Starting phenix.real_space_refine on Fri Nov 21 00:16:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dpw_7975/11_2025/6dpw_7975.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dpw_7975/11_2025/6dpw_7975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dpw_7975/11_2025/6dpw_7975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dpw_7975/11_2025/6dpw_7975.map" model { file = "/net/cci-nas-00/data/ceres_data/6dpw_7975/11_2025/6dpw_7975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dpw_7975/11_2025/6dpw_7975.cif" } resolution = 3.5 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= -0.022 sd= 0.922 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 6 5.21 5 S 282 5.16 5 C 25620 2.51 5 N 6966 2.21 5 O 7902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40812 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 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: 9.93, per 1000 atoms: 0.24 Number of scatterers: 40812 At special positions: 0 Unit cell: (171.57, 87.78, 211.47, 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 6 11.99 O 7902 8.00 N 6966 7.00 C 25620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.9 seconds 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9552 Finding SS restraints... Secondary structure from input PDB file: 258 helices and 30 sheets defined 56.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.888A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.630A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.593A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.096A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.398A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.654A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.172A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.981A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.919A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.430A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.755A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.491A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.778A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.648A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.741A pdb=" N GLN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.096A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 438 removed outlier: 3.726A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.885A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.633A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.592A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 162 removed outlier: 4.101A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.396A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.654A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 400 removed outlier: 4.170A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.980A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.924A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.430A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.755A pdb=" N PHE D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.491A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.778A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.650A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.741A pdb=" N GLN D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.097A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 438 removed outlier: 3.727A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.887A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.630A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 162 removed outlier: 4.096A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 205 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.399A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.656A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.171A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.980A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.918A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.432A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.755A pdb=" N PHE F 87 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.490A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.777A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 3.649A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.741A pdb=" N GLN F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG F 284 " --> pdb=" O GLN F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 400 Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.096A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 438 removed outlier: 3.726A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.430A pdb=" N ARG G 48 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 72 through 81 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.753A pdb=" N PHE G 87 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 129 removed outlier: 4.492A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.777A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 3.649A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.740A pdb=" N GLN G 282 " --> pdb=" O GLY G 279 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G 284 " --> pdb=" O GLN G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 384 through 400 Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.096A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 438 removed outlier: 3.725A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.430A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.754A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.494A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.778A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.648A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.740A pdb=" N GLN H 282 " --> pdb=" O GLY H 279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 284 " --> pdb=" O GLN H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 296 Processing helix chain 'H' and resid 297 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 400 Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.097A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 438 removed outlier: 3.726A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.430A pdb=" N ARG I 48 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 72 through 81 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.754A pdb=" N PHE I 87 " --> pdb=" O GLY I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 109 through 129 removed outlier: 4.493A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.778A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.647A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 279 through 284 removed outlier: 3.740A pdb=" N GLN I 282 " --> pdb=" O GLY I 279 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG I 284 " --> pdb=" O GLN I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 296 Processing helix chain 'I' and resid 297 through 301 Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 339 Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 384 through 400 Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.098A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 438 removed outlier: 3.725A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 47 through 51 removed outlier: 3.889A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.631A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.593A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 162 removed outlier: 4.096A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 205 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.397A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.653A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 Processing helix chain 'J' and resid 287 through 296 Processing helix chain 'J' and resid 297 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 Processing helix chain 'J' and resid 383 through 400 removed outlier: 4.172A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 3.982A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.918A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.887A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.634A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.592A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 162 removed outlier: 4.100A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 196 through 198 No H-bonds generated for 'chain 'K' and resid 196 through 198' Processing helix chain 'K' and resid 205 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.396A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.652A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 282 Processing helix chain 'K' and resid 287 through 296 Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 400 removed outlier: 4.169A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 3.981A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.923A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 47 through 51 removed outlier: 3.887A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.632A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.593A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 162 removed outlier: 4.098A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 205 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.396A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 3.652A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 282 Processing helix chain 'L' and resid 287 through 296 Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 Processing helix chain 'L' and resid 383 through 400 removed outlier: 4.171A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 3.981A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.918A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 248 removed outlier: 6.631A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.896A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.266A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.938A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.012A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) 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 246 through 248 removed outlier: 6.634A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.896A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.264A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER D 374 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE D 319 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR D 376 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA D 317 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 378 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL D 315 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN D 380 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.938A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) 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 246 through 248 removed outlier: 6.629A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA E 374 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.896A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.265A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.895A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU G 137 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE G 7 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.135A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.263A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.895A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.135A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.262A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER H 374 " --> pdb=" O PHE H 319 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE H 319 " --> pdb=" O SER H 374 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR H 376 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA H 317 " --> pdb=" O THR H 376 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE H 378 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL H 315 " --> pdb=" O ILE H 378 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN H 380 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.938A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.896A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU I 137 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE I 7 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.263A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.938A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) 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 246 through 248 removed outlier: 6.628A pdb=" N ASN J 380 " --> pdb=" O MET J 313 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS J 315 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU J 378 " --> pdb=" O CYS J 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU J 317 " --> pdb=" O CYS J 376 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N CYS J 376 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR J 319 " --> pdb=" O ALA J 374 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA J 374 " --> pdb=" O TYR J 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.012A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) 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 246 through 248 removed outlier: 6.632A pdb=" N ASN K 380 " --> pdb=" O MET K 313 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS K 315 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU K 378 " --> pdb=" O CYS K 315 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU K 317 " --> pdb=" O CYS K 376 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS K 376 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR K 319 " --> pdb=" O ALA K 374 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA K 374 " --> pdb=" O TYR K 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) 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 246 through 248 removed outlier: 6.628A pdb=" N ASN L 380 " --> pdb=" O MET L 313 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS L 315 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU L 378 " --> pdb=" O CYS L 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU L 317 " --> pdb=" O CYS L 376 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS L 376 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR L 319 " --> pdb=" O ALA L 374 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA L 374 " --> pdb=" O TYR L 319 " (cutoff:3.500A) 2062 hydrogen bonds defined for protein. 5934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.57 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 13626 1.35 - 1.50: 11303 1.50 - 1.65: 16375 1.65 - 1.80: 215 1.80 - 1.95: 223 Bond restraints: 41742 Sorted by residual: bond pdb=" PG GSP I 501 " pdb=" S1G GSP I 501 " ideal model delta sigma weight residual 1.700 1.948 -0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" PG GSP H 501 " pdb=" S1G GSP H 501 " ideal model delta sigma weight residual 1.700 1.947 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" PG GSP G 501 " pdb=" S1G GSP G 501 " ideal model delta sigma weight residual 1.700 1.947 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" PG GSP B 501 " pdb=" S1G GSP B 501 " ideal model delta sigma weight residual 1.700 1.939 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" PG GSP D 501 " pdb=" S1G GSP D 501 " ideal model delta sigma weight residual 1.700 1.937 -0.237 2.00e-02 2.50e+03 1.41e+02 ... (remaining 41737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 52218 2.53 - 5.06: 4225 5.06 - 7.59: 229 7.59 - 10.12: 40 10.12 - 12.65: 6 Bond angle restraints: 56718 Sorted by residual: angle pdb=" C LYS J 338 " pdb=" N ARG J 339 " pdb=" CA ARG J 339 " ideal model delta sigma weight residual 120.38 127.96 -7.58 1.37e+00 5.33e-01 3.06e+01 angle pdb=" C LYS L 338 " pdb=" N ARG L 339 " pdb=" CA ARG L 339 " ideal model delta sigma weight residual 120.38 127.94 -7.56 1.37e+00 5.33e-01 3.05e+01 angle pdb=" C LYS E 338 " pdb=" N ARG E 339 " pdb=" CA ARG E 339 " ideal model delta sigma weight residual 120.38 127.93 -7.55 1.37e+00 5.33e-01 3.03e+01 angle pdb=" C LYS A 338 " pdb=" N ARG A 339 " pdb=" CA ARG A 339 " ideal model delta sigma weight residual 120.38 127.92 -7.54 1.37e+00 5.33e-01 3.03e+01 angle pdb=" N LYS L 338 " pdb=" CA LYS L 338 " pdb=" C LYS L 338 " ideal model delta sigma weight residual 110.24 118.32 -8.08 1.47e+00 4.63e-01 3.02e+01 ... (remaining 56713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.83: 24095 33.83 - 67.66: 667 67.66 - 101.49: 42 101.49 - 135.32: 0 135.32 - 169.14: 18 Dihedral angle restraints: 24822 sinusoidal: 9930 harmonic: 14892 Sorted by residual: dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.59 -169.14 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.63 -169.10 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.64 -169.10 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 24819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4072 0.069 - 0.139: 1599 0.139 - 0.208: 349 0.208 - 0.278: 159 0.278 - 0.347: 19 Chirality restraints: 6198 Sorted by residual: chirality pdb=" CA ASN G 167 " pdb=" N ASN G 167 " pdb=" C ASN G 167 " pdb=" CB ASN G 167 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASN I 167 " pdb=" N ASN I 167 " pdb=" C ASN I 167 " pdb=" CB ASN I 167 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASN F 167 " pdb=" N ASN F 167 " pdb=" C ASN F 167 " pdb=" CB ASN F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 6195 not shown) Planarity restraints: 7386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP C 501 " 0.025 2.00e-02 2.50e+03 1.20e-02 4.31e+00 pdb=" C2 GTP C 501 " -0.009 2.00e-02 2.50e+03 pdb=" C4 GTP C 501 " -0.000 2.00e-02 2.50e+03 pdb=" C5 GTP C 501 " -0.005 2.00e-02 2.50e+03 pdb=" C6 GTP C 501 " 0.002 2.00e-02 2.50e+03 pdb=" C8 GTP C 501 " 0.002 2.00e-02 2.50e+03 pdb=" N1 GTP C 501 " 0.007 2.00e-02 2.50e+03 pdb=" N2 GTP C 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP C 501 " -0.001 2.00e-02 2.50e+03 pdb=" N7 GTP C 501 " -0.002 2.00e-02 2.50e+03 pdb=" N9 GTP C 501 " -0.029 2.00e-02 2.50e+03 pdb=" O6 GTP C 501 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 501 " 0.023 2.00e-02 2.50e+03 1.12e-02 3.78e+00 pdb=" C2 GTP L 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4 GTP L 501 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GTP L 501 " -0.004 2.00e-02 2.50e+03 pdb=" C6 GTP L 501 " 0.001 2.00e-02 2.50e+03 pdb=" C8 GTP L 501 " 0.003 2.00e-02 2.50e+03 pdb=" N1 GTP L 501 " 0.004 2.00e-02 2.50e+03 pdb=" N2 GTP L 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP L 501 " -0.002 2.00e-02 2.50e+03 pdb=" N7 GTP L 501 " -0.001 2.00e-02 2.50e+03 pdb=" N9 GTP L 501 " -0.029 2.00e-02 2.50e+03 pdb=" O6 GTP L 501 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 21 " 0.024 2.00e-02 2.50e+03 1.20e-02 3.61e+00 pdb=" CG TRP C 21 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP C 21 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 21 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 21 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 21 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 21 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 21 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 21 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 21 " 0.008 2.00e-02 2.50e+03 ... (remaining 7383 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 154 2.61 - 3.18: 35410 3.18 - 3.76: 65265 3.76 - 4.33: 90705 4.33 - 4.90: 153615 Nonbonded interactions: 345149 Sorted by model distance: nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.040 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 2.047 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 2.056 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 2.060 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 2.084 2.170 ... (remaining 345144 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: 0.13 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: 13.