start: 0.8718 (t60) cc_final: 0.8312 (t60) REVERT: G 134 GLN cc_start: 0.8121 (pp30) cc_final: 0.7734 (pp30) REVERT: G 174 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8730 (mmmt) REVERT: G 216 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8398 (mmtp) REVERT: G 300 MET cc_start: 0.8345 (tpp) cc_final: 0.7976 (mmt) REVERT: G 327 ASP cc_start: 0.8997 (m-30) cc_final: 0.8708 (p0) REVERT: G 363 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7895 (ptp) REVERT: G 367 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8457 (t80) REVERT: G 422 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.6557 (t80) REVERT: H 53 GLU cc_start: 0.7604 (tp30) cc_final: 0.7114 (tp30) REVERT: H 101 TRP cc_start: 0.8597 (t60) cc_final: 0.8159 (t60) REVERT: H 130 LEU cc_start: 0.8425 (tp) cc_final: 0.8148 (tp) REVERT: H 136 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8472 (p) REVERT: H 216 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7748 (pptt) REVERT: H 300 MET cc_start: 0.8180 (mmm) cc_final: 0.7858 (mmt) REVERT: H 362 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8388 (mtmm) REVERT: H 417 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8496 (t0) REVERT: I 92 PHE cc_start: 0.8683 (p90) cc_final: 0.8393 (p90) REVERT: I 101 TRP cc_start: 0.8785 (t60) cc_final: 0.8471 (t60) REVERT: I 130 LEU cc_start: 0.8354 (tp) cc_final: 0.7987 (tp) REVERT: I 136 THR cc_start: 0.8783 (m) cc_final: 0.8333 (p) REVERT: I 216 LYS cc_start: 0.8237 (mmtp) cc_final: 0.7614 (pptt) REVERT: I 246 LEU cc_start: 0.8425 (tp) cc_final: 0.8104 (tt) REVERT: I 257 MET cc_start: 0.8752 (mmt) cc_final: 0.8464 (mmt) REVERT: I 267 MET cc_start: 0.8488 (ptm) cc_final: 0.7649 (ppp) REVERT: I 299 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6506 (tpt) REVERT: I 343 GLU cc_start: 0.8466 (tp30) cc_final: 0.8261 (tp30) REVERT: I 362 LYS cc_start: 0.8380 (pptt) cc_final: 0.8144 (pptt) REVERT: I 363 MET cc_start: 0.7756 (ptp) cc_final: 0.7187 (ptt) REVERT: J 49 PHE cc_start: 0.8680 (p90) cc_final: 0.8374 (p90) REVERT: J 121 ARG cc_start: 0.9104 (mmm160) cc_final: 0.8830 (mmp80) REVERT: J 138 PHE cc_start: 0.8826 (m-80) cc_final: 0.8442 (m-10) REVERT: J 230 LEU cc_start: 0.9280 (mp) cc_final: 0.8887 (tt) REVERT: J 380 ASN cc_start: 0.8521 (t0) cc_final: 0.8196 (t0) REVERT: J 393 HIS cc_start: 0.8735 (t70) cc_final: 0.8436 (t70) REVERT: J 432 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7497 (t80) REVERT: K 309 HIS cc_start: 0.8382 (m-70) cc_final: 0.7810 (m90) REVERT: K 388 TRP cc_start: 0.8823 (m100) cc_final: 0.8568 (m100) REVERT: K 432 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7737 (t80) REVERT: L 84 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7131 (ttm-80) REVERT: L 138 PHE cc_start: 0.8846 (m-80) cc_final: 0.8330 (m-10) REVERT: L 149 PHE cc_start: 0.9073 (t80) cc_final: 0.8859 (t80) outliers start: 195 outliers final: 153 residues processed: 1046 average time/residue: 0.2455 time to fit residues: 426.6645 Evaluate side-chains 1037 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 864 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 425 TYR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 293 MET Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 HIS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 367 PHE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 237 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 31 optimal weight: 7.9990 chunk 385 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 429 optimal weight: 4.9990 chunk 396 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 chunk 325 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 226 ASN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 384 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN K 28 HIS ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.117278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.099579 restraints weight = 89464.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.102908 restraints weight = 45774.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.105163 restraints weight = 28373.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.106665 restraints weight = 19935.