Starting phenix.real_space_refine on Tue Aug 26 22:59:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jak_6349/08_2025/3jak_6349.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jak_6349/08_2025/3jak_6349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jak_6349/08_2025/3jak_6349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jak_6349/08_2025/3jak_6349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jak_6349/08_2025/3jak_6349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jak_6349/08_2025/3jak_6349.map" } resolution = 3.3 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 36 5.49 5 Mg 6 5.21 5 S 296 5.16 5 C 27084 2.51 5 N 7340 2.21 5 O 8304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43066 Number of models: 1 Model: "" Number of chains: 26 Chain: "E" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.54, per 1000 atoms: 0.18 Number of scatterers: 43066 At special positions: 0 Unit cell: (171.6, 113.52, 212.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 296 16.00 P 36 15.00 Mg 6 11.99 O 8304 8.00 N 7340 7.00 C 27084 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: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10080 Finding SS restraints... Secondary structure from input PDB file: 274 helices and 30 sheets defined 57.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.919A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.633A 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: 3.598A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 162 removed outlier: 4.088A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 205 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.370A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.641A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.186A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.965A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.429A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.756A pdb=" N PHE F 87 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.462A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.623A 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: 3.784A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 3.652A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.671A pdb=" N GLN F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 284 " --> pdb=" O GLN F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 400 Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.098A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 438 removed outlier: 3.736A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 29 Processing helix chain 'N' and resid 34 through 40 removed outlier: 3.562A pdb=" N SER N 40 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 52 Processing helix chain 'N' and resid 57 through 61 Processing helix chain 'N' and resid 67 through 86 Processing helix chain 'N' and resid 92 through 98 removed outlier: 3.868A pdb=" N LYS N 98 " --> pdb=" O GLU N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 119 Processing helix chain 'N' and resid 125 through 131 removed outlier: 3.991A pdb=" N ALA N 129 " --> pdb=" O ASN N 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 47 through 51 removed outlier: 3.919A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.633A 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: 3.599A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 162 removed outlier: 4.088A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 205 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.370A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.641A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 Processing helix chain 'J' and resid 287 through 296 Processing helix chain 'J' and resid 297 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 Processing helix chain 'J' and resid 383 through 400 removed outlier: 4.187A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 3.967A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.429A pdb=" N ARG G 48 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 72 through 81 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.757A pdb=" N PHE G 87 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 129 removed outlier: 4.461A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.623A 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: 3.785A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 3.652A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.670A pdb=" N GLN G 282 " --> pdb=" O GLY G 279 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG G 284 " --> pdb=" O GLN G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 384 through 400 Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.096A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 438 removed outlier: 3.737A 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 removed outlier: 3.920A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.634A 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: 3.599A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 162 removed outlier: 4.089A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.370A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.642A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 400 removed outlier: 4.187A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.967A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.918A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.428A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.756A pdb=" N PHE D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.461A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.622A 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: 3.785A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.651A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.673A pdb=" N GLN D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.096A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 438 removed outlier: 3.737A 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 removed outlier: 3.918A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.633A 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: 3.598A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 162 removed outlier: 4.088A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 205 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.371A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 3.642A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 282 Processing helix chain 'L' and resid 287 through 296 Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 Processing helix chain 'L' and resid 383 through 400 