Starting phenix.real_space_refine on Tue Aug 26 19:39:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jas_6353/08_2025/3jas_6353.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jas_6353/08_2025/3jas_6353.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 { model { file = "/net/cci-nas-00/data/ceres_data/3jas_6353/08_2025/3jas_6353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jas_6353/08_2025/3jas_6353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jas_6353/08_2025/3jas_6353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jas_6353/08_2025/3jas_6353.map" } 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= 0.028 sd= 0.918 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 30 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6924 2.21 5 O 7806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40506 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "K" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 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} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.68, per 1000 atoms: 0.19 Number of scatterers: 40506 At special positions: 0 Unit cell: (170.28, 87.12, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 276 16.00 P 30 15.00 Mg 6 11.99 O 7806 8.00 N 6924 7.00 C 25464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 30 sheets defined 55.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.628A 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: 3.592A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.098A 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 206 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.608A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.008A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 283 removed outlier: 3.739A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.859A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.898A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.543A 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: 4.490A 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 71 through 81 removed outlier: 4.552A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (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: 4.515A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.455A 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: 3.907A 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: 5.148A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 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 401 removed outlier: 3.633A pdb=" N ARG F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 436 removed outlier: 3.956A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 47 through 51 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.628A 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 161 removed outlier: 4.099A 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 206 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.610A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 4.006A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 283 removed outlier: 3.737A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.860A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) 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 removed outlier: 3.563A pdb=" N VAL J 328 " --> pdb=" O VAL J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 3.899A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.491A 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 71 through 81 removed outlier: 4.552A pdb=" N MET G 75 " --> pdb=" O GLU G 71 " (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: 4.515A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.455A 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: 3.906A 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: 5.147A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 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 401 removed outlier: 3.632A pdb=" N ARG G 401 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 436 removed outlier: 3.957A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.629A 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 161 removed outlier: 4.098A 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 206 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.607A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.007A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.737A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.858A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.899A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.542A 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: 4.493A 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 71 through 81 removed outlier: 4.551A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (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: 4.515A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.455A 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: 3.907A 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: 5.148A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 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 401 removed outlier: 3.631A pdb=" N ARG D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.067A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 436 removed outlier: 3.957A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.630A 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: 3.592A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.101A 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 206 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.609A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 4.004A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.736A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.860A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) 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 removed outlier: 3.563A pdb=" N VAL L 328 " --> pdb=" O VAL L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 3.900A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.492A 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 71 through 81 removed outlier: 4.553A pdb=" N MET I 75 " --> pdb=" O GLU I 71 " (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: 4.516A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.456A 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: 3.906A 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: 5.147A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG I 243 " --> pdb=" O THR I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 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 401 removed outlier: 3.630A pdb=" N ARG I 401 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 436 removed outlier: 3.956A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.629A 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: 3.592A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.098A 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 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.607A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.008A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.739A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.859A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.899A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.543A 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: 4.490A 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 71 through 81 removed outlier: 4.552A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (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: 4.515A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.455A 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: 3.907A 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: 5.149A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 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 401 removed outlier: 3.632A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 436 removed outlier: 3.957A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.629A 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 161 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 206 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.608A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 4.005A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 283 removed outlier: 