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 42.740 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.880 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.009 0.248 41742 Z= 0.628 Angle : 1.426 12.653 56718 Z= 0.989 Chirality : 0.081 0.347 6198 Planarity : 0.006 0.042 7386 Dihedral : 15.584 169.145 15270 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.56 % Rotamer: Outliers : 0.82 % Allowed : 5.04 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.11), residues: 5118 helix: 0.86 (0.09), residues: 2328 sheet: 0.32 (0.19), residues: 816 loop : -0.71 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 2 TYR 0.020 0.002 TYR J 224 PHE 0.023 0.002 PHE F 92 TRP 0.024 0.003 TRP C 21 HIS 0.010 0.002 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00919 (41742) covalent geometry : angle 1.42584 (56718) hydrogen bonds : bond 0.18979 ( 2062) hydrogen bonds : angle 7.52764 ( 5934) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1427 time to evaluate : 1.527 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: A 290 GLU cc_start: 0.7342 (tt0) cc_final: 0.6945 (tt0) REVERT: B 41 ASP cc_start: 0.8048 (m-30) cc_final: 0.7724 (p0) REVERT: B 161 TYR cc_start: 0.8672 (m-80) cc_final: 0.8453 (m-80) REVERT: B 224 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: B 306 ASP cc_start: 0.8267 (t0) cc_final: 0.7939 (t70) REVERT: B 325 MET cc_start: 0.7378 (mmm) cc_final: 0.7006 (mmm) REVERT: B 329 ASP cc_start: 0.7327 (m-30) cc_final: 0.6817 (m-30) REVERT: B 339 ASN cc_start: 0.7469 (m110) cc_final: 0.6676 (m110) REVERT: B 414 ASP cc_start: 0.7221 (p0) cc_final: 0.6770 (t70) REVERT: B 427 ASP cc_start: 0.8335 (m-30) cc_final: 0.8040 (m-30) REVERT: C 71 GLU cc_start: 0.7616 (pt0) cc_final: 0.7294 (pt0) REVERT: C 84 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7408 (ptp90) REVERT: C 205 ASP cc_start: 0.7778 (t0) cc_final: 0.7451 (t0) REVERT: C 304 LYS cc_start: 0.8187 (tttt) cc_final: 0.7473 (tptm) REVERT: C 341 ILE cc_start: 0.8807 (mp) cc_final: 0.8544 (mp) REVERT: D 114 LEU cc_start: 0.9440 (tp) cc_final: 0.9101 (tt) REVERT: D 120 ASP cc_start: 0.8047 (m-30) cc_final: 0.7814 (m-30) REVERT: D 138 THR cc_start: 0.9105 (m) cc_final: 0.8893 (p) REVERT: D 210 TYR cc_start: 0.8724 (m-80) cc_final: 0.8256 (m-80) REVERT: D 224 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: D 325 MET cc_start: 0.7561 (mmm) cc_final: 0.7347 (tpp) REVERT: D 353 THR cc_start: 0.8765 (m) cc_final: 0.8551 (p) REVERT: D 414 ASP cc_start: 0.7356 (p0) cc_final: 0.6987 (t70) REVERT: E 71 GLU cc_start: 0.7807 (pt0) cc_final: 0.7579 (tt0) REVERT: E 243 ARG cc_start: 0.8611 (mtm110) cc_final: 0.7826 (mtm110) REVERT: E 302 MET cc_start: 0.8127 (mtt) cc_final: 0.7876 (mtt) REVERT: E 304 LYS cc_start: 0.8487 (tttt) cc_final: 0.8056 (ttmm) REVERT: F 138 THR cc_start: 0.8938 (m) cc_final: 0.8667 (p) REVERT: F 179 ASP cc_start: 0.8346 (t70) cc_final: 0.8006 (t0) REVERT: F 210 TYR cc_start: 0.8594 (m-80) cc_final: 0.8106 (m-80) REVERT: F 224 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: F 306 ASP cc_start: 0.8002 (t0) cc_final: 0.7200 (t70) REVERT: G 179 ASP cc_start: 0.8277 (t70) cc_final: 0.7823 (t0) REVERT: G 224 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: G 228 ASN cc_start: 0.8675 (m-40) cc_final: 0.8249 (m-40) REVERT: G 325 MET cc_start: 0.7560 (mmm) cc_final: 0.7162 (mmm) REVERT: H 131 CYS cc_start: 0.8098 (t) cc_final: 0.7717 (t) REVERT: H 179 ASP cc_start: 0.8025 (t70) cc_final: 0.7691 (t0) REVERT: H 210 TYR cc_start: 0.8366 (m-80) cc_final: 0.8044 (m-80) REVERT: H 325 MET cc_start: 0.7541 (mmm) cc_final: 0.7332 (tpp) REVERT: I 69 ASP cc_start: 0.6708 (t0) cc_final: 0.6301 (t0) REVERT: I 86 ILE cc_start: 0.8292 (tt) cc_final: 0.8019 (tt) REVERT: I 138 THR cc_start: 0.8987 (m) cc_final: 0.8673 (p) REVERT: I 179 ASP cc_start: 0.8166 (t70) cc_final: 0.7845 (t0) REVERT: I 332 MET cc_start: 0.8909 (mmp) cc_final: 0.8516 (mmm) REVERT: J 2 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7097 (mtt90) REVERT: J 115 ILE cc_start: 0.9012 (tp) cc_final: 0.8703 (tp) REVERT: J 176 GLN cc_start: 0.8244 (mt0) cc_final: 0.7904 (mt0) REVERT: J 271 THR cc_start: 0.9014 (m) cc_final: 0.8796 (m) REVERT: J 275 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8511 (p) REVERT: K 2 ARG cc_start: 0.7465 (mtm180) cc_final: 0.7131 (mpt180) REVERT: K 71 GLU cc_start: 0.7672 (pt0) cc_final: 0.6682 (tt0) REVERT: K 302 MET cc_start: 0.8066 (mtt) cc_final: 0.7713 (mtt) REVERT: K 417 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7324 (tm-30) REVERT: L 2 ARG cc_start: 0.7515 (mtm180) cc_final: 0.7026 (mtt90) REVERT: L 207 GLU cc_start: 0.7187 (tt0) cc_final: 0.6363 (tt0) REVERT: L 285 GLN cc_start: 0.7793 (pm20) cc_final: 0.6850 (mm110) REVERT: L 417 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7309 (tm-30) outliers start: 36 outliers final: 3 residues processed: 1451 average time/residue: 0.2609 time to fit residues: 605.0548 Evaluate side-chains 733 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 725 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain J residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 88 HIS A 283 HIS A 358 GLN B 6 HIS ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 433 GLN C 15 GLN C 88 HIS C 283 HIS C 293 ASN C 358 GLN D 6 HIS D 192 HIS D 336 GLN D 433 GLN E 15 GLN E 88 HIS E 283 HIS E 293 ASN E 358 GLN F 6 HIS F 192 HIS ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN F 433 GLN G 6 HIS G 59 ASN ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 HIS H 14 ASN H 101 ASN H 339 ASN I 6 HIS I 59 ASN I 192 HIS I 258 ASN I 309 HIS J 15 GLN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 HIS J 358 GLN K 15 GLN K 50 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS K 293 ASN K 358 GLN L 8 HIS L 15 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 358 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093055 restraints weight = 66174.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096671 restraints weight = 32057.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.099138 restraints weight = 19306.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.100837 restraints weight = 13227.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102063 restraints weight = 9865.459| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41742 Z= 0.157 Angle : 0.621 7.942 56718 Z= 0.330 Chirality : 0.045 0.184 6198 Planarity : 0.005 0.046 7386 Dihedral : 11.258 172.195 5781 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.39 % Allowed : 13.20 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.12), residues: 5118 helix: 2.32 (0.11), residues: 2340 sheet: 0.57 (0.18), residues: 786 loop : -0.20 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 390 TYR 0.015 0.002 TYR E 172 PHE 0.022 0.002 PHE G 169 TRP 0.015 0.002 TRP G 346 HIS 0.008 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00332 (41742) covalent geometry : angle 0.62077 (56718) hydrogen bonds : bond 0.05958 ( 2062) hydrogen bonds : angle 5.26654 ( 5934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 785 time to evaluate : 1.534 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: A 112 LYS cc_start: 0.8549 (pttp) cc_final: 0.8336 (mtpt) REVERT: A 113 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 136 LEU cc_start: 0.9112 (mt) cc_final: 0.8887 (mp) REVERT: A 172 TYR cc_start: 0.8489 (t80) cc_final: 0.8118 (t80) REVERT: A 207 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: B 69 ASP cc_start: 0.7190 (t0) cc_final: 0.6749 (t0) REVERT: B 224 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: B 299 LYS cc_start: 0.8517 (ptpt) cc_final: 0.8313 (tmmt) REVERT: B 306 ASP cc_start: 0.7920 (t0) cc_final: 0.7667 (t70) REVERT: B 325 MET cc_start: 0.7659 (mmm) cc_final: 0.6582 (mmm) REVERT: B 329 ASP cc_start: 0.7333 (m-30) cc_final: 0.6600 (m-30) REVERT: B 417 GLU cc_start: 0.7314 (mp0) cc_final: 0.6967 (mp0) REVERT: C 50 ASN cc_start: 0.8097 (t0) cc_final: 0.7891 (t0) REVERT: C 203 MET cc_start: 0.8200 (mmm) cc_final: 0.7872 (mmm) REVERT: C 205 ASP cc_start: 0.7878 (t0) cc_final: 0.7579 (t0) REVERT: C 207 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: C 313 MET cc_start: 0.8513 (mtm) cc_final: 0.8230 (mtm) REVERT: D 55 GLU cc_start: 0.7624 (tp30) cc_final: 0.7420 (tp30) REVERT: D 120 ASP cc_start: 0.8154 (m-30) cc_final: 0.7877 (m-30) REVERT: D 166 MET cc_start: 0.7803 (tpp) cc_final: 0.7475 (tpp) REVERT: D 210 TYR cc_start: 0.8694 (m-80) cc_final: 0.8348 (m-80) REVERT: D 314 THR cc_start: 0.9365 (p) cc_final: 0.9143 (p) REVERT: E 71 GLU cc_start: 0.7831 (pt0) cc_final: 0.6815 (tt0) REVERT: E 157 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8867 (mp) REVERT: E 205 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: E 251 ASP cc_start: 0.7780 (p0) cc_final: 0.7531 (p0) REVERT: E 313 MET cc_start: 0.8410 (mtm) cc_final: 0.8193 (mtm) REVERT: F 138 THR cc_start: 0.9060 (m) cc_final: 0.8518 (p) REVERT: F 179 ASP cc_start: 0.8238 (t70) cc_final: 0.7529 (t0) REVERT: F 204 ILE cc_start: 0.8992 (mp) cc_final: 0.8630 (mt) REVERT: F 205 ASP cc_start: 0.7628 (m-30) cc_final: 0.7304 (m-30) REVERT: F 209 LEU cc_start: 0.9092 (mp) cc_final: 0.8857 (mm) REVERT: F 210 TYR cc_start: 0.8806 (m-80) cc_final: 0.8528 (m-80) REVERT: F 259 MET cc_start: 0.9047 (mmp) cc_final: 0.8769 (mmt) REVERT: F 334 ASN cc_start: 0.8363 (t0) cc_final: 0.8091 (t0) REVERT: G 179 ASP cc_start: 0.8167 (t70) cc_final: 0.7698 (t0) REVERT: G 255 LEU cc_start: 0.8636 (mt) cc_final: 0.8314 (mt) REVERT: G 325 MET cc_start: 0.8011 (mmm) cc_final: 0.7359 (mmm) REVERT: H 179 ASP cc_start: 0.7948 (t70) cc_final: 0.7639 (t0) REVERT: I 47 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7700 (mm-30) REVERT: I 138 THR cc_start: 0.8848 (m) cc_final: 0.8462 (p) REVERT: I 179 ASP cc_start: 0.8195 (t70) cc_final: 0.7788 (t0) REVERT: J 205 ASP cc_start: 0.7554 (t0) cc_final: 0.7266 (t0) REVERT: J 275 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8675 (p) REVERT: J 377 MET cc_start: 0.8409 (ttp) cc_final: 0.8097 (ttm) REVERT: J 378 LEU cc_start: 0.9003 (mt) cc_final: 0.8789 (mt) REVERT: K 2 ARG cc_start: 0.7343 (mtm180) cc_final: 0.6928 (mpt180) REVERT: K 76 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8718 (m-30) REVERT: K 302 MET cc_start: 0.8326 (mtt) cc_final: 0.7832 (mtt) REVERT: K 417 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6782 (tm-30) REVERT: L 2 ARG cc_start: 0.7304 (mtm180) cc_final: 0.7087 (mtt90) REVERT: L 176 GLN cc_start: 0.7707 (pm20) cc_final: 0.7428 (pm20) REVERT: L 285 GLN cc_start: 0.7726 (pm20) cc_final: 0.6404 (mm-40) REVERT: L 313 MET cc_start: 0.8493 (mtm) cc_final: 0.8208 (mtm) REVERT: L 378 LEU cc_start: 0.9105 (mt) cc_final: 0.8670 (mt) outliers start: 105 outliers final: 65 residues processed: 854 average time/residue: 0.2324 time to fit residues: 333.5805 Evaluate side-chains 702 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 630 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 213 CYS Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 213 CYS Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 213 CYS Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 314 optimal weight: 3.9990 chunk 336 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 431 optimal weight: 8.9990 chunk 478 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 357 optimal weight: 6.9990 chunk 434 optimal weight: 1.9990 chunk 437 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 88 HIS A 293 ASN B 8 GLN B 101 ASN B 167 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS C 8 HIS C 18 ASN C 88 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 258 ASN D 406 HIS E 8 HIS E 18 ASN E 88 HIS ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 406 HIS G 8 GLN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 HIS H 8 GLN H 133 GLN H 228 ASN H 309 HIS H 349 ASN H 406 HIS I 8 GLN I 15 GLN I 59 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS J 8 HIS J 88 HIS J 186 ASN K 8 HIS K 88 HIS K 186 ASN K 342 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088621 restraints weight = 67278.