removed outlier: 4.186A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 3.968A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.429A pdb=" N ARG I 48 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 72 through 81 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.757A pdb=" N PHE I 87 " --> pdb=" O GLY I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 109 through 129 removed outlier: 4.461A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.623A 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: 3.785A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.651A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 279 through 284 removed outlier: 3.671A pdb=" N GLN I 282 " --> pdb=" O GLY I 279 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG I 284 " --> pdb=" O GLN I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 296 Processing helix chain 'I' and resid 297 through 301 Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 339 Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 384 through 400 Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.095A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 438 removed outlier: 3.737A 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 removed outlier: 3.919A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.634A 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: 3.598A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.089A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.370A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.641A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.186A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.967A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.428A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.756A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.462A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.621A 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: 3.785A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.652A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.671A pdb=" N GLN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.097A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 438 removed outlier: 3.737A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 29 Processing helix chain 'M' and resid 34 through 40 removed outlier: 3.561A pdb=" N SER M 40 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 52 Processing helix chain 'M' and resid 57 through 61 Processing helix chain 'M' and resid 67 through 86 Processing helix chain 'M' and resid 92 through 98 removed outlier: 3.866A pdb=" N LYS M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 119 Processing helix chain 'M' and resid 125 through 131 removed outlier: 3.990A pdb=" N ALA M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.919A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.633A 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: 3.598A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 162 removed outlier: 4.089A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 196 through 198 No H-bonds generated for 'chain 'K' and resid 196 through 198' Processing helix chain 'K' and resid 205 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.371A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.640A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 282 Processing helix chain 'K' and resid 287 through 296 Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 400 removed outlier: 4.187A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 3.967A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.429A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.757A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.461A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.623A 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: 3.784A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.652A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.669A pdb=" N GLN H 282 " --> pdb=" O GLY H 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 284 " --> pdb=" O GLN H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 296 Processing helix chain 'H' and resid 297 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 400 Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.096A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 438 removed outlier: 3.737A 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: 8.016A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.101A 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 246 through 248 removed outlier: 6.598A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA E 374 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.280A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.643A 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 56 removed outlier: 3.939A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.015A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.100A 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 246 through 248 removed outlier: 6.598A pdb=" N ASN J 380 " --> pdb=" O MET J 313 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS J 315 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU J 378 " --> pdb=" O CYS J 315 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU J 317 " --> pdb=" O CYS J 376 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS J 376 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR J 319 " --> pdb=" O ALA J 374 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA J 374 " --> pdb=" O TYR J 319 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU G 137 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE G 7 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.279A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.622A 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: 8.483A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.643A 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 56 removed outlier: 3.939A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.098A 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 246 through 248 removed outlier: 6.598A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.893A 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: 8.509A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.863A 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: 7.525A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.366A 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: 6.797A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.281A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.643A 