3.738A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.860A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) 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 removed outlier: 3.563A pdb=" N VAL K 328 " --> pdb=" O VAL K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 3.899A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.492A 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 71 through 81 removed outlier: 4.552A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (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: 4.514A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.455A 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: 3.906A 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: 5.148A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG H 243 " --> pdb=" O THR H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 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 401 removed outlier: 3.631A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 436 removed outlier: 3.957A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=C, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.808A 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: 7.361A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.210A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=F, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER J 165 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE J 171 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=H, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU G 137 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE G 7 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.210A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=K, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER C 165 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 171 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=M, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.211A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=P, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.842A 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: 5.961A pdb=" N GLU L 3 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY L 134 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER L 165 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE L 171 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=R, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.812A 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: 7.361A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU I 137 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE I 7 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.209A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=U, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.843A 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: 5.963A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=W, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.810A 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: 7.362A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.212A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.238A 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: 6.494A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.842A 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: 5.964A pdb=" N GLU K 3 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY K 134 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER K 165 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE K 171 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AB, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.210A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'H' and resid 53 through 55 2046 hydrogen bonds defined for protein. 5886 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.33 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7360 1.32 - 1.45: 10850 1.45 - 1.57: 22746 1.57 - 1.69: 48 1.69 - 1.82: 432 Bond restraints: 41436 Sorted by residual: bond pdb=" C5 GTP E 501 " pdb=" C6 GTP E 501 " ideal model delta sigma weight residual 1.390 1.477 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CA PRO E 359 " pdb=" C PRO E 359 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.86e+01 bond pdb=" C5 GTP J 501 " pdb=" C6 GTP J 501 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CA PRO J 359 " pdb=" C PRO J 359 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.75e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 41431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 46018 1.89 - 3.77: 9146 3.77 - 5.66: 965 5.66 - 7.55: 150 7.55 - 9.44: 25 Bond angle restraints: 56304 Sorted by residual: angle pdb=" N THR E 73 " pdb=" CA THR E 73 " pdb=" C THR E 73 " ideal model delta sigma weight residual 111.11 117.24 -6.13 1.20e+00 6.94e-01 2.61e+01 angle pdb=" N THR C 73 " pdb=" CA THR C 73 " pdb=" C THR C 73 " ideal model delta sigma weight residual 111.11 117.22 -6.11 1.20e+00 6.94e-01 2.59e+01 angle pdb=" N THR A 73 " pdb=" CA THR A 73 " pdb=" C THR A 73 " ideal model delta sigma weight residual 111.11 117.20 -6.09 1.20e+00 6.94e-01 2.58e+01 angle pdb=" N THR J 73 " pdb=" CA THR J 73 " pdb=" C THR J 73 " ideal model delta sigma weight residual 111.11 117.17 -6.06 1.20e+00 6.94e-01 2.55e+01 angle pdb=" N THR K 73 " pdb=" CA THR K 73 " pdb=" C THR K 73 " ideal model delta sigma weight residual 111.11 117.16 -6.05 1.20e+00 6.94e-01 2.55e+01 ... (remaining 56299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 23795 33.72 - 67.44: 757 67.44 - 101.16: 36 101.16 - 134.87: 6 134.87 - 168.59: 18 Dihedral angle restraints: 24612 sinusoidal: 9810 harmonic: 14802 Sorted by residual: dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.14 -168.59 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.34 -168.39 1 2.00e+01 2.50e-03 4.75e+01 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 -122.54 -168.19 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3714 0.064 - 0.127: 1671 0.127 - 0.191: 580 0.191 - 0.254: 149 0.254 - 0.318: 42 Chirality restraints: 6156 Sorted by residual: chirality pdb=" CA PHE I 83 " pdb=" N PHE I 83 " pdb=" C PHE I 83 " pdb=" CB PHE I 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA PHE F 83 " pdb=" N PHE F 83 " pdb=" C PHE F 83 " pdb=" CB PHE F 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA PHE B 83 " pdb=" N PHE B 83 " pdb=" C PHE B 83 " pdb=" CB PHE B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 6153 not shown) Planarity restraints: 7338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 288 " 0.048 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO F 289 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 288 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO G 289 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 289 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 288 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO H 289 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO H 289 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 289 " 0.041 5.00e-02 4.00e+02 ... (remaining 7335 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 51 2.46 - 3.07: 25244 3.07 - 3.68: 63912 3.68 - 4.29: 90901 4.29 - 4.90: 159585 Nonbonded interactions: 339693 Sorted by model distance: nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.846 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.857 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.857 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.884 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.926 2.170 ... (remaining 339688 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: 0.14 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'C' selection = chain 'L' selection = chain 'A' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'D' selection = chain 'I' selection = chain 'B' selection = chain 'H' } 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: 13.190 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 36.840 Find NCS groups from input model: 0.440 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.008 0.087 41436 Z= 0.601 Angle : 1.458 9.437 56304 Z= 1.017 Chirality : 0.083 0.318 6156 Planarity : 0.006 0.074 7338 Dihedral : 16.413 168.593 15120 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 2.07 % Allowed : 8.44 % Favored : 89.49 % Cbeta Deviations : 0.13 % 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 