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.107764 restraints weight = 15357.774| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 41862 Z= 0.136 Angle : 0.717 15.141 56844 Z= 0.350 Chirality : 0.046 0.319 6222 Planarity : 0.004 0.065 7386 Dihedral : 12.338 165.794 5845 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.79 % Allowed : 25.27 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.27 (0.12), residues: 5130 helix: 1.07 (0.10), residues: 2460 sheet: 0.13 (0.19), residues: 756 loop : -0.92 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 422 TYR 0.040 0.001 TYR E 24 PHE 0.022 0.001 PHE A 343 TRP 0.020 0.002 TRP I 21 HIS 0.009 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00313 (41844) covalent geometry : angle 0.71653 (56844) hydrogen bonds : bond 0.03782 ( 2028) hydrogen bonds : angle 4.56442 ( 5850) Misc. bond : bond 0.00167 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 931 time to evaluate : 1.678 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 49 PHE cc_start: 0.8186 (p90) cc_final: 0.7894 (p90) REVERT: A 127 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7980 (p0) REVERT: A 129 CYS cc_start: 0.7194 (m) cc_final: 0.6946 (m) REVERT: A 149 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8696 (t80) REVERT: A 377 MET cc_start: 0.8771 (tmt) cc_final: 0.8287 (tmm) REVERT: A 430 LYS cc_start: 0.9273 (ttmt) cc_final: 0.8794 (tppt) REVERT: A 432 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7212 (t80) REVERT: B 33 SER cc_start: 0.8864 (m) cc_final: 0.8544 (p) REVERT: B 59 TYR cc_start: 0.8290 (m-80) cc_final: 0.7937 (m-80) REVERT: B 72 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8854 (p) REVERT: B 125 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 184 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7464 (p0) REVERT: B 279 GLN cc_start: 0.8626 (pt0) cc_final: 0.8374 (pt0) REVERT: B 297 LYS cc_start: 0.8381 (mmmt) cc_final: 0.8139 (tppt) REVERT: B 350 LYS cc_start: 0.8590 (tppt) cc_final: 0.8158 (tppt) REVERT: C 97 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7156 (mm-30) REVERT: C 232 SER cc_start: 0.8832 (t) cc_final: 0.8558 (t) REVERT: C 326 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8759 (ttpt) REVERT: C 358 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8584 (mm-40) REVERT: C 370 LYS cc_start: 0.7901 (tttp) cc_final: 0.7356 (tptp) REVERT: C 377 MET cc_start: 0.8502 (tmm) cc_final: 0.7998 (tmm) REVERT: C 432 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7422 (t80) REVERT: D 22 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7534 (tp30) REVERT: D 33 SER cc_start: 0.9125 (m) cc_final: 0.8792 (p) REVERT: D 101 TRP cc_start: 0.8170 (t60) cc_final: 0.7532 (t60) REVERT: D 147 MET cc_start: 0.8882 (mmm) cc_final: 0.8541 (mmm) REVERT: D 213 ARG cc_start: 0.8174 (tmm-80) cc_final: 0.7589 (ttm170) REVERT: D 232 THR cc_start: 0.8486 (m) cc_final: 0.8175 (m) REVERT: D 257 MET cc_start: 0.8037 (mmm) cc_final: 0.7693 (mmm) REVERT: D 297 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8455 (tttp) REVERT: D 364 SER cc_start: 0.8540 (p) cc_final: 0.8161 (p) REVERT: D 388 MET cc_start: 0.8858 (mmt) cc_final: 0.8451 (mmt) REVERT: E 49 PHE cc_start: 0.8264 (p90) cc_final: 0.7989 (p90) REVERT: E 84 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.7914 (mtm-85) REVERT: E 232 SER cc_start: 0.8991 (p) cc_final: 0.8660 (t) REVERT: E 282 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: E 357 TYR cc_start: 0.8238 (m-80) cc_final: 0.7942 (m-80) REVERT: E 370 LYS cc_start: 0.8112 (tttp) cc_final: 0.7563 (tptp) REVERT: E 388 TRP cc_start: 0.8743 (m100) cc_final: 0.8536 (m100) REVERT: E 398 MET cc_start: 0.9143 (mmm) cc_final: 0.8897 (mmt) REVERT: E 407 TRP cc_start: 0.8412 (m100) cc_final: 0.7870 (m-10) REVERT: E 430 LYS cc_start: 0.9440 (ttmt) cc_final: 0.9085 (tppt) REVERT: F 111 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: F 136 THR cc_start: 0.7856 (m) cc_final: 0.7634 (p) REVERT: F 177 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8363 (t0) REVERT: F 279 GLN cc_start: 0.8582 (pt0) cc_final: 0.8342 (mt0) REVERT: F 364 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7941 (p) REVERT: F 422 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.7654 (t80) REVERT: G 12 CYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8767 (p) REVERT: G 22 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8789 (tp30) REVERT: G 67 ASP cc_start: 0.7707 (t70) cc_final: 0.7204 (t70) REVERT: G 101 TRP cc_start: 0.8703 (t60) cc_final: 0.8341 (t60) REVERT: G 134 GLN cc_start: 0.8149 (pp30) cc_final: 0.7675 (pp30) REVERT: G 174 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8703 (mmmt) REVERT: G 216 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8365 (mmtp) REVERT: G 300 MET cc_start: 0.8348 (tpp) cc_final: 0.8006 (mmt) REVERT: G 327 ASP cc_start: 0.9082 (m-30) cc_final: 