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 56 removed outlier: 3.939A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.100A 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 246 through 248 removed outlier: 6.598A pdb=" N ASN L 380 " --> pdb=" O MET L 313 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS L 315 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU L 378 " --> pdb=" O CYS L 315 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU L 317 " --> pdb=" O CYS L 376 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS L 376 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR L 319 " --> pdb=" O ALA L 374 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA L 374 " --> pdb=" O TYR L 319 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.865A 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: 7.525A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU I 137 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE I 7 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.280A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.642A 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 56 removed outlier: 3.939A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.099A 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 246 through 248 removed outlier: 6.598A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.281A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.643A 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 56 removed outlier: 3.939A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.099A 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 246 through 248 removed outlier: 6.596A pdb=" N ASN K 380 " --> pdb=" O MET K 313 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS K 315 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU K 378 " --> pdb=" O CYS K 315 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU K 317 " --> pdb=" O CYS K 376 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS K 376 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR K 319 " --> pdb=" O ALA K 374 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA K 374 " --> pdb=" O TYR K 319 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.894A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.281A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.643A 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 56 removed outlier: 3.940A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) 2194 hydrogen bonds defined for protein. 6300 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: 7.90 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 14136 1.35 - 1.50: 12108 1.50 - 1.65: 17348 1.65 - 1.81: 417 1.81 - 1.96: 43 Bond restraints: 44052 Sorted by residual: bond pdb=" PG GSP I 501 " pdb=" S1G GSP I 501 " ideal model delta sigma weight residual 1.700 1.959 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" PG GSP G 501 " pdb=" S1G GSP G 501 " ideal model delta sigma weight residual 1.700 1.958 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" PG GSP H 501 " pdb=" S1G GSP H 501 " ideal model delta sigma weight residual 1.700 1.957 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" PG GSP F 501 " pdb=" S1G GSP F 501 " ideal model delta sigma weight residual 1.700 1.941 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" PG GSP B 501 " pdb=" S1G GSP B 501 " ideal model delta sigma weight residual 1.700 1.940 -0.240 2.00e-02 2.50e+03 1.44e+02 ... (remaining 44047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 55298 2.52 - 5.05: 4264 5.05 - 7.57: 225 7.57 - 10.09: 37 10.09 - 12.62: 6 Bond angle restraints: 59830 Sorted by residual: angle pdb=" C LYS A 338 " pdb=" N ARG A 339 " pdb=" CA ARG A 339 " ideal model delta sigma weight residual 120.38 128.13 -7.75 1.37e+00 5.33e-01 3.20e+01 angle pdb=" C LYS E 338 " pdb=" N ARG E 339 " pdb=" CA ARG E 339 " ideal model delta sigma weight residual 120.38 128.09 -7.71 1.37e+00 5.33e-01 3.17e+01 angle pdb=" C LYS C 338 " pdb=" N ARG C 339 " pdb=" CA ARG C 339 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.37e+00 5.33e-01 3.14e+01 angle pdb=" C LYS L 338 " pdb=" N ARG L 339 " pdb=" CA ARG L 339 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.37e+00 5.33e-01 3.14e+01 angle pdb=" C LYS J 338 " pdb=" N ARG J 339 " pdb=" CA ARG J 339 " ideal model delta sigma weight residual 120.38 128.02 -7.64 1.37e+00 5.33e-01 3.11e+01 ... (remaining 59825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 25433 33.95 - 67.91: 699 67.91 - 101.86: 42 101.86 - 135.82: 0 135.82 - 169.77: 18 Dihedral angle restraints: 26192 sinusoidal: 10488 harmonic: 15704 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -120.96 -169.77 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.20 -169.53 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.74 -168.99 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 26189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4170 0.065 - 0.131: 1675 0.131 - 0.196: 436 0.196 - 0.262: 208 0.262 - 0.327: 39 Chirality restraints: 6528 Sorted by residual: chirality pdb=" CA ASN F 167 " pdb=" N ASN F 167 " pdb=" C ASN F 167 " pdb=" CB ASN F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ASN H 167 " pdb=" N ASN H 167 " pdb=" C ASN H 167 " pdb=" CB ASN H 167 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ASN B 167 " pdb=" N ASN B 167 " pdb=" C ASN B 167 " pdb=" CB ASN B 167 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 6525 not shown) Planarity restraints: 7782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA N 117 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C ALA N 117 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA N 117 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN N 118 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 117 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ALA M 117 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA M 117 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN M 118 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP C 501 " -0.024 2.00e-02 2.50e+03 1.16e-02 4.06e+00 pdb=" C2 GTP C 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GTP C 501 " 0.000 2.00e-02 2.50e+03 pdb=" C5 GTP C 501 " 0.002 2.00e-02 2.50e+03 pdb=" C6 GTP C 501 " -0.004 2.00e-02 2.50e+03 pdb=" C8 GTP C 501 " -0.003 2.00e-02 2.50e+03 pdb=" N1 GTP C 501 " -0.007 2.00e-02 2.50e+03 pdb=" N2 GTP C 501 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GTP C 501 " 0.004 2.00e-02 2.50e+03 pdb=" N7 GTP C 501 " 0.000 2.00e-02 2.50e+03 pdb=" N9 GTP C 501 " 0.030 2.00e-02 2.50e+03 pdb=" O6 GTP C 501 " -0.004 2.00e-02 2.50e+03 ... (remaining 7779 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 