aren not related in a simple way. whole: 0.41 (0.11), residues: 5088 helix: 1.21 (0.10), residues: 2280 sheet: 0.70 (0.19), residues: 774 loop : -0.95 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 2 TYR 0.021 0.003 TYR F 224 PHE 0.024 0.003 PHE D 92 TRP 0.025 0.004 TRP D 21 HIS 0.012 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00844 (41436) covalent geometry : angle 1.45754 (56304) hydrogen bonds : bond 0.18850 ( 2046) hydrogen bonds : angle 7.13849 ( 5886) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1009 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8200 (tt) REVERT: F 329 ASP cc_start: 0.7856 (m-30) cc_final: 0.7564 (m-30) REVERT: J 50 ASN cc_start: 0.7924 (t0) cc_final: 0.7705 (t0) REVERT: J 203 MET cc_start: 0.7088 (mtt) cc_final: 0.6714 (mtm) REVERT: J 424 ASP cc_start: 0.7628 (t70) cc_final: 0.7221 (t0) REVERT: G 44 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8278 (tt) REVERT: G 301 MET cc_start: 0.8499 (mmp) cc_final: 0.8023 (mmt) REVERT: G 323 MET cc_start: 0.7702 (mtp) cc_final: 0.7488 (mtm) REVERT: G 325 MET cc_start: 0.8361 (tpp) cc_final: 0.7977 (mmm) REVERT: G 356 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7658 (m) REVERT: G 373 MET cc_start: 0.7945 (ttp) cc_final: 0.7485 (ttp) REVERT: G 398 MET cc_start: 0.8161 (mtt) cc_final: 0.7925 (mtp) REVERT: G 408 TYR cc_start: 0.8598 (m-80) cc_final: 0.8228 (m-80) REVERT: G 415 GLU cc_start: 0.7980 (tt0) cc_final: 0.7531 (tm-30) REVERT: C 50 ASN cc_start: 0.7720 (t0) cc_final: 0.7502 (m-40) REVERT: C 209 ILE cc_start: 0.8959 (mt) cc_final: 0.8493 (mt) REVERT: C 425 MET cc_start: 0.8132 (tpp) cc_final: 0.7880 (mmp) REVERT: D 240 THR cc_start: 0.8869 (t) cc_final: 0.8480 (t) REVERT: D 329 ASP cc_start: 0.7993 (m-30) cc_final: 0.7517 (m-30) REVERT: D 356 CYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7471 (t) REVERT: D 373 MET cc_start: 0.7431 (ttp) cc_final: 0.7223 (ttm) REVERT: D 413 MET cc_start: 0.7629 (ttp) cc_final: 0.7176 (ttm) REVERT: L 172 TYR cc_start: 0.8422 (t80) cc_final: 0.7987 (t80) REVERT: L 391 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8420 (tt) REVERT: L 424 ASP cc_start: 0.7322 (t70) cc_final: 0.7065 (t0) REVERT: I 44 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8485 (tt) REVERT: I 214 PHE cc_start: 0.8828 (t80) cc_final: 0.8512 (t80) REVERT: I 332 MET cc_start: 0.9011 (mmp) cc_final: 0.8302 (mmm) REVERT: I 356 CYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8062 (m) REVERT: I 413 MET cc_start: 0.7889 (ttp) cc_final: 0.7418 (ttm) REVERT: B 44 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7812 (tt) REVERT: B 108 TYR cc_start: 0.7576 (m-80) cc_final: 0.7282 (m-80) REVERT: B 214 PHE cc_start: 0.7984 (t80) cc_final: 0.7778 (t80) REVERT: B 332 MET cc_start: 0.8324 (mmp) cc_final: 0.8098 (mmp) REVERT: B 356 CYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7588 (t) REVERT: B 411 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7140 (tp30) REVERT: K 50 ASN cc_start: 0.7808 (t0) cc_final: 0.7492 (m-40) REVERT: K 154 MET cc_start: 0.8329 (mmp) cc_final: 0.8079 (mmt) REVERT: K 172 TYR cc_start: 0.8216 (t80) cc_final: 0.7904 (t80) REVERT: K 178 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.8013 (p) REVERT: H 44 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8259 (tt) REVERT: H 211 ASP cc_start: 0.7942 (m-30) cc_final: 0.7540 (m-30) REVERT: H 301 MET cc_start: 0.8577 (mmp) cc_final: 0.8178 (mmt) REVERT: H 325 MET cc_start: 0.8050 (tpp) cc_final: 0.7652 (tpt) REVERT: H 373 MET cc_start: 0.7998 (ttp) cc_final: 0.7686 (ttm) REVERT: H 398 MET cc_start: 0.8204 (mtt) cc_final: 0.7831 (mtt) outliers start: 90 outliers final: 33 residues processed: 1086 average time/residue: 0.2721 time to fit residues: 477.0803 Evaluate side-chains 602 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 558 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 382 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 382 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 88 HIS E 101 ASN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 91 ASN F 406 HIS J 8 HIS J 88 HIS J 101 ASN J 176 GLN J 266 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN G 6 HIS G 14 ASN G 91 ASN G 349 ASN C 8 HIS C 15 GLN C 88 HIS C 101 ASN C 283 HIS D 11 GLN D 14 ASN D 91 ASN D 349 ASN L 88 HIS L 101 ASN L 283 HIS L 300 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN I 91 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 349 ASN I 385 GLN I 433 GLN I 436 GLN A 18 ASN A 88 HIS A 101 ASN A 256 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS A 342 GLN B 91 ASN B 349 ASN K 8 HIS K 15 GLN K 88 HIS K 101 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN H 91 ASN H 349 ASN H 436 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.091395 restraints weight = 65600.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094984 restraints weight = 30872.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097394 restraints weight = 18127.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099046 restraints weight = 12121.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.100220 restraints weight = 8802.792| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 41436 Z= 0.148 Angle : 0.634 7.520 56304 Z= 0.332 Chirality : 0.045 0.180 6156 Planarity : 0.005 0.074 7338 Dihedral : 12.349 170.844 5781 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.00 % Allowed : 14.50 % Favored : 82.50 % 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 aren not related in a simple way. whole: 1.39 (0.12), residues: 5088 helix: 2.17 (0.11), residues: 2340 sheet: 0.89 (0.18), residues: 810 loop : -0.63 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 390 TYR 0.020 0.001 TYR I 408 PHE 0.018 0.001 PHE G 418 TRP 0.017 0.002 TRP I 346 HIS 0.005 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00306 (41436) covalent geometry : angle 0.63370 (56304) hydrogen bonds : bond 0.05540 ( 2046) hydrogen bonds : angle 4.96964 ( 5886) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 668 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8425 (tt) REVERT: F 325 MET cc_start: 0.8021 (mmm) cc_final: 0.7426 (mmm) REVERT: F 329 ASP cc_start: 0.8095 (m-30) cc_final: 0.7796 (m-30) REVERT: J 50 ASN cc_start: 0.7815 (t0) cc_final: 0.7424 (m-40) REVERT: J 178 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8380 (p) REVERT: J 183 GLU cc_start: 0.7281 (tt0) cc_final: 0.7044 (tt0) REVERT: J 279 GLU cc_start: 0.8016 (mp0) cc_final: 0.7761 (mp0) REVERT: J 424 ASP cc_start: 0.7891 (t70) cc_final: 0.7267 (t0) REVERT: G 90 ASP cc_start: 0.7889 (t0) cc_final: 0.7688 (t0) REVERT: G 238 VAL cc_start: 0.8609 (t) cc_final: 0.8374 (t) REVERT: G 295 MET cc_start: 0.8504 (mtm) cc_final: 0.8277 (mtm) REVERT: G 373 MET cc_start: 0.8260 (ttp) cc_final: 0.7878 (ttp) REVERT: G 408 TYR cc_start: 0.8524 (m-80) cc_final: 0.8127 (m-80) REVERT: G 415 GLU cc_start: 0.7437 (tt0) cc_final: 0.6952 (tm-30) REVERT: C 69 ASP cc_start: 0.8174 (t0) cc_final: 0.7774 (t0) REVERT: C 388 TRP cc_start: 0.9000 (m100) cc_final: 0.8695 (m100) REVERT: C 425 MET cc_start: 0.8240 (tpp) cc_final: 0.8019 (mmp) REVERT: D 305 CYS cc_start: 0.7757 (m) cc_final: 0.7500 (m) REVERT: D 329 ASP cc_start: 0.8140 (m-30) cc_final: 0.7790 (m-30) REVERT: D 356 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7597 (t) REVERT: D 373 MET cc_start: 0.8181 (ttp) cc_final: 0.7768 (ttm) REVERT: D 413 MET cc_start: 0.7665 (ttp) cc_final: 0.7311 (ttp) REVERT: D 435 TYR cc_start: 0.8368 (m-10) cc_final: 0.8130 (m-10) REVERT: L 279 GLU cc_start: 0.7894 (mp0) cc_final: 0.7605 (mp0) REVERT: L 391 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8608 (tt) REVERT: L 424 ASP cc_start: 0.7795 (t70) cc_final: 0.7218 (t0) REVERT: I 145 THR cc_start: 0.8747 (m) cc_final: 0.8390 (p) REVERT: I 151 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8517 (m) REVERT: I 166 MET cc_start: 0.8820 (tpt) cc_final: 0.8510 (mmm) REVERT: I 199 ASP cc_start: 0.7641 (m-30) cc_final: 0.7202 (m-30) REVERT: I 205 ASP cc_start: 0.7835 (m-30) cc_final: 0.7452 (m-30) REVERT: I 214 PHE cc_start: 0.8748 (t80) cc_final: 0.8419 (t80) REVERT: I 332 MET cc_start: 0.9207 (mmp) cc_final: 0.8889 (mmm) REVERT: I 356 CYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7989 (m) REVERT: I 413 MET cc_start: 0.7870 (ttp) cc_final: 0.7594 (ttm) REVERT: I 415 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6451 (tm-30) REVERT: A 377 MET cc_start: 0.7907 (ttp) cc_final: 0.7668 (ttp) REVERT: B 69 ASP cc_start: 0.7955 (t0) cc_final: 0.7698 (t0) REVERT: B 71 GLU cc_start: 0.6856 (pt0) cc_final: 0.6267 (tt0) REVERT: B 322 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7614 (mmm160) REVERT: B 332 MET cc_start: 0.8648 (mmp) cc_final: 0.8405 (mmp) REVERT: B 356 CYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7679 (t) REVERT: B 416 MET cc_start: 0.8011 (mmm) cc_final: 0.7662 (mmm) REVERT: K 50 ASN cc_start: 0.8078 (t0) cc_final: 0.7840 (m-40) REVERT: K 183 GLU cc_start: 0.7147 (tt0) cc_final: 0.6908 (mt-10) REVERT: K 413 MET cc_start: 0.7117 (mtp) cc_final: 0.6896 (mtp) REVERT: H 211 ASP cc_start: 0.7560 (m-30) cc_final: 0.7351 (m-30) REVERT: H 269 MET cc_start: 0.8174 (mpp) cc_final: 0.7934 (mtp) REVERT: H 325 MET cc_start: 0.7777 (tpp) cc_final: 0.7519 (tpt) REVERT: H 329 ASP cc_start: 0.7891 (m-30) cc_final: 0.7686 (m-30) REVERT: H 373 MET cc_start: 0.8281 (ttp) cc_final: 0.8077 (ttm) REVERT: H 398 MET cc_start: 0.8549 (mtt) cc_final: 0.8321 (mtt) REVERT: H 434 GLN cc_start: 0.8489 (tp40) cc_final: 0.8287 (tt0) outliers start: 130 outliers final: 59 residues processed: 765 average time/residue: 0.2518 time to fit residues: 321.1019 Evaluate side-chains 577 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 511 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 170 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 441 optimal weight: 6.9990 chunk 171 optimal weight: 0.2980 chunk 306 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 447 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 466 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN F 350 ASN J 107 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 HIS C 107 HIS D 14 ASN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS L 8 HIS L 28 HIS L 88 HIS L 107 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 349 ASN I 350 ASN I 436 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 37 HIS ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS K 31 GLN K 88 HIS K 107 HIS H 336 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086121 restraints weight = 67120.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089606 restraints weight = 32216.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092009 restraints weight = 19301.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093668 restraints weight = 13105.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.094848 restraints weight = 9650.330| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41436 Z= 0.150 Angle : 0.577 7.506 56304 Z= 0.299 Chirality : 0.044 0.176 6156 Planarity : 0.005 0.062 7338 Dihedral : 11.903 177.379 5746 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.72 % Allowed : 15.79 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.12), residues: 5088 helix: 2.11 (0.11), residues: 2346 sheet: 1.10 (0.18), residues: 804 loop : -0.54 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 390 TYR 0.021 0.001 TYR F 435 PHE 0.022 0.001 PHE A 49 TRP 0.036 0.002 TRP G 346 HIS 0.008 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00332 (41436) covalent geometry : angle 0.57693 (56304) hydrogen bonds : bond 0.04930 ( 2046) hydrogen bonds : angle 4.64903 ( 5886) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 584 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.8624 (mmm) cc_final: 0.7939 (mmp) REVERT: E 302 MET cc_start: 0.8120 (mmm) cc_final: 0.7673 (mtt) REVERT: E 388 TRP cc_start: 0.8941 (m100) cc_final: 0.8667 (m100) REVERT: F 305 CYS cc_start: 0.7548 (m) cc_final: 0.7223 (m) REVERT: F 325 MET cc_start: 0.7940 (mmm) cc_final: 0.7552 (mmm) REVERT: J 50 ASN cc_start: 0.8040 (t0) cc_final: 0.7709 (m-40) REVERT: J 279 GLU cc_start: 0.7790 (mp0) cc_final: 0.7544 (mp0) REVERT: J 424 ASP cc_start: 0.7960 (t70) cc_final: 0.7428 (t0) REVERT: G 90 ASP cc_start: 0.7952 (t0) cc_final: 0.7701 (t0) REVERT: G 145 THR cc_start: 0.8659 (m) cc_final: 0.8112 (p) REVERT: G 269 MET cc_start: 0.8059 (mpp) cc_final: 0.7669 (mtp) REVERT: G 301 MET cc_start: 0.8767 (mmp) cc_final: 0.8553 (mmp) REVERT: G 323 MET cc_start: 0.7634 (mtm) cc_final: 0.7337 (mtm) REVERT: G 373 MET cc_start: 0.8402 (ttp) cc_final: 0.7997 (ttm) REVERT: G 398 MET cc_start: 0.8492 (mtp) cc_final: 0.8237 (mtp) REVERT: G 408 TYR cc_start: 0.8578 (m-80) cc_final: 0.8152 (m-80) REVERT: G 415 GLU cc_start: 0.7486 (tt0) cc_final: 0.6929 (tm-30) REVERT: C 69 ASP cc_start: 0.8203 (t70) cc_final: 0.7744 (t0) REVERT: C 77 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: C 388 TRP cc_start: 0.9034 (m100) cc_final: 0.8724 (m100) REVERT: C 425 MET cc_start: 0.8339 (tpp) cc_final: 0.8022 (mmp) REVERT: D 329 ASP cc_start: 0.8165 (m-30) cc_final: 0.7836 (m-30) REVERT: D 356 CYS cc_start: 0.8137 (m) cc_final: 0.7676 (t) REVERT: D 413 MET cc_start: 0.7768 (ttp) cc_final: 0.7385 (ttp) REVERT: D 435 TYR cc_start: 0.8338 (m-10) cc_final: 0.8109 (m-10) REVERT: L 235 VAL cc_start: 0.8904 (t) cc_final: 0.8582 (m) REVERT: L 279 GLU cc_start: 0.7900 (mp0) cc_final: 0.7464 (mp0) REVERT: L 377 MET cc_start: 0.8268 (ttp) cc_final: 0.7844 (ttp) REVERT: L 391 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8404 (tt) REVERT: L 424 ASP cc_start: 0.7850 (t70) cc_final: 0.7278 (t0) REVERT: I 116 ASP cc_start: 0.8534 (t70) cc_final: 0.8309 (m-30) REVERT: I 145 THR cc_start: 0.8482 (m) cc_final: 0.8141 (p) REVERT: I 151 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8871 (m) REVERT: I 157 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8742 (mm) REVERT: I 166 MET cc_start: 0.8806 (tpt) cc_final: 0.8551 (mmm) REVERT: I 205 ASP cc_start: 0.7763 (m-30) cc_final: 0.7415 (m-30) REVERT: I 214 PHE cc_start: 0.8777 (t80) cc_final: 0.8432 (t80) REVERT: I 299 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7967 (mtpt) REVERT: I 332 MET cc_start: 0.9212 (mmp) cc_final: 0.8942 (mmm) REVERT: I 413 MET cc_start: 0.7952 (ttp) cc_final: 0.7710 (ttm) REVERT: I 415 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6229 (tm-30) REVERT: I 425 MET cc_start: 0.8031 (tpp) cc_final: 0.7563 (ttp) REVERT: A 113 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7583 (mp0) REVERT: B 322 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7723 (mmm160) REVERT: B 332 MET cc_start: 0.8706 (mmp) cc_final: 0.8415 (mmt) REVERT: B 356 CYS cc_start: 0.8397 (m) cc_final: 0.7834 (t) REVERT: B 416 MET cc_start: 0.7831 (mmm) cc_final: 0.7551 (mmm) REVERT: K 50 ASN cc_start: 0.8339 (t0) cc_final: 0.8077 (m-40) REVERT: K 377 MET cc_start: 0.8236 (ttp) cc_final: 0.7902 (ttp) REVERT: H 44 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8405 (tt) REVERT: H 114 LEU cc_start: 0.9192 (tp) cc_final: 0.8686 (tt) REVERT: H 301 MET cc_start: 0.8190 (mmm) cc_final: 0.7785 (mmt) REVERT: H 398 MET cc_start: 0.8495 (mtt) cc_final: 0.8290 (ttm) REVERT: H 416 MET cc_start: 0.7845 (mmp) cc_final: 0.7638 (mmm) outliers start: 118 outliers final: 56 residues processed: 670 average time/residue: 0.2297 time to fit residues: 257.9195 Evaluate side-chains 547 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 486 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 362 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 262 optimal weight: 0.9990 chunk 437 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 255 optimal weight: 6.9990 chunk 494 optimal weight: 9.9990 chunk 419 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 407 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 339 ASN D 339 ASN L 15 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 HIS I 349 ASN A 31 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 281 GLN B 349 ASN B 350 ASN H 229 HIS H 350 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087077 restraints weight = 66447.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090619 restraints weight = 31912.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093063 restraints weight = 19128.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094741 restraints weight = 13015.