0.8633 (p0) REVERT: G 351 VAL cc_start: 0.9215 (t) cc_final: 0.8955 (m) REVERT: G 363 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7639 (ptp) REVERT: G 422 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.6559 (t80) REVERT: H 53 GLU cc_start: 0.7622 (tp30) cc_final: 0.7177 (tp30) REVERT: H 101 TRP cc_start: 0.8531 (t60) cc_final: 0.8085 (t60) REVERT: H 130 LEU cc_start: 0.8388 (tp) cc_final: 0.8118 (tp) REVERT: H 136 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8243 (p) REVERT: H 216 LYS cc_start: 0.8297 (mmtp) cc_final: 0.7693 (pptt) REVERT: H 300 MET cc_start: 0.8078 (mmm) cc_final: 0.7707 (mmt) REVERT: I 81 PHE cc_start: 0.6090 (m-10) cc_final: 0.5811 (m-10) REVERT: I 92 PHE cc_start: 0.8622 (p90) cc_final: 0.8338 (p90) REVERT: I 101 TRP cc_start: 0.8755 (t60) cc_final: 0.8434 (t60) REVERT: I 130 LEU cc_start: 0.8313 (tp) cc_final: 0.7961 (tp) REVERT: I 136 THR cc_start: 0.8576 (m) cc_final: 0.8302 (p) REVERT: I 216 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7590 (pptt) REVERT: I 246 LEU cc_start: 0.8356 (tp) cc_final: 0.7952 (tt) REVERT: I 267 MET cc_start: 0.8405 (ptm) cc_final: 0.7488 (ppp) REVERT: I 299 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.6103 (tpt) REVERT: I 300 MET cc_start: 0.8321 (tpp) cc_final: 0.7585 (tpt) REVERT: I 343 GLU cc_start: 0.8543 (tp30) cc_final: 0.8333 (tp30) REVERT: I 362 LYS cc_start: 0.8449 (pptt) cc_final: 0.8246 (pptt) REVERT: I 363 MET cc_start: 0.7723 (ptp) cc_final: 0.7003 (ptt) REVERT: J 49 PHE cc_start: 0.8610 (p90) cc_final: 0.8343 (p90) REVERT: J 138 PHE cc_start: 0.8794 (m-80) cc_final: 0.8394 (m-10) REVERT: J 192 HIS cc_start: 0.8684 (t70) cc_final: 0.8311 (t70) REVERT: J 203 MET cc_start: 0.8746 (mmp) cc_final: 0.8264 (mmm) REVERT: J 230 LEU cc_start: 0.9254 (mp) cc_final: 0.8855 (tt) REVERT: J 377 MET cc_start: 0.8210 (ttp) cc_final: 0.7936 (ttm) REVERT: J 380 ASN cc_start: 0.8575 (t0) cc_final: 0.8225 (t0) REVERT: J 432 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7429 (t80) REVERT: K 203 MET cc_start: 0.8641 (mmp) cc_final: 0.8021 (mmm) REVERT: K 253 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7887 (p) REVERT: K 282 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: K 309 HIS cc_start: 0.8400 (m-70) cc_final: 0.7842 (m90) REVERT: K 432 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7730 (t80) REVERT: L 138 PHE cc_start: 0.8795 (m-80) cc_final: 0.8250 (m-10) REVERT: L 432 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7664 (t80) outliers start: 167 outliers final: 129 residues processed: 1046 average time/residue: 0.2466 time to fit residues: 427.2644 Evaluate side-chains 1028 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 876 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 356 ILE Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 237 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 311 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 352 optimal weight: 3.9990 chunk 446 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 384 GLN I 245 GLN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 384 GLN J 293 ASN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.116049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.098690 restraints weight = 90963.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.101949 restraints weight = 46755.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.104126 restraints weight = 29015.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.105626 restraints weight = 20481.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.106683 restraints weight = 15783.691| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 41862 Z= 0.164 Angle : 0.731 13.824 56844 Z= 0.359 Chirality : 0.046 0.303 6222 Planarity : 0.004 0.061 7386 Dihedral : 12.328 166.463 5839 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.02 % Allowed : 25.66 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.22 (0.12), residues: 5130 helix: 1.00 (0.10), residues: 2460 sheet: 0.42 (0.20), residues: 720 loop : -1.02 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 422 TYR 0.037 0.001 TYR E 24 PHE 0.027 0.002 PHE J 351 TRP 0.043 0.002 TRP D 397 HIS 0.008 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00382 (41844) covalent geometry : angle 0.73084 (56844) hydrogen bonds : bond 0.03879 ( 2028) hydrogen bonds : angle 4.61608 ( 5850) Misc. bond : bond 0.00172 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9877.60 seconds wall clock time: 171 minutes 20.60 seconds (10280.60 seconds total)