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092006 restraints weight = 33605.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094336 restraints weight = 20592.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095949 restraints weight = 14277.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097103 restraints weight = 10739.349| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41742 Z= 0.154 Angle : 0.571 11.680 56718 Z= 0.298 Chirality : 0.044 0.193 6198 Planarity : 0.004 0.043 7386 Dihedral : 10.917 176.176 5771 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.26 % Allowed : 14.96 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.12), residues: 5118 helix: 2.29 (0.11), residues: 2364 sheet: 0.34 (0.17), residues: 816 loop : 0.03 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 284 TYR 0.015 0.001 TYR I 202 PHE 0.018 0.001 PHE L 138 TRP 0.015 0.002 TRP A 21 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00342 (41742) covalent geometry : angle 0.57118 (56718) hydrogen bonds : bond 0.05047 ( 2062) hydrogen bonds : angle 4.95396 ( 5934) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 702 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8597 (pttp) cc_final: 0.8365 (mtmm) REVERT: A 113 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7891 (mm-30) REVERT: A 172 TYR cc_start: 0.8692 (t80) cc_final: 0.8296 (t80) REVERT: A 207 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: A 251 ASP cc_start: 0.7625 (p0) cc_final: 0.7314 (p0) REVERT: B 76 ASP cc_start: 0.8677 (m-30) cc_final: 0.8463 (m-30) REVERT: B 306 ASP cc_start: 0.8023 (t0) cc_final: 0.7625 (t70) REVERT: B 325 MET cc_start: 0.7700 (mmm) cc_final: 0.6423 (mmm) REVERT: B 329 ASP cc_start: 0.7402 (m-30) cc_final: 0.6676 (m-30) REVERT: B 417 GLU cc_start: 0.7384 (mp0) cc_final: 0.7036 (mp0) REVERT: C 24 TYR cc_start: 0.8965 (m-80) cc_final: 0.8578 (m-80) REVERT: C 50 ASN cc_start: 0.8264 (t0) cc_final: 0.7828 (t0) REVERT: C 203 MET cc_start: 0.8230 (mmm) cc_final: 0.7869 (mmm) REVERT: C 313 MET cc_start: 0.8574 (mtm) cc_final: 0.8308 (mtm) REVERT: C 382 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.9014 (p) REVERT: C 411 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7664 (mm-30) REVERT: D 26 ASP cc_start: 0.8452 (t70) cc_final: 0.8196 (m-30) REVERT: D 41 ASP cc_start: 0.8178 (p0) cc_final: 0.7590 (p0) REVERT: D 138 THR cc_start: 0.9065 (m) cc_final: 0.8790 (p) REVERT: D 166 MET cc_start: 0.7912 (tpp) cc_final: 0.7574 (ttm) REVERT: D 210 TYR cc_start: 0.8727 (m-80) cc_final: 0.8217 (m-80) REVERT: D 301 MET cc_start: 0.8501 (mmp) cc_final: 0.8052 (tpp) REVERT: D 306 ASP cc_start: 0.7844 (t0) cc_final: 0.7364 (t70) REVERT: E 157 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8782 (mp) REVERT: E 313 MET cc_start: 0.8517 (mtm) cc_final: 0.8265 (mtm) REVERT: F 3 GLU cc_start: 0.6447 (mp0) cc_final: 0.6202 (mm-30) REVERT: F 26 ASP cc_start: 0.8514 (t70) cc_final: 0.8292 (m-30) REVERT: F 138 THR cc_start: 0.9054 (m) cc_final: 0.8499 (p) REVERT: F 149 MET cc_start: 0.8787 (ttt) cc_final: 0.8499 (ttt) REVERT: F 179 ASP cc_start: 0.8287 (t70) cc_final: 0.7551 (t0) REVERT: F 204 ILE cc_start: 0.9023 (mp) cc_final: 0.8617 (mt) REVERT: F 210 TYR cc_start: 0.8810 (m-80) cc_final: 0.8311 (m-80) REVERT: F 259 MET cc_start: 0.9043 (mmp) cc_final: 0.8490 (mmt) REVERT: F 433 GLN cc_start: 0.8310 (tp40) cc_final: 0.8061 (tp40) REVERT: F 437 ASP cc_start: 0.6661 (m-30) cc_final: 0.6203 (m-30) REVERT: G 67 LEU cc_start: 0.8383 (mp) cc_final: 0.8164 (mt) REVERT: G 179 ASP cc_start: 0.8199 (t70) cc_final: 0.7768 (t0) REVERT: G 325 MET cc_start: 0.8111 (mmm) cc_final: 0.7278 (mmm) REVERT: H 60 LYS cc_start: 0.7959 (mttt) cc_final: 0.7466 (mptt) REVERT: H 76 ASP cc_start: 0.8399 (t0) cc_final: 0.8160 (t0) REVERT: H 179 ASP cc_start: 0.7955 (t70) cc_final: 0.7697 (t0) REVERT: H 325 MET cc_start: 0.8106 (tpp) cc_final: 0.7897 (tpp) REVERT: I 47 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7792 (mm-30) REVERT: I 179 ASP cc_start: 0.8113 (t70) cc_final: 0.7683 (t0) REVERT: I 204 ILE cc_start: 0.8965 (mp) cc_final: 0.8759 (mt) REVERT: I 327 GLU cc_start: 0.8118 (tt0) cc_final: 0.7905 (tt0) REVERT: J 71 GLU cc_start: 0.7679 (pt0) cc_final: 0.7395 (pt0) REVERT: J 275 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8680 (p) REVERT: J 371 VAL cc_start: 0.8982 (m) cc_final: 0.8569 (t) REVERT: J 382 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9233 (p) REVERT: J 411 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7417 (mm-30) REVERT: K 2 ARG cc_start: 0.7479 (mtm180) cc_final: 0.7029 (mpt180) REVERT: K 205 ASP cc_start: 0.7900 (t0) cc_final: 0.7241 (m-30) REVERT: K 302 MET cc_start: 0.8484 (mtt) cc_final: 0.8059 (mtt) REVERT: K 411 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7372 (mm-30) REVERT: L 2 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7274 (mpt180) REVERT: L 285 GLN cc_start: 0.7853 (pm20) cc_final: 0.6486 (mm-40) REVERT: L 313 MET cc_start: 0.8607 (mtm) cc_final: 0.8254 (mtm) REVERT: L 368 LEU cc_start: 0.8776 (mp) cc_final: 0.8573 (mp) outliers start: 143 outliers final: 81 residues processed: 804 average time/residue: 0.2214 time to fit residues: 301.1894 Evaluate side-chains 677 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 591 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 353 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 166 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 440 optimal weight: 7.9990 chunk 496 optimal weight: 0.2980 chunk 318 optimal weight: 6.9990 chunk 475 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN B 258 ASN C 50 ASN C 88 HIS C 107 HIS C 258 ASN D 385 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 258 ASN F 8 GLN F 14 ASN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 339 ASN H 281 GLN H 349 ASN H 433 GLN I 59 ASN I 167 ASN I 406 HIS ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086169 restraints weight = 68148.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089514 restraints weight = 33902.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091839 restraints weight = 20806.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093458 restraints weight = 14446.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.094605 restraints weight = 10895.556| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41742 Z= 0.191 Angle : 0.577 10.922 56718 Z= 0.301 Chirality : 0.044 0.164 6198 Planarity : 0.004 0.046 7386 Dihedral : 10.860 179.457 5767 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.78 % Allowed : 14.87 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.12), residues: 5118 helix: 2.19 (0.11), residues: 2376 sheet: 0.21 (0.17), residues: 834 loop : -0.10 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 221 TYR 0.017 0.001 TYR B 161 PHE 0.015 0.002 PHE L 138 TRP 0.013 0.002 TRP A 21 HIS 0.007 0.001 HIS K 88 Details of bonding type rmsd covalent geometry : bond 0.00433 (41742) covalent geometry : angle 0.57658 (56718) hydrogen bonds : bond 0.05032 ( 2062) hydrogen bonds : angle 4.88266 ( 5934) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 633 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8428 (pttp) cc_final: 0.8176 (mtpt) REVERT: A 113 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 172 TYR cc_start: 0.8756 (t80) cc_final: 0.8357 (t80) REVERT: A 207 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: A 245 ASP cc_start: 0.7812 (p0) cc_final: 0.7490 (p0) REVERT: A 306 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8178 (t0) REVERT: B 76 ASP cc_start: 0.8570 (m-30) cc_final: 0.8209 (m-30) REVERT: B 211 ASP cc_start: 0.8421 (t0) cc_final: 0.7786 (t0) REVERT: B 325 MET cc_start: 0.7811 (mmm) cc_final: 0.6644 (mmm) REVERT: B 329 ASP cc_start: 0.7500 (m-30) cc_final: 0.6917 (m-30) REVERT: B 417 GLU cc_start: 0.7618 (mp0) cc_final: 0.7075 (mp0) REVERT: C 24 TYR cc_start: 0.9004 (m-80) cc_final: 0.8593 (m-80) REVERT: C 50 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7971 (t0) REVERT: C 203 MET cc_start: 0.8418 (mmm) cc_final: 0.8104 (mmt) REVERT: C 313 MET cc_start: 0.8477 (mtm) cc_final: 0.8213 (mtm) REVERT: C 411 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7665 (mm-30) REVERT: D 26 ASP cc_start: 0.8409 (t70) cc_final: 0.8187 (m-30) REVERT: D 41 ASP cc_start: 0.8274 (p0) cc_final: 0.7750 (p0) REVERT: D 138 THR cc_start: 0.9075 (m) cc_final: 0.8799 (p) REVERT: D 149 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8349 (ttt) REVERT: D 166 MET cc_start: 0.7908 (tpp) cc_final: 0.7668 (ttm) REVERT: D 210 TYR cc_start: 0.8747 (m-80) cc_final: 0.8070 (m-80) REVERT: D 301 MET cc_start: 0.8571 (mmp) cc_final: 0.8030 (tpp) REVERT: D 314 THR cc_start: 0.9506 (p) cc_final: 0.9282 (p) REVERT: E 118 VAL cc_start: 0.9010 (t) cc_final: 0.8784 (p) REVERT: E 157 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8793 (mp) REVERT: E 205 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7199 (m-30) REVERT: E 342 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: F 26 ASP cc_start: 0.8551 (t70) cc_final: 0.8334 (m-30) REVERT: F 149 MET cc_start: 0.8766 (ttt) cc_final: 0.8473 (ttt) REVERT: F 179 ASP cc_start: 0.8212 (t70) cc_final: 0.7465 (t0) REVERT: F 210 TYR cc_start: 0.8872 (m-80) cc_final: 0.8287 (m-80) REVERT: F 433 GLN cc_start: 0.8309 (tp40) cc_final: 0.8055 (tp40) REVERT: G 179 ASP cc_start: 0.8269 (t70) cc_final: 0.7854 (t0) REVERT: G 325 MET cc_start: 0.8138 (mmm) cc_final: 0.7439 (mmm) REVERT: H 60 LYS cc_start: 0.7787 (mttt) cc_final: 0.7506 (mptt) REVERT: I 47 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7801 (mm-30) REVERT: I 50 ASN cc_start: 0.8767 (p0) cc_final: 0.8478 (p0) REVERT: I 179 ASP cc_start: 0.8104 (t70) cc_final: 0.7716 (t0) REVERT: I 204 ILE cc_start: 0.9010 (mp) cc_final: 0.8798 (mt) REVERT: I 211 ASP cc_start: 0.8245 (t0) cc_final: 0.7941 (t0) REVERT: I 214 PHE cc_start: 0.8647 (t80) cc_final: 0.8425 (t80) REVERT: I 425 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8036 (tpt) REVERT: J 275 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8586 (p) REVERT: J 371 VAL cc_start: 0.8736 (m) cc_final: 0.8410 (t) REVERT: J 377 MET cc_start: 0.8441 (ttp) cc_final: 0.7989 (ttm) REVERT: J 411 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7414 (mm-30) REVERT: K 2 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7029 (mpt180) REVERT: K 24 TYR cc_start: 0.8816 (m-10) cc_final: 0.8250 (m-10) REVERT: K 205 ASP cc_start: 0.7929 (t0) cc_final: 0.7350 (m-30) REVERT: K 302 MET cc_start: 0.8489 (mtt) cc_final: 0.8088 (mtt) REVERT: K 411 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7010 (mm-30) REVERT: L 2 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7331 (mpt180) REVERT: L 285 GLN cc_start: 0.7908 (pm20) cc_final: 0.6316 (mm-40) REVERT: L 313 MET cc_start: 0.8615 (mtm) cc_final: 0.8255 (mtm) REVERT: L 335 ILE cc_start: 0.8699 (mt) cc_final: 0.8484 (mt) outliers start: 166 outliers final: 115 residues processed: 759 average time/residue: 0.2360 time to fit residues: 302.5708 Evaluate side-chains 715 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 591 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 438 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 438 ASP Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 379 optimal weight: 4.9990 chunk 485 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 410 optimal weight: 0.0030 chunk 198 optimal weight: 0.7980 chunk 437 optimal weight: 8.9990 chunk 327 optimal weight: 2.9990 chunk 462 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 415 optimal weight: 10.0000 chunk 446 optimal weight: 0.0270 overall best weight: 1.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN E 88 HIS ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086746 restraints weight = 67090.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090110 restraints weight = 32829.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092427 restraints weight = 19765.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094020 restraints weight = 13528.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095157 restraints weight = 10090.980| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41742 Z= 0.142 Angle : 0.543 11.445 56718 Z= 0.281 Chirality : 0.043 0.148 6198 Planarity : 0.004 0.043 7386 Dihedral : 10.769 179.291 5767 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.19 % Allowed : 16.12 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.12), residues: 5118 helix: 2.21 (0.11), residues: 2376 sheet: 0.33 (0.17), residues: 816 loop : -0.11 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 278 TYR 0.022 0.001 TYR G 435 PHE 0.020 0.001 PHE G 262 TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS J 88 Details of bonding type rmsd covalent geometry : bond 0.00317 (41742) covalent geometry : angle 0.54300 (56718) hydrogen bonds : bond 0.04627 ( 2062) hydrogen bonds : angle 4.76687 ( 5934) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 649 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8397 (pttp) cc_final: 0.8169 (mtpt) REVERT: A 113 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 172 TYR cc_start: 0.8791 (t80) cc_final: 0.8407 (t80) REVERT: A 245 ASP cc_start: 0.7773 (p0) cc_final: 0.7472 (p0) REVERT: A 279 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: A 342 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6766 (mp10) REVERT: B 41 ASP cc_start: 0.7806 (p0) cc_final: 0.7249 (p0) REVERT: B 69 ASP cc_start: 0.7462 (t0) cc_final: 0.7185 (t0) REVERT: B 76 ASP cc_start: 0.8566 (m-30) cc_final: 0.8335 (m-30) REVERT: B 211 ASP cc_start: 0.8195 (t0) cc_final: 0.7926 (t0) REVERT: B 325 MET cc_start: 0.7821 (mmm) cc_final: 0.6676 (mmm) REVERT: B 329 ASP cc_start: 0.7355 (m-30) cc_final: 0.6827 (m-30) REVERT: B 417 GLU cc_start: 0.7679 (mp0) cc_final: 0.7089 (mp0) REVERT: C 24 TYR cc_start: 0.8953 (m-80) cc_final: 0.8520 (m-80) REVERT: C 50 ASN cc_start: 0.8420 (t0) cc_final: 0.8022 (t0) REVERT: C 203 MET cc_start: 0.8472 (mmm) cc_final: 0.8203 (mmt) REVERT: C 269 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8664 (pp) REVERT: C 313 MET cc_start: 0.8591 (mtm) cc_final: 0.8321 (mtm) REVERT: C 411 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7616 (mm-30) REVERT: D 41 ASP cc_start: 0.8275 (p0) cc_final: 0.7541 (p0) REVERT: D 47 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7935 (mm-30) REVERT: D 138 THR cc_start: 0.9032 (m) cc_final: 0.8782 (p) REVERT: D 210 TYR cc_start: 0.8709 (m-80) cc_final: 0.8060 (m-80) REVERT: D 301 MET cc_start: 0.8592 (mmp) cc_final: 0.8096 (tpp) REVERT: D 306 ASP cc_start: 0.7869 (t0) cc_final: 0.7336 (t70) REVERT: D 314 THR cc_start: 0.9498 (p) cc_final: 0.9255 (p) REVERT: E 157 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8807 (mp) REVERT: E 205 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: E 342 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: F 25 SER cc_start: 0.9266 (m) cc_final: 0.9054 (p) REVERT: F 149 MET cc_start: 0.8788 (ttt) cc_final: 0.8541 (ttt) REVERT: F 179 ASP cc_start: 0.8250 (t70) cc_final: 0.7615 (t0) REVERT: F 210 TYR cc_start: 0.8834 (m-80) cc_final: 0.8239 (m-80) REVERT: F 228 ASN cc_start: 0.8847 (m-40) cc_final: 0.8387 (m-40) REVERT: G 69 ASP cc_start: 0.7586 (t0) cc_final: 0.7334 (t0) REVERT: G 179 ASP cc_start: 0.8241 (t70) cc_final: 0.7849 (t0) REVERT: G 205 ASP cc_start: 0.8189 (t0) cc_final: 0.7920 (m-30) REVERT: G 309 HIS cc_start: 0.8662 (m-70) cc_final: 0.8150 (m90) REVERT: G 325 MET cc_start: 0.8112 (mmm) cc_final: 0.7521 (mmm) REVERT: G 329 ASP cc_start: 0.7654 (m-30) cc_final: 0.7434 (m-30) REVERT: G 330 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6867 (mp0) REVERT: H 41 ASP cc_start: 0.8273 (p0) cc_final: 0.7988 (p0) REVERT: H 60 LYS cc_start: 0.7789 (mttt) cc_final: 0.7550 (mmtm) REVERT: H 76 ASP cc_start: 0.8426 (t0) cc_final: 0.8146 (t0) REVERT: I 47 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7873 (mm-30) REVERT: I 50 ASN cc_start: 0.8715 (p0) cc_final: 0.8449 (p0) REVERT: I 69 ASP cc_start: 0.7551 (t0) cc_final: 0.7249 (t0) REVERT: I 129 CYS cc_start: 0.6622 (m) cc_final: 0.6342 (m) REVERT: I 179 ASP cc_start: 0.8080 (t70) cc_final: 0.7683 (t0) REVERT: I 204 ILE cc_start: 0.9002 (mp) cc_final: 0.8794 (mt) REVERT: J 172 TYR cc_start: 0.8478 (t80) cc_final: 0.8131 (t80) REVERT: J 275 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8503 (p) REVERT: J 371 VAL cc_start: 0.8735 (m) cc_final: 0.8408 (t) REVERT: J 377 MET cc_start: 0.8449 (ttp) cc_final: 0.8162 (ttm) REVERT: J 388 TRP cc_start: 0.9258 (m100) cc_final: 0.8901 (m100) REVERT: J 411 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7375 (mm-30) REVERT: K 2 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7024 (mpt180) REVERT: K 24 TYR cc_start: 0.8798 (m-10) cc_final: 0.8377 (m-10) REVERT: K 69 ASP cc_start: 0.7783 (t0) cc_final: 0.7470 (t0) REVERT: K 176 GLN cc_start: 0.8200 (pt0) cc_final: 0.7725 (pm20) REVERT: K 205 ASP cc_start: 0.7837 (t0) cc_final: 0.7296 (m-30) REVERT: K 302 MET cc_start: 0.8331 (mtt) cc_final: 0.7962 (mtt) REVERT: K 411 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7556 (mm-30) REVERT: L 2 ARG cc_start: 0.7717 (mtm180) cc_final: 0.7022 (mtt90) REVERT: L 285 GLN cc_start: 0.7906 (pm20) cc_final: 0.6304 (mm-40) REVERT: L 313 MET cc_start: 0.8572 (mtm) cc_final: 0.8166 (mtm) outliers start: 140 outliers final: 93 residues processed: 754 average time/residue: 0.2289 time to fit residues: 291.8377 Evaluate side-chains 694 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 594 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 271 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 439 optimal weight: 9.9990 chunk 330 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 102 optimal weight: 0.0770 chunk 47 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 325 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 433 GLN E 88 HIS F 14 ASN F 85 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 14 ASN H 309 HIS I 59 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS K 88 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.103095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087187 restraints weight = 67248.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090619 restraints weight = 33458.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092979 restraints weight = 20471.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094627 restraints weight = 14230.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095810 restraints weight = 10744.759| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41742 Z= 0.118 Angle : 0.530 11.935 56718 Z= 0.273 Chirality : 0.042 0.148 6198 Planarity : 0.004 0.049 7386 Dihedral : 10.652 177.958 5767 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.92 % Allowed : 17.08 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.12), residues: 5118 helix: 2.23 (0.11), residues: 2376 sheet: 0.43 (0.17), residues: 816 loop : -0.04 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 278 TYR 0.023 0.001 TYR E 357 PHE 0.016 0.001 PHE L 138 TRP 0.011 0.001 TRP C 21 HIS 0.009 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00255 (41742) covalent geometry : angle 0.52995 (56718) hydrogen bonds : bond 0.04278 ( 2062) hydrogen bonds : angle 4.66596 ( 5934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 661 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8254 (t0) cc_final: 0.7931 (t70) REVERT: A 71 GLU cc_start: 0.7557 (tt0) cc_final: 0.6974 (tt0) REVERT: A 112 LYS cc_start: 0.8315 (pttp) cc_final: 0.8113 (mtpt) REVERT: A 113 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 172 TYR cc_start: 0.8702 (t80) cc_final: 0.8351 (t80) REVERT: A 245 ASP cc_start: 0.7800 (p0) cc_final: 0.7428 (p0) REVERT: A 251 ASP cc_start: 0.7756 (p0) cc_final: 0.7549 (p0) REVERT: A 279 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: A 357 TYR cc_start: 0.7356 (m-10) cc_final: 0.7109 (m-80) REVERT: B 41 ASP cc_start: 0.7777 (p0) cc_final: 0.7129 (p0) REVERT: B 76 ASP cc_start: 0.8544 (m-30) cc_final: 0.8294 (m-30) REVERT: B 325 MET cc_start: 0.7633 (mmm) cc_final: 0.6607 (mmm) REVERT: B 329 ASP