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095895 restraints weight = 9614.917| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41436 Z= 0.121 Angle : 0.552 10.224 56304 Z= 0.282 Chirality : 0.042 0.181 6156 Planarity : 0.004 0.062 7338 Dihedral : 11.624 179.849 5731 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.51 % Allowed : 16.48 % Favored : 81.01 % 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 aren not related in a simple way. whole: 1.45 (0.12), residues: 5088 helix: 2.08 (0.11), residues: 2346 sheet: 1.14 (0.18), residues: 786 loop : -0.49 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 390 TYR 0.018 0.001 TYR K 210 PHE 0.022 0.001 PHE A 49 TRP 0.039 0.002 TRP G 346 HIS 0.006 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00257 (41436) covalent geometry : angle 0.55178 (56304) hydrogen bonds : bond 0.04378 ( 2046) hydrogen bonds : angle 4.46034 ( 5886) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 569 time to evaluate : 1.634 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: E 91 GLN cc_start: 0.7601 (mt0) cc_final: 0.7087 (pt0) REVERT: E 302 MET cc_start: 0.8167 (mmm) cc_final: 0.7709 (mtt) REVERT: F 323 MET cc_start: 0.7851 (mtp) cc_final: 0.7485 (mtm) REVERT: J 23 LEU cc_start: 0.9283 (tp) cc_final: 0.9007 (tp) REVERT: J 35 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7923 (mm-40) REVERT: J 377 MET cc_start: 0.7818 (ttp) cc_final: 0.7607 (ttp) REVERT: J 424 ASP cc_start: 0.7967 (t70) cc_final: 0.7426 (t0) REVERT: G 90 ASP cc_start: 0.7955 (t0) cc_final: 0.7709 (t0) REVERT: G 145 THR cc_start: 0.8422 (m) cc_final: 0.8073 (p) REVERT: G 210 TYR cc_start: 0.8194 (m-10) cc_final: 0.7858 (m-10) REVERT: G 269 MET cc_start: 0.8021 (mpp) cc_final: 0.7626 (mtp) REVERT: G 415 GLU cc_start: 0.7474 (tt0) cc_final: 0.6793 (tm-30) REVERT: C 69 ASP cc_start: 0.8182 (t70) cc_final: 0.7733 (t0) REVERT: C 77 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: C 213 CYS cc_start: 0.8129 (m) cc_final: 0.7791 (m) REVERT: C 253 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 388 TRP cc_start: 0.9014 (m100) cc_final: 0.8669 (m100) REVERT: C 425 MET cc_start: 0.8325 (tpp) cc_final: 0.8065 (mmp) REVERT: D 329 ASP cc_start: 0.8228 (m-30) cc_final: 0.7913 (m-30) REVERT: D 356 CYS cc_start: 0.8339 (m) cc_final: 0.7664 (t) REVERT: D 413 MET cc_start: 0.7825 (ttp) cc_final: 0.7513 (ttp) REVERT: L 235 VAL cc_start: 0.8838 (t) cc_final: 0.8513 (m) REVERT: L 279 GLU cc_start: 0.7867 (mp0) cc_final: 0.7403 (mp0) REVERT: L 377 MET cc_start: 0.8113 (ttp) cc_final: 0.7632 (ttp) REVERT: L 424 ASP cc_start: 0.7894 (t70) cc_final: 0.7318 (t0) REVERT: I 145 THR cc_start: 0.8460 (m) cc_final: 0.8207 (p) REVERT: I 151 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8830 (m) REVERT: I 214 PHE cc_start: 0.8761 (t80) cc_final: 0.8382 (t80) REVERT: I 299 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7898 (mtpt) REVERT: I 332 MET cc_start: 0.9153 (mmp) cc_final: 0.8876 (mmm) REVERT: I 413 MET cc_start: 0.7960 (ttp) cc_final: 0.7683 (ttm) REVERT: I 425 MET cc_start: 0.8002 (tpp) cc_final: 0.7559 (ttp) REVERT: A 113 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7641 (mp0) REVERT: A 377 MET cc_start: 0.7942 (ttp) cc_final: 0.7676 (ttp) REVERT: B 145 THR cc_start: 0.8729 (m) cc_final: 0.8489 (p) REVERT: B 228 ASN cc_start: 0.8385 (m-40) cc_final: 0.8162 (m-40) REVERT: B 281 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: B 322 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7740 (mmm160) REVERT: B 332 MET cc_start: 0.8721 (mmp) cc_final: 0.8396 (mmt) REVERT: B 356 CYS cc_start: 0.8475 (m) cc_final: 0.7858 (t) REVERT: B 416 MET cc_start: 0.7796 (mmm) cc_final: 0.7541 (mmm) REVERT: K 50 ASN cc_start: 0.8288 (t0) cc_final: 0.8033 (m110) REVERT: K 413 MET cc_start: 0.7227 (mtp) cc_final: 0.6918 (mtp) REVERT: H 301 MET cc_start: 0.7897 (mmm) cc_final: 0.7647 (mmt) REVERT: H 425 MET cc_start: 0.8004 (tpp) cc_final: 0.7596 (ttm) outliers start: 109 outliers final: 59 residues processed: 651 average time/residue: 0.2383 time to fit residues: 260.1319 Evaluate side-chains 549 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 486 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 129 CYS Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 42 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 469 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 426 optimal weight: 0.9980 chunk 394 optimal weight: 0.3980 chunk 339 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 459 optimal weight: 0.3980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN E 300 ASN F 349 ASN J 31 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS G 350 ASN D 14 ASN D 136 GLN D 336 GLN L 31 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 349 ASN A 15 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086557 restraints weight = 66583.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090055 restraints weight = 31946.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092440 restraints weight = 19094.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094102 restraints weight = 12983.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.095288 restraints weight = 9572.844| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41436 Z= 0.132 Angle : 0.549 9.466 56304 Z= 0.280 Chirality : 0.042 0.186 6156 Planarity : 0.004 0.062 7338 Dihedral : 11.458 179.595 5724 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.63 % Allowed : 17.77 % Favored : 79.60 % 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 aren not related in a simple way. whole: 1.46 (0.12), residues: 5088 helix: 2.11 (0.11), residues: 2346 sheet: 1.06 (0.18), residues: 786 loop : -0.47 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 278 TYR 0.014 0.001 TYR D 435 PHE 0.021 0.001 PHE A 49 TRP 0.029 0.002 TRP G 346 HIS 0.005 0.001 HIS I 309 Details of bonding type rmsd covalent geometry : bond 0.00288 (41436) covalent geometry : angle 0.54857 (56304) hydrogen bonds : bond 0.04362 ( 2046) hydrogen bonds : angle 4.41732 ( 5886) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 548 time to evaluate : 1.680 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: E 302 MET cc_start: 0.8135 (mmm) cc_final: 0.7831 (mtt) REVERT: J 23 LEU cc_start: 0.9305 (tp) cc_final: 0.9034 (tp) REVERT: J 35 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7950 (mm-40) REVERT: J 424 ASP cc_start: 0.7971 (t70) cc_final: 0.7456 (t0) REVERT: G 90 ASP cc_start: 0.7966 (t0) cc_final: 0.7733 (t0) REVERT: G 145 THR cc_start: 0.8350 (m) cc_final: 0.8048 (p) REVERT: G 207 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: G 210 TYR cc_start: 0.8100 (m-10) cc_final: 0.7632 (m-80) REVERT: G 259 MET cc_start: 0.8433 (mmm) cc_final: 0.8141 (mmt) REVERT: G 323 MET cc_start: 0.7785 (mtm) cc_final: 0.7483 (mtm) REVERT: G 415 GLU cc_start: 0.7468 (tt0) cc_final: 0.6780 (tm-30) REVERT: C 69 ASP cc_start: 0.8169 (t70) cc_final: 0.7715 (t0) REVERT: C 77 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: C 209 ILE cc_start: 0.9126 (mt) cc_final: 0.8764 (mt) REVERT: C 213 CYS cc_start: 0.7976 (m) cc_final: 0.7648 (m) REVERT: C 253 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8867 (p) REVERT: C 388 TRP cc_start: 0.9006 (m100) cc_final: 0.8688 (m100) REVERT: C 425 MET cc_start: 0.8357 (tpp) cc_final: 0.8065 (mmp) REVERT: D 259 MET cc_start: 0.8368 (mmm) cc_final: 0.7774 (mmt) REVERT: D 329 ASP cc_start: 0.8204 (m-30) cc_final: 0.7878 (m-30) REVERT: D 356 CYS cc_start: 0.8453 (m) cc_final: 0.7730 (t) REVERT: D 413 MET cc_start: 0.7747 (ttp) cc_final: 0.7309 (ttp) REVERT: L 35 GLN cc_start: 0.8507 (mt0) cc_final: 0.7867 (mp10) REVERT: L 235 VAL cc_start: 0.8852 (t) cc_final: 0.8531 (m) REVERT: L 279 GLU cc_start: 0.7894 (mp0) cc_final: 0.7415 (mp0) REVERT: L 424 ASP cc_start: 0.7916 (t70) cc_final: 0.7362 (t0) REVERT: I 145 THR cc_start: 0.8265 (m) cc_final: 0.7897 (p) REVERT: I 214 PHE cc_start: 0.8782 (t80) cc_final: 0.8415 (t80) REVERT: I 299 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7918 (mtpt) REVERT: I 332 MET cc_start: 0.9153 (mmp) cc_final: 0.8881 (mmm) REVERT: I 413 MET cc_start: 0.7972 (ttp) cc_final: 0.7692 (ttm) REVERT: I 425 MET cc_start: 0.7968 (tpp) cc_final: 0.7513 (ttp) REVERT: A 113 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7653 (mp0) REVERT: A 377 MET cc_start: 0.7945 (ttp) cc_final: 0.7707 (ttp) REVERT: B 145 THR cc_start: 0.8673 (m) cc_final: 0.8409 (p) REVERT: B 161 TYR cc_start: 0.8522 (m-80) cc_final: 0.8243 (m-80) REVERT: B 228 ASN cc_start: 0.8393 (m-40) cc_final: 0.8180 (m-40) REVERT: B 322 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7777 (mmm160) REVERT: B 324 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.6298 (m) REVERT: B 332 MET cc_start: 0.8741 (mmp) cc_final: 0.8386 (mmt) REVERT: B 356 CYS cc_start: 0.8533 (m) cc_final: 0.7846 (t) REVERT: B 416 MET cc_start: 0.7804 (mmm) cc_final: 0.7524 (mmm) REVERT: K 50 ASN cc_start: 0.8290 (t0) cc_final: 0.8021 (m-40) REVERT: K 391 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8600 (tt) REVERT: K 413 MET cc_start: 0.7448 (mtp) cc_final: 0.7123 (mtp) REVERT: H 44 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8400 (tt) REVERT: H 301 MET cc_start: 0.8006 (mmm) cc_final: 0.7766 (mmt) REVERT: H 425 MET cc_start: 0.8006 (tpp) cc_final: 0.7605 (ttm) outliers start: 114 outliers final: 77 residues processed: 631 average time/residue: 0.2189 time to fit residues: 232.9654 Evaluate side-chains 571 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 488 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 406 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 404 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 468 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN E 300 ASN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN F 349 ASN J 15 GLN J 358 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 35 GLN D 197 ASN L 358 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN I 349 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN B 193 GLN B 281 GLN B 349 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.082298 restraints weight = 68714.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085672 restraints weight = 33093.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088008 restraints weight = 19887.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.089613 restraints weight = 13571.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090771 restraints weight = 10078.279| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 41436 Z= 0.227 Angle : 0.614 9.815 56304 Z= 0.316 Chirality : 0.045 0.153 6156 Planarity : 0.005 0.070 7338 Dihedral : 11.462 177.450 5724 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.11 % Allowed : 17.73 % Favored : 79.16 % 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 aren not related in a simple way. whole: 1.29 (0.12), residues: 5088 helix: 1.94 (0.11), residues: 2340 sheet: 1.13 (0.18), residues: 738 loop : -0.53 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 390 TYR 0.014 0.001 TYR B 224 PHE 0.020 0.002 PHE A 49 TRP 0.031 0.002 TRP B 346 HIS 0.006 0.001 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.00523 (41436) covalent geometry : angle 0.61423 (56304) hydrogen bonds : bond 0.05098 ( 2046) hydrogen bonds : angle 4.55575 ( 5886) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 509 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 302 MET cc_start: 0.8204 (mmm) cc_final: 0.7998 (mtt) REVERT: G 145 THR cc_start: 0.8434 (m) cc_final: 0.8041 (p) REVERT: G 207 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: G 210 TYR cc_start: 0.8204 (m-10) cc_final: 0.7832 (m-80) REVERT: G 415 GLU cc_start: 0.7597 (tt0) cc_final: 0.6925 (tm-30) REVERT: C 69 ASP cc_start: 0.8125 (t70) cc_final: 0.7709 (t0) REVERT: C 77 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: C 213 CYS cc_start: 0.8153 (m) cc_final: 0.7747 (m) REVERT: C 388 TRP cc_start: 0.9039 (m100) cc_final: 0.8797 (m100) REVERT: C 425 MET cc_start: 0.8377 (tpp) cc_final: 0.8152 (tpp) REVERT: D 259 MET cc_start: 0.8290 (mmm) cc_final: 0.7253 (mmm) REVERT: D 329 ASP cc_start: 0.8177 (m-30) cc_final: 0.7852 (m-30) REVERT: D 356 CYS cc_start: 0.8559 (m) cc_final: 0.7809 (t) REVERT: D 413 MET cc_start: 0.7912 (ttp) cc_final: 0.7447 (ttp) REVERT: L 35 GLN cc_start: 0.8552 (mt0) cc_final: 0.7919 (mp10) REVERT: L 279 GLU cc_start: 0.7861 (mp0) cc_final: 0.7306 (mp0) REVERT: L 424 ASP cc_start: 0.8052 (t70) cc_final: 0.7537 (t0) REVERT: I 42 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9088 (mm) REVERT: I 145 THR cc_start: 0.8213 (m) cc_final: 0.7931 (p) REVERT: I 217 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8546 (tt) REVERT: I 413 MET cc_start: 0.8013 (ttp) cc_final: 0.7715 (ttm) REVERT: A 377 MET cc_start: 0.8015 (ttp) cc_final: 0.7729 (ttp) REVERT: A 413 MET cc_start: 0.7793 (ttm) cc_final: 0.7173 (ttm) REVERT: B 332 MET cc_start: 0.8783 (mmp) cc_final: 0.8566 (mmp) REVERT: B 416 MET cc_start: 0.8021 (mmm) cc_final: 0.7538 (mmm) REVERT: K 50 ASN cc_start: 0.8435 (t0) cc_final: 0.8176 (m-40) REVERT: K 391 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8641 (tt) REVERT: K 413 MET cc_start: 0.7684 (mtp) cc_final: 0.7410 (mtp) REVERT: H 44 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8511 (tt) REVERT: H 259 MET cc_start: 0.8569 (mmm) cc_final: 0.7702 (mpp) REVERT: H 301 MET cc_start: 0.8004 (mmm) cc_final: 0.7614 (mmt) outliers start: 135 outliers final: 100 residues processed: 613 average time/residue: 0.2164 time to fit residues: 222.5175 Evaluate side-chains 577 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 471 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 363 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 420 optimal weight: 10.0000 chunk 406 optimal weight: 4.9990 chunk 272 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 444 optimal weight: 0.8980 chunk 330 optimal weight: 4.9990 chunk 346 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN F 37 HIS ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN F 349 ASN J 28 HIS ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 349 ASN A 88 HIS A 266 HIS B 349 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083523 restraints weight = 67848.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086937 restraints weight = 32649.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089261 restraints weight = 19599.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090880 restraints weight = 13403.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092044 restraints weight = 9928.419| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 41436 Z= 0.164 Angle : 0.578 11.672 56304 Z= 0.295 Chirality : 0.043 0.152 6156 Planarity : 0.004 0.066 7338 Dihedral : 11.323 176.558 5724 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.02 % Allowed : 17.91 % Favored : 79.07 % 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 aren not related in a simple way. whole: 1.27 (0.12), residues: 5088 helix: 1.94 (0.11), residues: 2346 sheet: 0.95 (0.18), residues: 750 loop : -0.51 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 390 TYR 0.016 0.001 TYR K 210 PHE 0.020 0.001 PHE A 49 TRP 0.039 0.002 TRP B 346 HIS 0.006 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00373 (41436) covalent geometry : angle 0.57758 (56304) hydrogen bonds : bond 0.04692 ( 2046) hydrogen bonds : angle 4.46536 ( 5886) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 514 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 23 LEU cc_start: 0.9286 (tp) cc_final: 0.9084 (tp) REVERT: J 35 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7758 (mm-40) REVERT: J 279 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7460 (mp0) REVERT: J 280 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7852 (ttpt) REVERT: G 145 THR cc_start: 0.8381 (m) cc_final: 0.8033 (p) REVERT: G 207 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: G 210 TYR cc_start: 0.8200 (m-10) cc_final: 0.7835 (m-80) REVERT: G 259 MET cc_start: 0.8584 (mmm) cc_final: 0.8217 (mmm) REVERT: G 415 GLU cc_start: 0.7557 (tt0) cc_final: 0.6912 (tm-30) REVERT: C 69 ASP cc_start: 0.8066 (t70) cc_final: 0.7686 (t0) REVERT: C 77 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: C 213 CYS cc_start: 0.8048 (m) cc_final: 0.7663 (m) REVERT: C 253 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8827 (p) REVERT: C 388 TRP cc_start: 0.9032 (m100) cc_final: 0.8790 (m100) REVERT: C 425 MET cc_start: 0.8354 (tpp) cc_final: 0.8138 (tpp) REVERT: D 259 MET cc_start: 0.8203 (mmm) cc_final: 0.7064 (mmm) REVERT: D 329 ASP cc_start: 0.8168 (m-30) cc_final: 0.7847 (m-30) REVERT: D 356 CYS cc_start: 0.8596 (m) cc_final: 0.7789 (t) REVERT: D 413 MET cc_start: 0.7833 (ttp) cc_final: 0.7368 (ttp) REVERT: L 35 GLN cc_start: 0.8593 (mt0) cc_final: 0.8046 (mp10) REVERT: L 235 VAL cc_start: 0.8922 (t) cc_final: 0.8611 (m) REVERT: L 279 GLU cc_start: 0.7876 (mp0) cc_final: 0.7301 (mp0) REVERT: L 424 ASP cc_start: 0.8022 (t70) cc_final: 0.7506 (t0) REVERT: I 42 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9059 (mm) REVERT: I 145 THR cc_start: 0.8371 (m) cc_final: 0.8036 (p) REVERT: I 214 PHE cc_start: 0.8770 (t80) cc_final: 