cc_start: 0.7364 (m-30) cc_final: 0.6919 (m-30) REVERT: B 417 GLU cc_start: 0.7701 (mp0) cc_final: 0.7099 (mp0) REVERT: C 24 TYR cc_start: 0.8976 (m-80) cc_final: 0.8587 (m-80) REVERT: C 50 ASN cc_start: 0.8447 (t0) cc_final: 0.8138 (t0) REVERT: C 90 GLU cc_start: 0.7485 (tp30) cc_final: 0.7020 (tp30) REVERT: C 203 MET cc_start: 0.8479 (mmm) cc_final: 0.8215 (mmt) REVERT: C 269 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8649 (pp) REVERT: C 313 MET cc_start: 0.8561 (mtm) cc_final: 0.8305 (mtm) REVERT: C 411 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7715 (mm-30) REVERT: D 41 ASP cc_start: 0.8280 (p0) cc_final: 0.7542 (p0) REVERT: D 47 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7916 (mm-30) REVERT: D 138 THR cc_start: 0.9032 (m) cc_final: 0.8811 (p) REVERT: D 210 TYR cc_start: 0.8685 (m-80) cc_final: 0.7987 (m-80) REVERT: D 301 MET cc_start: 0.8581 (mmp) cc_final: 0.8113 (tpp) REVERT: D 306 ASP cc_start: 0.7866 (t0) cc_final: 0.7380 (t70) REVERT: D 433 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7552 (tp40) REVERT: E 157 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8943 (mp) REVERT: E 205 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: E 342 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: F 127 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7698 (mp0) REVERT: F 138 THR cc_start: 0.8960 (m) cc_final: 0.8532 (p) REVERT: F 149 MET cc_start: 0.8740 (ttt) cc_final: 0.8486 (ttt) REVERT: F 179 ASP cc_start: 0.8241 (t70) cc_final: 0.7629 (t0) REVERT: F 200 GLU cc_start: 0.7897 (pt0) cc_final: 0.7585 (pt0) REVERT: F 210 TYR cc_start: 0.8789 (m-80) cc_final: 0.8189 (m-80) REVERT: F 228 ASN cc_start: 0.8902 (m-40) cc_final: 0.8485 (m-40) REVERT: G 69 ASP cc_start: 0.7539 (t0) cc_final: 0.7254 (t0) REVERT: G 179 ASP cc_start: 0.8205 (t70) cc_final: 0.7817 (t0) REVERT: G 228 ASN cc_start: 0.8677 (m-40) cc_final: 0.8331 (m-40) REVERT: G 325 MET cc_start: 0.8106 (mmm) cc_final: 0.7394 (mmm) REVERT: H 41 ASP cc_start: 0.8307 (p0) cc_final: 0.7935 (p0) REVERT: H 47 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7740 (mm-30) REVERT: H 60 LYS cc_start: 0.7990 (mttt) cc_final: 0.7685 (mmtm) REVERT: H 76 ASP cc_start: 0.8402 (t0) cc_final: 0.8113 (t0) REVERT: I 47 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7964 (mm-30) REVERT: I 50 ASN cc_start: 0.8668 (p0) cc_final: 0.8386 (p0) REVERT: I 129 CYS cc_start: 0.6555 (m) cc_final: 0.6301 (m) REVERT: I 179 ASP cc_start: 0.8039 (t70) cc_final: 0.7639 (t0) REVERT: I 204 ILE cc_start: 0.9025 (mp) cc_final: 0.8822 (mt) REVERT: J 172 TYR cc_start: 0.8469 (t80) cc_final: 0.8175 (t80) REVERT: J 275 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8491 (p) REVERT: J 371 VAL cc_start: 0.8745 (m) cc_final: 0.8461 (t) REVERT: J 377 MET cc_start: 0.8386 (ttp) cc_final: 0.8094 (ttm) REVERT: J 388 TRP cc_start: 0.9220 (m100) cc_final: 0.8891 (m100) REVERT: J 411 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7361 (mm-30) REVERT: K 2 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7038 (mpt180) REVERT: K 24 TYR cc_start: 0.8750 (m-10) cc_final: 0.8290 (m-10) REVERT: K 176 GLN cc_start: 0.8195 (pt0) cc_final: 0.7546 (pm20) REVERT: K 205 ASP cc_start: 0.7727 (t0) cc_final: 0.7262 (m-30) REVERT: K 221 ARG cc_start: 0.7358 (mpp80) cc_final: 0.7151 (mpp80) REVERT: K 302 MET cc_start: 0.8295 (mtt) cc_final: 0.7963 (mtt) REVERT: K 317 LEU cc_start: 0.8972 (mm) cc_final: 0.8750 (mm) REVERT: K 377 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7690 (ttp) REVERT: K 378 LEU cc_start: 0.9303 (mt) cc_final: 0.9091 (mt) REVERT: L 2 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7356 (mpt180) REVERT: L 50 ASN cc_start: 0.8701 (t0) cc_final: 0.8328 (t0) REVERT: L 285 GLN cc_start: 0.7910 (pm20) cc_final: 0.6203 (mm-40) REVERT: L 313 MET cc_start: 0.8540 (mtm) cc_final: 0.8195 (mtm) outliers start: 128 outliers final: 93 residues processed: 751 average time/residue: 0.2260 time to fit residues: 288.3837 Evaluate side-chains 699 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 598 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 MET Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 390 optimal weight: 0.9980 chunk 378 optimal weight: 0.0070 chunk 475 optimal weight: 0.5980 chunk 214 optimal weight: 6.9990 chunk 261 optimal weight: 0.0170 chunk 332 optimal weight: 5.9990 chunk 443 optimal weight: 9.9990 chunk 449 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 501 optimal weight: 10.0000 chunk 430 optimal weight: 0.9980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 433 GLN E 88 HIS F 85 GLN F 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 14 ASN H 339 ASN I 59 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN K 88 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN L 283 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088612 restraints weight = 66683.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092012 restraints weight = 32612.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.094344 restraints weight = 19587.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095948 restraints weight = 13377.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097099 restraints weight = 9956.644| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 41742 Z= 0.108 Angle : 0.529 12.472 56718 Z= 0.271 Chirality : 0.042 0.148 6198 Planarity : 0.004 0.040 7386 Dihedral : 10.513 178.751 5767 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.53 % Allowed : 18.19 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.12), residues: 5118 helix: 2.22 (0.11), residues: 2382 sheet: 0.49 (0.17), residues: 870 loop : 0.07 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 278 TYR 0.020 0.001 TYR E 357 PHE 0.018 0.001 PHE F 377 TRP 0.012 0.001 TRP I 21 HIS 0.008 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00231 (41742) covalent geometry : angle 0.52891 (56718) hydrogen bonds : bond 0.03979 ( 2062) hydrogen bonds : angle 4.60799 ( 5934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 672 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7617 (tt0) cc_final: 0.7060 (tt0) REVERT: A 113 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 251 ASP cc_start: 0.7508 (p0) cc_final: 0.7182 (p0) REVERT: A 279 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: A 284 GLU cc_start: 0.7643 (tp30) cc_final: 0.7352 (tp30) REVERT: B 41 ASP cc_start: 0.7770 (p0) cc_final: 0.7144 (p0) REVERT: B 76 ASP cc_start: 0.8549 (m-30) cc_final: 0.8259 (m-30) REVERT: B 124 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8612 (ttpt) REVERT: B 325 MET cc_start: 0.7793 (mmm) cc_final: 0.6832 (mmm) REVERT: B 329 ASP cc_start: 0.7338 (m-30) cc_final: 0.6924 (m-30) REVERT: B 417 GLU cc_start: 0.7704 (mp0) cc_final: 0.7110 (mp0) REVERT: C 24 TYR cc_start: 0.8761 (m-80) cc_final: 0.8516 (m-80) REVERT: C 50 ASN cc_start: 0.8420 (t0) cc_final: 0.7924 (t0) REVERT: C 90 GLU cc_start: 0.7466 (tp30) cc_final: 0.7024 (tp30) REVERT: C 203 MET cc_start: 0.8505 (mmm) cc_final: 0.8180 (mmt) REVERT: C 269 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8602 (pp) REVERT: C 313 MET cc_start: 0.8557 (mtm) cc_final: 0.8314 (mtm) REVERT: C 411 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7716 (mm-30) REVERT: D 41 ASP cc_start: 0.8267 (p0) cc_final: 0.7445 (p0) REVERT: D 47 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7850 (mm-30) REVERT: D 80 SER cc_start: 0.7946 (m) cc_final: 0.7689 (p) REVERT: D 138 THR cc_start: 0.9016 (m) cc_final: 0.8813 (p) REVERT: D 210 TYR cc_start: 0.8649 (m-80) cc_final: 0.8001 (m-80) REVERT: D 306 ASP cc_start: 0.7891 (t0) cc_final: 0.7430 (t70) REVERT: E 24 TYR cc_start: 0.8732 (m-80) cc_final: 0.8446 (m-10) REVERT: E 205 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: E 342 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: F 41 ASP cc_start: 0.8095 (p0) cc_final: 0.7599 (p0) REVERT: F 47 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7891 (mm-30) REVERT: F 85 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7556 (pp30) REVERT: F 127 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7715 (mp0) REVERT: F 138 THR cc_start: 0.8921 (m) cc_final: 0.8479 (p) REVERT: F 149 MET cc_start: 0.8717 (ttt) cc_final: 0.8493 (ttm) REVERT: F 179 ASP cc_start: 0.8208 (t70) cc_final: 0.7596 (t0) REVERT: F 200 GLU cc_start: 0.7829 (pt0) cc_final: 0.7505 (pt0) REVERT: F 210 TYR cc_start: 0.8747 (m-80) cc_final: 0.8204 (m-80) REVERT: F 228 ASN cc_start: 0.8791 (m-40) cc_final: 0.8365 (m-40) REVERT: F 259 MET cc_start: 0.9150 (mmm) cc_final: 0.8548 (mmt) REVERT: G 69 ASP cc_start: 0.7499 (t0) cc_final: 0.7238 (t0) REVERT: G 119 LEU cc_start: 0.8990 (mt) cc_final: 0.8763 (mm) REVERT: G 179 ASP cc_start: 0.8177 (t70) cc_final: 0.7802 (t0) REVERT: G 205 ASP cc_start: 0.8090 (t0) cc_final: 0.7825 (m-30) REVERT: G 228 ASN cc_start: 0.8530 (m-40) cc_final: 0.8256 (m-40) REVERT: G 309 HIS cc_start: 0.8704 (m-70) cc_final: 0.8204 (m90) REVERT: G 325 MET cc_start: 0.8037 (mmm) cc_final: 0.7485 (mmm) REVERT: G 413 MET cc_start: 0.7761 (ttm) cc_final: 0.7324 (ttm) REVERT: H 41 ASP cc_start: 0.8330 (p0) cc_final: 0.7919 (p0) REVERT: H 47 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7712 (mm-30) REVERT: H 60 LYS cc_start: 0.7962 (mttt) cc_final: 0.7654 (mmtm) REVERT: H 76 ASP cc_start: 0.8417 (t0) cc_final: 0.8020 (t0) REVERT: H 301 MET cc_start: 0.8164 (mmp) cc_final: 0.7945 (mmp) REVERT: I 26 ASP cc_start: 0.8356 (t0) cc_final: 0.7993 (m-30) REVERT: I 47 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7875 (mm-30) REVERT: I 50 ASN cc_start: 0.8655 (p0) cc_final: 0.8374 (p0) REVERT: I 129 CYS cc_start: 0.6732 (m) cc_final: 0.6415 (m) REVERT: J 172 TYR cc_start: 0.8485 (t80) cc_final: 0.8201 (t80) REVERT: J 275 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8490 (p) REVERT: J 371 VAL cc_start: 0.8757 (m) cc_final: 0.8445 (t) REVERT: J 377 MET cc_start: 0.8381 (ttp) cc_final: 0.8078 (ttm) REVERT: J 388 TRP cc_start: 0.9213 (m100) cc_final: 0.8902 (m100) REVERT: J 411 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7427 (mm-30) REVERT: K 2 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7228 (mpt180) REVERT: K 24 TYR cc_start: 0.8776 (m-10) cc_final: 0.8550 (m-80) REVERT: K 76 ASP cc_start: 0.8926 (t0) cc_final: 0.8631 (t0) REVERT: K 205 ASP cc_start: 0.7547 (t0) cc_final: 0.7173 (m-30) REVERT: K 302 MET cc_start: 0.8253 (mtt) cc_final: 0.7966 (mtt) REVERT: K 377 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7640 (ttp) REVERT: L 2 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7364 (mpt180) REVERT: L 35 GLN cc_start: 0.8042 (mp10) cc_final: 0.7766 (mp10) REVERT: L 50 ASN cc_start: 0.8688 (t0) cc_final: 0.8305 (t0) REVERT: L 285 GLN cc_start: 0.7906 (pm20) cc_final: 0.6214 (mm-40) REVERT: L 313 MET cc_start: 0.8521 (mtm) cc_final: 0.8080 (mtm) outliers start: 111 outliers final: 82 residues processed: 751 average time/residue: 0.2283 time to fit residues: 291.0379 Evaluate side-chains 683 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 594 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 MET Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 474 optimal weight: 0.9990 chunk 249 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 468 optimal weight: 8.9990 chunk 457 optimal weight: 0.2980 chunk 149 optimal weight: 0.8980 chunk 498 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN E 88 HIS ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 14 ASN H 281 GLN I 59 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.104180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089069 restraints weight = 67056.