0.8280 (t80) REVERT: I 217 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8627 (tt) REVERT: I 248 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7888 (tt) REVERT: I 413 MET cc_start: 0.7987 (ttp) cc_final: 0.7674 (ttm) REVERT: A 377 MET cc_start: 0.7967 (ttp) cc_final: 0.7688 (ttp) REVERT: A 413 MET cc_start: 0.7859 (ttm) cc_final: 0.7298 (ttm) REVERT: B 248 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7887 (tt) REVERT: B 332 MET cc_start: 0.8792 (mmp) cc_final: 0.8557 (mmp) REVERT: B 416 MET cc_start: 0.8018 (mmm) cc_final: 0.7614 (mmm) REVERT: K 50 ASN cc_start: 0.8387 (t0) cc_final: 0.8125 (m-40) REVERT: K 391 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8640 (tt) REVERT: K 413 MET cc_start: 0.7548 (mtp) cc_final: 0.7276 (mtp) REVERT: H 44 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8491 (tt) REVERT: H 301 MET cc_start: 0.8027 (mmm) cc_final: 0.7733 (mmt) REVERT: H 323 MET cc_start: 0.8074 (mtm) cc_final: 0.7873 (mtp) outliers start: 131 outliers final: 105 residues processed: 612 average time/residue: 0.2085 time to fit residues: 215.3120 Evaluate side-chains 590 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 476 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 378 LEU 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 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 216 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 250 optimal weight: 0.1980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN F 37 HIS F 136 GLN F 339 ASN F 349 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS A 18 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS B 337 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086074 restraints weight = 66794.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089549 restraints weight = 31981.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.091931 restraints weight = 19078.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093570 restraints weight = 12935.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094745 restraints weight = 9515.220| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41436 Z= 0.118 Angle : 0.558 12.360 56304 Z= 0.282 Chirality : 0.042 0.188 6156 Planarity : 0.004 0.064 7338 Dihedral : 11.061 177.700 5724 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.40 % Allowed : 18.86 % Favored : 78.75 % 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 aren not related in a simple way. whole: 1.40 (0.12), residues: 5088 helix: 2.04 (0.11), residues: 2346 sheet: 1.00 (0.18), residues: 750 loop : -0.44 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 390 TYR 0.018 0.001 TYR A 108 PHE 0.017 0.001 PHE A 49 TRP 0.045 0.002 TRP B 346 HIS 0.005 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00254 (41436) covalent geometry : angle 0.55751 (56304) hydrogen bonds : bond 0.04175 ( 2046) hydrogen bonds : angle 4.34935 ( 5886) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 546 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 23 LEU cc_start: 0.9274 (tp) cc_final: 0.9006 (tp) REVERT: J 35 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7730 (mm-40) REVERT: J 279 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7444 (mp0) REVERT: J 280 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7827 (ttpt) REVERT: J 377 MET cc_start: 0.8117 (ttp) cc_final: 0.7871 (ttp) REVERT: J 424 ASP cc_start: 0.8106 (t70) cc_final: 0.7592 (t0) REVERT: G 207 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: G 210 TYR cc_start: 0.8169 (m-10) cc_final: 0.7741 (m-80) REVERT: G 259 MET cc_start: 0.8450 (mmm) cc_final: 0.8231 (mmm) REVERT: G 415 GLU cc_start: 0.7452 (tt0) cc_final: 0.6809 (tm-30) REVERT: C 69 ASP cc_start: 0.8137 (t70) cc_final: 0.7810 (t0) REVERT: C 77 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: C 253 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8786 (p) REVERT: C 388 TRP cc_start: 0.8991 (m100) cc_final: 0.8623 (m100) REVERT: C 425 MET cc_start: 0.8424 (tpp) cc_final: 0.8086 (mmp) REVERT: D 259 MET cc_start: 0.8045 (mmm) cc_final: 0.7121 (mmm) REVERT: D 329 ASP cc_start: 0.8106 (m-30) cc_final: 0.7811 (m-30) REVERT: D 356 CYS cc_start: 0.8540 (m) cc_final: 0.7625 (t) REVERT: D 413 MET cc_start: 0.7727 (ttp) cc_final: 0.7275 (ttp) REVERT: L 35 GLN cc_start: 0.8563 (mt0) cc_final: 0.8031 (mp10) REVERT: L 235 VAL cc_start: 0.8858 (t) cc_final: 0.8549 (m) REVERT: L 279 GLU cc_start: 0.7876 (mp0) cc_final: 0.7307 (mp0) REVERT: L 424 ASP cc_start: 0.7997 (t70) cc_final: 0.7504 (t0) REVERT: I 214 PHE cc_start: 0.8717 (t80) cc_final: 0.8220 (t80) REVERT: I 248 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7901 (tt) REVERT: I 413 MET cc_start: 0.8079 (ttp) cc_final: 0.7751 (ttm) REVERT: I 415 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6402 (tm-30) REVERT: A 300 ASN cc_start: 0.8542 (m-40) cc_final: 0.8338 (t0) REVERT: A 377 MET cc_start: 0.7894 (ttp) cc_final: 0.7628 (ttp) REVERT: A 413 MET cc_start: 0.7752 (ttm) cc_final: 0.7182 (ttm) REVERT: B 248 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7892 (tt) REVERT: B 332 MET cc_start: 0.8846 (mmp) cc_final: 0.8442 (mmt) REVERT: K 50 ASN cc_start: 0.8347 (t0) cc_final: 0.8097 (m110) REVERT: K 217 LEU cc_start: 0.8757 (mt) cc_final: 0.8074 (tp) REVERT: K 413 MET cc_start: 0.7496 (mtp) cc_final: 0.7202 (mtp) REVERT: H 44 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8435 (tt) REVERT: H 323 MET cc_start: 0.7930 (mtm) cc_final: 0.7721 (mtp) REVERT: H 324 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7889 (p) outliers start: 104 outliers final: 78 residues processed: 616 average time/residue: 0.2180 time to fit residues: 225.8622 Evaluate side-chains 576 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 491 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 378 LEU 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 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 357 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 497 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 59 optimal weight: 0.0030 chunk 475 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 348 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN F 37 HIS F 339 ASN F 349 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS A 18 ASN A 256 GLN B 14 ASN ** B 136 GLN ** 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 = 0.3564 r_free = 0.3564 target = 0.104325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089794 restraints weight = 66336.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093319 restraints weight = 31661.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095713 restraints weight = 18817.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097362 restraints weight = 12701.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098523 restraints weight = 9290.566| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 41436 Z= 0.115 Angle : 0.559 12.786 56304 Z= 0.282 Chirality : 0.043 0.327 6156 Planarity : 0.004 0.063 7338 Dihedral : 10.852 178.352 5722 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.24 % Allowed : 19.29 % Favored : 78.47 % 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 aren not related in a simple way. whole: 1.40 (0.12), residues: 5088 helix: 1.97 (0.11), residues: 2370 sheet: 1.03 (0.19), residues: 750 loop : -0.38 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 390 TYR 0.014 0.001 TYR H 210 PHE 0.020 0.001 PHE A 49 TRP 0.042 0.002 TRP B 346 HIS 0.004 0.001 HIS I 309 Details of bonding type rmsd covalent geometry : bond 0.00248 (41436) covalent geometry : angle 0.55902 (56304) hydrogen bonds : bond 0.04005 ( 2046) hydrogen bonds : angle 4.31908 ( 5886) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 540 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 413 MET cc_start: 0.7814 (ttm) cc_final: 0.7577 (ttm) REVERT: J 23 LEU cc_start: 0.9303 (tp) cc_final: 0.9037 (tp) REVERT: J 35 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7948 (mm-40) REVERT: J 279 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7519 (mp0) REVERT: J 280 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7809 (ttpt) REVERT: J 424 ASP cc_start: 0.8024 (t70) cc_final: 0.7563 (t0) REVERT: G 207 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: G 210 TYR cc_start: 0.8123 (m-10) cc_final: 0.7688 (m-80) REVERT: G 259 MET cc_start: 0.8522 (mmm) cc_final: 0.8304 (mmm) REVERT: G 415 GLU cc_start: 