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.092392 restraints weight = 33629.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094674 restraints weight = 20700.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.096256 restraints weight = 14364.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.097379 restraints weight = 10800.954| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.002 0.046 41742 Z= 0.113 Angle : 0.535 12.217 56718 Z= 0.274 Chirality : 0.042 0.145 6198 Planarity : 0.004 0.059 7386 Dihedral : 10.423 178.721 5767 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.71 % Allowed : 18.33 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.12), residues: 5118 helix: 2.17 (0.11), residues: 2388 sheet: 0.49 (0.17), residues: 870 loop : 0.11 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 278 TYR 0.018 0.001 TYR B 161 PHE 0.017 0.001 PHE A 169 TRP 0.012 0.001 TRP D 21 HIS 0.008 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00250 (41742) covalent geometry : angle 0.53521 (56718) hydrogen bonds : bond 0.03979 ( 2062) hydrogen bonds : angle 4.59916 ( 5934) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 625 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7454 (tt0) cc_final: 0.7228 (tt0) REVERT: A 245 ASP cc_start: 0.7810 (p0) cc_final: 0.7533 (p0) REVERT: A 251 ASP cc_start: 0.7466 (p0) cc_final: 0.7129 (p0) REVERT: A 279 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: B 41 ASP cc_start: 0.7789 (p0) cc_final: 0.7278 (p0) REVERT: B 76 ASP cc_start: 0.8532 (m-30) cc_final: 0.8234 (m-30) REVERT: B 124 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8628 (ttpt) REVERT: B 210 TYR cc_start: 0.8597 (m-80) cc_final: 0.7574 (m-80) REVERT: B 417 GLU cc_start: 0.7725 (mp0) cc_final: 0.7130 (mp0) REVERT: C 24 TYR cc_start: 0.8784 (m-80) cc_final: 0.8567 (m-80) REVERT: C 50 ASN cc_start: 0.8425 (t0) cc_final: 0.7929 (t0) REVERT: C 90 GLU cc_start: 0.7493 (tp30) cc_final: 0.7084 (tp30) REVERT: C 203 MET cc_start: 0.8514 (mmm) cc_final: 0.8196 (mmt) REVERT: C 205 ASP cc_start: 0.7602 (t0) cc_final: 0.7302 (t0) REVERT: C 269 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (pp) REVERT: C 313 MET cc_start: 0.8533 (mtm) cc_final: 0.8323 (mtm) REVERT: D 41 ASP cc_start: 0.8298 (p0) cc_final: 0.7476 (p0) REVERT: D 47 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7981 (mm-30) REVERT: D 80 SER cc_start: 0.7987 (m) cc_final: 0.7730 (p) REVERT: D 210 TYR cc_start: 0.8621 (m-80) cc_final: 0.8025 (m-80) REVERT: D 211 ASP cc_start: 0.7845 (t0) cc_final: 0.7433 (t0) REVERT: D 215 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7591 (ptp90) REVERT: D 306 ASP cc_start: 0.7669 (t0) cc_final: 0.7378 (t70) REVERT: D 433 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: E 24 TYR cc_start: 0.8754 (m-80) cc_final: 0.8482 (m-10) REVERT: E 205 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: E 342 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: F 41 ASP cc_start: 0.8241 (p0) cc_final: 0.7735 (p0) REVERT: F 47 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7855 (mm-30) REVERT: F 127 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7669 (mp0) REVERT: F 138 THR cc_start: 0.8917 (m) cc_final: 0.8472 (p) REVERT: F 179 ASP cc_start: 0.8164 (t70) cc_final: 0.7474 (t0) REVERT: F 200 GLU cc_start: 0.7845 (pt0) cc_final: 0.7543 (pt0) REVERT: F 207 GLU cc_start: 0.7548 (tp30) cc_final: 0.7327 (mp0) REVERT: F 210 TYR cc_start: 0.8747 (m-80) cc_final: 0.8141 (m-80) REVERT: F 228 ASN cc_start: 0.8761 (m-40) cc_final: 0.8327 (m-40) REVERT: F 259 MET cc_start: 0.9136 (mmm) cc_final: 0.8582 (mmt) REVERT: G 69 ASP cc_start: 0.7512 (t0) cc_final: 0.7252 (t0) REVERT: G 179 ASP cc_start: 0.8160 (t70) cc_final: 0.7786 (t0) REVERT: G 205 ASP cc_start: 0.8095 (t0) cc_final: 0.7707 (m-30) REVERT: G 228 ASN cc_start: 0.8519 (m-40) cc_final: 0.8241 (m-40) REVERT: G 309 HIS cc_start: 0.8737 (m-70) cc_final: 0.8216 (m90) REVERT: G 325 MET cc_start: 0.8004 (mmm) cc_final: 0.7657 (tpp) REVERT: G 413 MET cc_start: 0.7767 (ttm) cc_final: 0.7268 (ttm) REVERT: H 41 ASP cc_start: 0.8352 (p0) cc_final: 0.7937 (p0) REVERT: H 47 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7723 (mm-30) REVERT: H 60 LYS cc_start: 0.7995 (mttt) cc_final: 0.7701 (mmtm) REVERT: H 281 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: I 26 ASP cc_start: 0.8396 (t0) cc_final: 0.8059 (m-30) REVERT: I 47 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7872 (mm-30) REVERT: I 50 ASN cc_start: 0.8709 (p0) cc_final: 0.8416 (p0) REVERT: I 129 CYS cc_start: 0.6679 (m) cc_final: 0.6345 (m) REVERT: I 228 ASN cc_start: 0.8543 (m-40) cc_final: 0.8239 (m-40) REVERT: J 172 TYR cc_start: 0.8446 (t80) cc_final: 0.8189 (t80) REVERT: J 275 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8488 (p) REVERT: J 371 VAL cc_start: 0.8781 (m) cc_final: 0.8474 (t) REVERT: J 377 MET cc_start: 0.8350 (ttp) cc_final: 0.8036 (ttm) REVERT: J 388 TRP cc_start: 0.9199 (m100) cc_final: 0.8905 (m100) REVERT: J 411 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7382 (mm-30) REVERT: K 2 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7274 (mpt180) REVERT: K 24 TYR cc_start: 0.8794 (m-10) cc_final: 0.8567 (m-80) REVERT: K 35 GLN cc_start: 0.7888 (mp10) cc_final: 0.7672 (pm20) REVERT: K 76 ASP cc_start: 0.8909 (t0) cc_final: 0.8611 (t0) REVERT: K 205 ASP cc_start: 0.7533 (t0) cc_final: 0.7177 (m-30) REVERT: K 302 MET cc_start: 0.8261 (mtt) cc_final: 0.7992 (mtt) REVERT: K 377 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7671 (ttp) REVERT: L 2 ARG cc_start: 0.7744 (mtm180) cc_final: 0.7050 (mtt90) REVERT: L 35 GLN cc_start: 0.8049 (mp10) cc_final: 0.7793 (mp10) REVERT: L 50 ASN cc_start: 0.8706 (t0) cc_final: 0.8366 (t0) REVERT: L 285 GLN cc_start: 0.7919 (pm20) cc_final: 0.6163 (mm-40) REVERT: L 313 MET cc_start: 0.8529 (mtm) cc_final: 0.8086 (mtm) outliers start: 119 outliers final: 98 residues processed: 715 average time/residue: 0.2294 time to fit residues: 277.4518 Evaluate side-chains 690 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 583 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 MET Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 244 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 258 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 377 optimal weight: 0.9990 chunk 419 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 431 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN E 88 HIS F 8 GLN F 14 ASN F 85 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 14 ASN I 167 ASN K 88 HIS L 88 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.102742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087312 restraints weight = 68260.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090718 restraints weight = 33438.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093043 restraints weight = 20250.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094656 restraints weight = 13957.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095775 restraints weight = 10478.453| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 41742 Z= 0.145 Angle : 0.554 11.675 56718 Z= 0.285 Chirality : 0.043 0.154 6198 Planarity : 0.004 0.061 7386 Dihedral : 10.397 179.928 5767 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.78 % Allowed : 18.63 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.12), residues: 5118 helix: 2.17 (0.11), residues: 2382 sheet: 0.41 (0.17), residues: 870 loop : 0.06 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 278 TYR 0.018 0.001 TYR B 161 PHE 0.023 0.001 PHE A 169 TRP 0.010 0.001 TRP A 21 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00331 (41742) covalent geometry : angle 0.55437 (56718) hydrogen bonds : bond 0.04222 ( 2062) hydrogen bonds : angle 4.65465 ( 5934) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 605 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7536 (tt0) cc_final: 0.7290 (tt0) REVERT: A 251 ASP cc_start: 0.7525 (p0) cc_final: 0.7244 (p0) REVERT: A 279 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: B 41 ASP cc_start: 0.7821 (p0) cc_final: 0.7195 (p0) REVERT: B 76 ASP cc_start: 0.8525 (m-30) cc_final: 0.8257 (m-30) REVERT: B 124 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8612 (ttpt) REVERT: B 417 GLU cc_start: 0.7755 (mp0) cc_final: 0.7143 (mp0) REVERT: C 24 TYR cc_start: 0.8830 (m-80) cc_final: 0.8604 (m-80) REVERT: C 50 ASN cc_start: 0.8483 (t0) cc_final: 0.8117 (t0) REVERT: C 90 GLU cc_start: 0.7522 (tp30) cc_final: 0.7201 (tp30) REVERT: C 203 MET cc_start: 0.8583 (mmm) cc_final: 0.8179 (mmm) REVERT: C 205 ASP cc_start: 0.7606 (t0) cc_final: 0.7310 (t0) REVERT: C 269 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8652 (pp) REVERT: C 313 MET cc_start: 0.8593 (mtm) cc_final: 0.8370 (mtm) REVERT: C 398 MET cc_start: 0.8735 (mtp) cc_final: 0.8527 (ttm) REVERT: D 41 ASP cc_start: 0.8317 (p0) cc_final: 0.7585 (p0) REVERT: D 47 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7992 (mm-30) REVERT: D 80 SER cc_start: 0.8027 (m) cc_final: 0.7777 (p) REVERT: D 210 TYR cc_start: 0.8685 (m-80) cc_final: 0.7952 (m-80) REVERT: D 211 ASP cc_start: 0.7879 (t0) cc_final: 0.7442 (t0) REVERT: D 215 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7580 (ptp90) REVERT: D 306 ASP cc_start: 