0.7550 (tt0) cc_final: 0.6824 (tm-30) REVERT: C 69 ASP cc_start: 0.8165 (t70) cc_final: 0.7740 (t0) REVERT: C 77 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: C 253 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8766 (p) REVERT: C 388 TRP cc_start: 0.8984 (m100) cc_final: 0.8655 (m100) REVERT: C 425 MET cc_start: 0.8388 (tpp) cc_final: 0.8033 (mmp) REVERT: D 166 MET cc_start: 0.8427 (mmm) cc_final: 0.7870 (mmm) REVERT: D 259 MET cc_start: 0.8162 (mmm) cc_final: 0.7285 (mmm) REVERT: D 329 ASP cc_start: 0.8041 (m-30) cc_final: 0.7782 (m-30) REVERT: L 35 GLN cc_start: 0.8547 (mt0) cc_final: 0.8084 (mp10) REVERT: L 235 VAL cc_start: 0.8885 (t) cc_final: 0.8578 (m) REVERT: L 279 GLU cc_start: 0.7828 (mp0) cc_final: 0.7308 (mp0) REVERT: L 424 ASP cc_start: 0.8029 (t70) cc_final: 0.7520 (t0) REVERT: I 42 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9031 (mm) REVERT: I 210 TYR cc_start: 0.8275 (m-80) cc_final: 0.8046 (m-80) REVERT: I 217 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8619 (tt) REVERT: I 248 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 300 ASN cc_start: 0.8477 (m-40) cc_final: 0.8226 (t0) REVERT: A 377 MET cc_start: 0.7893 (ttp) cc_final: 0.7632 (ttp) REVERT: A 413 MET cc_start: 0.7742 (ttm) cc_final: 0.7137 (ttm) REVERT: B 248 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7821 (tt) REVERT: B 295 MET cc_start: 0.8297 (mmm) cc_final: 0.7748 (mtt) REVERT: B 332 MET cc_start: 0.8964 (mmp) cc_final: 0.8521 (mmt) REVERT: K 413 MET cc_start: 0.7289 (mtp) cc_final: 0.7010 (mtp) REVERT: H 44 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8395 (tt) REVERT: H 166 MET cc_start: 0.8452 (mmm) cc_final: 0.8054 (tpt) REVERT: H 323 MET cc_start: 0.7969 (mtm) cc_final: 0.7260 (ptp) outliers start: 97 outliers final: 74 residues processed: 607 average time/residue: 0.2204 time to fit residues: 227.0980 Evaluate side-chains 583 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 501 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL 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 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 31 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 397 optimal weight: 4.9990 chunk 374 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 474 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN F 37 HIS F 349 ASN F 385 GLN F 433 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 HIS ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN K 50 ASN H 59 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.103740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089358 restraints weight = 66226.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092866 restraints weight = 31547.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095236 restraints weight = 18674.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096855 restraints weight = 12593.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098018 restraints weight = 9219.532| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 41436 Z= 0.129 Angle : 0.567 12.361 56304 Z= 0.285 Chirality : 0.043 0.259 6156 Planarity : 0.004 0.063 7338 Dihedral : 10.765 178.289 5722 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.35 % Allowed : 19.48 % Favored : 78.17 % 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 aren not related in a simple way. whole: 1.46 (0.12), residues: 5088 helix: 1.97 (0.11), residues: 2376 sheet: 1.16 (0.18), residues: 798 loop : -0.37 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.013 0.001 TYR K 210 PHE 0.018 0.001 PHE A 49 TRP 0.043 0.002 TRP B 346 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00289 (41436) covalent geometry : angle 0.56749 (56304) hydrogen bonds : bond 0.04077 ( 2046) hydrogen bonds : angle 4.33954 ( 5886) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 513 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 413 MET cc_start: 0.7788 (ttm) cc_final: 0.7499 (ttm) REVERT: J 23 LEU cc_start: 0.9353 (tp) cc_final: 0.9112 (tp) REVERT: J 35 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7956 (mm-40) REVERT: J 279 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7496 (mp0) REVERT: J 280 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7784 (ttpt) REVERT: J 424 ASP cc_start: 0.7995 (t70) cc_final: 0.7596 (t0) REVERT: G 207 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: G 210 TYR cc_start: 0.8179 (m-10) cc_final: 0.7744 (m-80) REVERT: G 259 MET cc_start: 0.8533 (mmm) cc_final: 0.8303 (mmm) REVERT: G 415 GLU cc_start: 0.7461 (tt0) cc_final: 0.6800 (tm-30) REVERT: C 69 ASP cc_start: 0.8216 (t70) cc_final: 0.7936 (t0) REVERT: C 77 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: D 166 MET cc_start: 0.8413 (mmm) cc_final: 0.7877 (mmm) REVERT: D 259 MET cc_start: 0.8107 (mmm) cc_final: 0.7227 (mmm) REVERT: D 329 ASP cc_start: 0.8025 (m-30) cc_final: 0.7761 (m-30) REVERT: D 413 MET cc_start: 0.7805 (ttp) cc_final: 0.7497 (ttm) REVERT: L 35 GLN cc_start: 0.8537 (mt0) cc_final: 0.8100 (mp10) REVERT: L 235 VAL cc_start: 0.8908 (t) cc_final: 0.8600 (m) REVERT: L 279 GLU cc_start: 0.7832 (mp0) cc_final: 0.7282 (mp0) REVERT: L 424 ASP cc_start: 0.8079 (t70) cc_final: 0.7568 (t0) REVERT: I 42 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9050 (mm) REVERT: I 210 TYR cc_start: 0.8283 (m-80) cc_final: 0.8069 (m-80) REVERT: I 217 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8561 (tt) REVERT: I 248 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7932 (tt) REVERT: I 415 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6495 (tm-30) REVERT: A 203 MET cc_start: 0.8663 (mmp) cc_final: 0.8449 (mmp) REVERT: A 300 ASN cc_start: 0.8333 (m-40) cc_final: 0.8129 (t0) REVERT: A 377 MET cc_start: 0.7876 (ttp) cc_final: 0.7615 (ttp) REVERT: A 413 MET cc_start: 0.7814 (ttm) cc_final: 0.7264 (ttm) REVERT: B 248 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7815 (tt) REVERT: B 295 MET cc_start: 0.8288 (mmm) cc_final: 0.7818 (mtt) REVERT: B 332 MET cc_start: 0.8954 (mmp) cc_final: 0.8516 (mmt) REVERT: K 413 MET cc_start: 0.7365 (mtp) cc_final: 0.7107 (mtp) REVERT: H 44 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8392 (tt) REVERT: H 323 MET cc_start: 0.8007 (mtm) cc_final: 0.7309 (ptp) outliers start: 102 outliers final: 85 residues processed: 591 average time/residue: 0.2172 time to fit residues: 216.4205 Evaluate side-chains 586 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 494 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL 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 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 331 optimal weight: 7.9990 chunk 254 optimal weight: 0.8980 chunk 397 optimal weight: 5.9990 chunk 340 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 320 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 419 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 430 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN F 37 HIS F 349 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS A 256 GLN B 349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088045 restraints weight = 67402.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091505 restraints weight = 32105.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093870 restraints weight = 19043.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095497 restraints weight = 12840.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096658 restraints weight = 9398.259| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 41436 Z= 0.158 Angle : 0.585 12.891 56304 Z= 0.295 Chirality : 0.044 0.240 6156 Planarity : 0.004 0.063 7338 Dihedral : 10.745 178.152 5722 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.35 % Allowed : 19.57 % Favored : 78.08 % 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 aren not related in a simple way. whole: 1.42 (0.12), residues: 5088 helix: 1.94 (0.11), residues: 2376 sheet: 1.10 (0.18), residues: 798 loop : -0.38 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.014 0.001 TYR K 210 PHE 0.025 0.001 PHE A 255 TRP 0.043 0.002 TRP B 346 HIS 0.004 0.001 HIS I 309 Details of bonding type rmsd covalent geometry : bond 0.00362 (41436) covalent geometry : angle 0.58500 (56304) hydrogen bonds : bond 0.04324 ( 2046) hydrogen bonds : angle 4.38523 ( 5886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6662.00 seconds wall clock time: 116 minutes 21.21 seconds (6981.21 seconds total)