0.7801 (t0) cc_final: 0.7423 (t70) REVERT: D 433 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: E 205 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: E 342 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7038 (mp10) REVERT: F 41 ASP cc_start: 0.8274 (p0) cc_final: 0.7772 (p0) REVERT: F 47 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7871 (mm-30) REVERT: F 85 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7528 (pp30) REVERT: F 127 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7717 (mp0) REVERT: F 138 THR cc_start: 0.8930 (m) cc_final: 0.8507 (p) REVERT: F 179 ASP cc_start: 0.8234 (t70) cc_final: 0.7587 (t0) REVERT: F 207 GLU cc_start: 0.7581 (tp30) cc_final: 0.7355 (mp0) REVERT: F 210 TYR cc_start: 0.8783 (m-80) cc_final: 0.8144 (m-80) REVERT: F 228 ASN cc_start: 0.8796 (m-40) cc_final: 0.8323 (m-40) REVERT: F 351 VAL cc_start: 0.9232 (t) cc_final: 0.8984 (p) REVERT: G 69 ASP cc_start: 0.7564 (t0) cc_final: 0.7330 (t0) REVERT: G 179 ASP cc_start: 0.8011 (t70) cc_final: 0.7565 (t0) REVERT: G 205 ASP cc_start: 0.8125 (t0) cc_final: 0.7748 (m-30) REVERT: G 228 ASN cc_start: 0.8683 (m-40) cc_final: 0.8320 (m-40) REVERT: G 325 MET cc_start: 0.8035 (mmm) cc_final: 0.7680 (mmm) REVERT: G 413 MET cc_start: 0.7823 (ttm) cc_final: 0.7320 (ttm) REVERT: H 41 ASP cc_start: 0.8394 (p0) cc_final: 0.7972 (p0) REVERT: H 47 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7660 (mm-30) REVERT: H 60 LYS cc_start: 0.8011 (mttt) cc_final: 0.7710 (mmtm) REVERT: I 47 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7891 (mm-30) REVERT: I 50 ASN cc_start: 0.8759 (p0) cc_final: 0.8464 (p0) REVERT: I 228 ASN cc_start: 0.8543 (m-40) cc_final: 0.8209 (m-40) REVERT: J 172 TYR cc_start: 0.8439 (t80) cc_final: 0.8190 (t80) REVERT: J 275 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8484 (p) REVERT: J 324 VAL cc_start: 0.8122 (t) cc_final: 0.7852 (m) REVERT: J 377 MET cc_start: 0.8356 (ttp) cc_final: 0.8027 (ttm) REVERT: J 388 TRP cc_start: 0.9204 (m100) cc_final: 0.8918 (m100) REVERT: J 411 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7416 (mm-30) REVERT: K 2 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7432 (mpt180) REVERT: K 24 TYR cc_start: 0.8815 (m-10) cc_final: 0.8401 (m-10) REVERT: K 76 ASP cc_start: 0.8927 (t0) cc_final: 0.8630 (t0) REVERT: K 205 ASP cc_start: 0.7591 (t0) cc_final: 0.7244 (m-30) REVERT: K 302 MET cc_start: 0.8303 (mtt) cc_final: 0.8013 (mtt) REVERT: K 327 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7976 (t0) REVERT: K 377 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7645 (ttp) REVERT: L 2 ARG cc_start: 0.7775 (mtm180) cc_final: 0.7054 (mtt90) REVERT: L 35 GLN cc_start: 0.8023 (mp10) cc_final: 0.7718 (mp10) REVERT: L 50 ASN cc_start: 0.8755 (t0) cc_final: 0.8386 (t0) REVERT: L 285 GLN cc_start: 0.7931 (pm20) cc_final: 0.6177 (mm-40) REVERT: L 313 MET cc_start: 0.8582 (mtm) cc_final: 0.8110 (mtm) outliers start: 122 outliers final: 101 residues processed: 695 average time/residue: 0.2313 time to fit residues: 271.8737 Evaluate side-chains 687 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 576 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 MET Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 292 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 358 optimal weight: 4.9990 chunk 473 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 394 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 486 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 281 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 339 ASN G 433 GLN H 14 ASN I 167 ASN I 281 GLN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 433 GLN K 88 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084965 restraints weight = 68803.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088272 restraints weight = 33793.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090522 restraints weight = 20563.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092106 restraints weight = 14296.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093234 restraints weight = 10746.773| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 41742 Z= 0.214 Angle : 0.599 11.205 56718 Z= 0.312 Chirality : 0.045 0.200 6198 Planarity : 0.004 0.042 7386 Dihedral : 10.457 177.149 5767 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.74 % Allowed : 18.58 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.12), residues: 5118 helix: 2.07 (0.11), residues: 2376 sheet: 0.39 (0.17), residues: 846 loop : -0.04 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 88 TYR 0.018 0.001 TYR B 161 PHE 0.022 0.002 PHE F 377 TRP 0.011 0.002 TRP A 21 HIS 0.012 0.001 HIS K 88 Details of bonding type rmsd covalent geometry : bond 0.00498 (41742) covalent geometry : angle 0.59948 (56718) hydrogen bonds : bond 0.04773 ( 2062) hydrogen bonds : angle 4.78199 ( 5934) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 572 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7497 (tt0) cc_final: 0.7253 (tt0) REVERT: A 279 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: B 41 ASP cc_start: 0.7871 (p0) cc_final: 0.7245 (p0) REVERT: B 76 ASP cc_start: 0.8524 (m-30) cc_final: 0.8245 (m-30) REVERT: B 124 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8607 (ttpt) REVERT: B 417 GLU cc_start: 0.7747 (mp0) cc_final: 0.7526 (mp0) REVERT: C 24 TYR cc_start: 0.8905 (m-80) cc_final: 0.8641 (m-80) REVERT: C 50 ASN cc_start: 0.8529 (t0) cc_final: 0.8164 (t0) REVERT: C 90 GLU cc_start: 0.7662 (tp30) cc_final: 0.7281 (tp30) REVERT: C 203 MET cc_start: 0.8561 (mmm) cc_final: 0.8210 (mmt) REVERT: C 269 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8673 (pp) REVERT: D 41 ASP cc_start: 0.8369 (p0) cc_final: 0.7652 (p0) REVERT: D 47 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8023 (mm-30) REVERT: D 80 SER cc_start: 0.8003 (m) cc_final: 0.7771 (p) REVERT: D 306 ASP cc_start: 0.7799 (t0) cc_final: 0.7366 (t70) REVERT: D 433 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: E 205 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: E 342 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: F 41 ASP cc_start: 0.8314 (p0) cc_final: 0.7834 (p0) REVERT: F 47 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7928 (mm-30) REVERT: F 127 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7814 (mp0) REVERT: F 179 ASP cc_start: 0.8261 (t70) cc_final: 0.7632 (t0) REVERT: F 207 GLU cc_start: 0.7603 (tp30) cc_final: 0.7357 (mp0) REVERT: F 210 TYR cc_start: 0.8854 (m-80) cc_final: 0.8172 (m-80) REVERT: F 228 ASN cc_start: 0.8981 (m-40) cc_final: 0.8423 (m-40) REVERT: G 179 ASP cc_start: 0.7963 (t70) cc_final: 0.7502 (t0) REVERT: G 309 HIS cc_start: 0.8772 (m-70) cc_final: 0.8236 (m90) REVERT: G 325 MET cc_start: 0.8097 (mmm) cc_final: 0.7798 (mmm) REVERT: G 339 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6925 (t0) REVERT: G 413 MET cc_start: 0.7885 (ttm) cc_final: 0.7428 (ttm) REVERT: G 433 GLN cc_start: 0.7991 (tp40) cc_final: 0.7671 (tm-30) REVERT: H 41 ASP cc_start: 0.8433 (p0) cc_final: 0.8019 (p0) REVERT: H 47 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7667 (mm-30) REVERT: H 60 LYS cc_start: 0.8002 (mttt) cc_final: 0.7715 (mmtm) REVERT: I 47 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7904 (mm-30) REVERT: I 228 ASN cc_start: 0.8532 (m-40) cc_final: 0.8265 (m-40) REVERT: J 2 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7026 (mtt90) REVERT: J 324 VAL cc_start: 0.8304 (t) cc_final: 0.8028 (m) REVERT: J 377 MET cc_start: 0.8385 (ttp) cc_final: 0.8065 (ttm) REVERT: J 411 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7443 (mm-30) REVERT: K 2 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7460 (mpt180) REVERT: K 24 TYR cc_start: 0.8821 (m-10) cc_final: 0.8383 (m-10) REVERT: K 205 ASP cc_start: 0.7735 (t0) cc_final: 0.7401 (m-30) REVERT: K 248 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7564 (tt) REVERT: K 302 MET cc_start: 0.8371 (mtt) cc_final: 0.8061 (mtt) REVERT: K 377 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7691 (ttp) REVERT: L 2 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7233 (mtt90) REVERT: L 50 ASN cc_start: 0.8837 (t0) cc_final: 0.8426 (t0) REVERT: L 285 GLN cc_start: 0.7976 (pm20) cc_final: 0.5990 (mm-40) REVERT: L 425 MET cc_start: 0.9035 (mmm) cc_final: 0.8758 (mmm) outliers start: 120 outliers final: 100 residues processed: 663 average time/residue: 0.2352 time to fit residues: 262.6211 Evaluate side-chains 661 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 553 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 377 MET Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 348 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 485 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 452 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 437 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN D 258 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN F 85 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 339 ASN H 14 ASN H 167 ASN I 167 ASN I 281 GLN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.102955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087995 restraints weight = 68320.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091365 restraints weight = 33151.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093657 restraints weight = 20013.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095255 restraints weight = 13769.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096405 restraints weight = 10288.191| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 41742 Z= 0.167 Angle : 0.577 11.331 56718 Z= 0.299 Chirality : 0.044 0.155 6198 Planarity : 0.004 0.067 7386 Dihedral : 10.399 175.785 5767 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.85 % Allowed : 18.54 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.12), residues: 5118 helix: 2.06 (0.11), residues: 2376 sheet: 0.35 (0.17), residues: 846 loop : -0.04 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 278 TYR 0.021 0.001 TYR E 357 PHE 0.019 0.001 PHE F 377 TRP 0.012 0.002 TRP A 21 HIS 0.017 0.001 HIS K 88 Details of bonding type rmsd covalent geometry : bond 0.00385 (41742) covalent geometry : angle 0.57660 (56718) hydrogen bonds : bond 0.04594 ( 2062) hydrogen bonds : angle 4.74876 ( 5934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7816.54 seconds wall clock time: 136 minutes 2.77 seconds (8162.77 seconds total)