94 2.59 - 3.17: 35164 3.17 - 3.74: 69122 3.74 - 4.32: 95682 4.32 - 4.90: 162693 Nonbonded interactions: 362755 Sorted by model distance: nonbonded pdb=" O1G GTP J 501 " pdb="MG MG J 502 " model vdw 2.010 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.052 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 2.054 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.056 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 2.067 2.170 ... (remaining 362750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain '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' } ncs_group { reference = chain 'N' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.090 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 32.660 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.259 44052 Z= 0.627 Angle : 1.398 12.615 59830 Z= 0.973 Chirality : 0.082 0.327 6528 Planarity : 0.006 0.043 7782 Dihedral : 15.616 169.773 16112 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.19 % Favored : 97.70 % Rotamer: Outliers : 1.12 % Allowed : 4.71 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.27 (0.11), residues: 5388 helix: 0.93 (0.09), residues: 2494 sheet: 0.28 (0.18), residues: 816 loop : -0.70 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 2 TYR 0.019 0.002 TYR E 224 PHE 0.020 0.002 PHE H 92 TRP 0.020 0.003 TRP E 21 HIS 0.010 0.002 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00914 (44052) covalent geometry : angle 1.39795 (59830) hydrogen bonds : bond 0.18795 ( 2194) hydrogen bonds : angle 7.41423 ( 6300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 992 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 288 VAL cc_start: 0.8618 (m) cc_final: 0.8270 (t) REVERT: E 357 TYR cc_start: 0.7379 (m-80) cc_final: 0.7175 (m-10) REVERT: F 240 THR cc_start: 0.8845 (t) cc_final: 0.8503 (t) REVERT: F 325 MET cc_start: 0.7678 (mmm) cc_final: 0.7073 (mmm) REVERT: N 113 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7582 (mttt) REVERT: J 172 TYR cc_start: 0.8227 (t80) cc_final: 0.7627 (t80) REVERT: J 339 ARG cc_start: 0.7579 (ptm160) cc_final: 0.6297 (mmm160) REVERT: G 332 MET cc_start: 0.8750 (mmp) cc_final: 0.8464 (mmm) REVERT: C 154 MET cc_start: 0.7680 (mmm) cc_final: 0.7428 (mmm) REVERT: C 313 MET cc_start: 0.8108 (mtm) cc_final: 0.7772 (mtm) REVERT: D 378 ILE cc_start: 0.8577 (mm) cc_final: 0.8313 (mm) REVERT: L 339 ARG cc_start: 0.7461 (ptm160) cc_final: 0.6868 (mmm160) REVERT: I 180 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8885 (p) REVERT: I 204 ILE cc_start: 0.9050 (mp) cc_final: 0.8844 (mt) REVERT: I 414 ASP cc_start: 0.6596 (p0) cc_final: 0.6249 (t70) REVERT: B 90 ASP cc_start: 0.7055 (t70) cc_final: 0.6813 (t0) REVERT: B 101 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8180 (t0) REVERT: B 204 ILE cc_start: 0.8803 (mp) cc_final: 0.8526 (mt) REVERT: B 281 GLN cc_start: 0.8065 (pt0) cc_final: 0.7818 (pt0) REVERT: B 325 MET cc_start: 0.7853 (mmm) cc_final: 0.7303 (mmm) REVERT: B 333 LEU cc_start: 0.9033 (tp) cc_final: 0.8815 (tp) REVERT: M 122 LYS cc_start: 0.6445 (mtpt) cc_final: 0.5964 (mmmm) REVERT: K 154 MET cc_start: 0.8410 (mmm) cc_final: 0.7834 (mmp) REVERT: K 176 GLN cc_start: 0.7420 (mt0) cc_final: 0.7091 (mt0) REVERT: K 313 MET cc_start: 0.8113 (mtm) cc_final: 0.7854 (mtp) REVERT: K 339 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7044 (mmm160) REVERT: H 378 ILE cc_start: 0.8742 (mm) cc_final: 0.8498 (mm) outliers start: 52 outliers final: 10 residues processed: 1035 average time/residue: 0.2548 time to fit residues: 419.8612 Evaluate side-chains 580 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 568 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain H residue 224 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 0.6980 chunk 310 optimal weight: 0.0040 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 0.7980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS E 358 GLN F 6 HIS F 281 GLN F 309 HIS F 336 GLN N 74 ASN J 88 HIS J 300 ASN J 358 GLN G 6 HIS G 14 ASN G 101 ASN G 309 HIS G 336 GLN G 433 GLN C 283 HIS C 358 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 HIS D 281 GLN D 309 HIS D 336 GLN L 283 HIS L 358 GLN I 6 HIS I 14 ASN I 59 ASN I 101 ASN I 281 GLN I 309 HIS I 336 GLN A 283 HIS A 358 GLN B 6 HIS B 293 GLN B 309 HIS B 336 GLN B 337 ASN K 300 ASN K 358 GLN H 6 HIS H 281 GLN H 336 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.106615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091654 restraints weight = 68561.400| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.16 r_work: 0.3244 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44052 Z= 0.142 Angle : 0.593 9.514 59830 Z= 0.309 Chirality : 0.043 0.170 6528 Planarity : 0.005 0.039 7782 Dihedral : 10.940 172.529 6072 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.17 % Allowed : 9.55 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.61 (0.12), residues: 5388 helix: 2.25 (0.11), residues: 2536 sheet: 0.41 (0.18), residues: 804 loop : -0.12 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 221 TYR 0.021 0.001 TYR E 172 PHE 0.015 0.001 PHE B 418 TRP 0.016 0.002 TRP D 346 HIS 0.007 0.001 HIS L 309 Details of bonding type rmsd covalent geometry : bond 0.00294 (44052) covalent geometry : angle 0.59308 (59830) hydrogen bonds : bond 0.05747 ( 2194) hydrogen bonds : angle 5.12203 ( 6300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 650 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 LEU cc_start: 0.9251 (mt) cc_final: 0.9025 (mt) REVERT: E 357 TYR cc_start: 0.8331 (m-80) cc_final: 0.8051 (m-10) REVERT: E 364 PRO cc_start: 0.8436 (Cg_exo) cc_final: 0.8145 (Cg_endo) REVERT: F 259 MET cc_start: 0.8214 (mmm) cc_final: 0.7416 (mmm) REVERT: N 113 LYS cc_start: 0.7293 (mmtm) cc_final: 0.6704 (mttt) REVERT: J 306 ASP cc_start: 0.7818 (t70) cc_final: 0.7044 (t0) REVERT: J 339 ARG cc_start: 0.7207 (ptm160) cc_final: 0.5903 (tpt170) REVERT: J 377 MET cc_start: 0.9222 (ttp) cc_final: 0.8823 (tmm) REVERT: J 413 MET cc_start: 0.8749 (ttm) cc_final: 0.8471 (ttm) REVERT: G 90 ASP cc_start: 0.8899 (t70) cc_final: 0.8549 (t0) REVERT: G 323 MET cc_start: 0.8903 (ptp) cc_final: 0.8696 (ptp) REVERT: C 172 TYR cc_start: 0.8561 (t80) cc_final: 0.8334 (t80) REVERT: C 313 MET cc_start: 0.9027 (mtm) cc_final: 0.8748 (mtm) REVERT: C 339 ARG cc_start: 0.7952 (ptt180) cc_final: 0.6386 (tpt170) REVERT: C 433 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8279 (tm-30) REVERT: D 213 CYS cc_start: 0.8995 (m) cc_final: 0.8715 (m) REVERT: D 293 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8282 (mm-40) REVERT: L 127 ASP cc_start: 0.8261 (m-30) cc_final: 0.8003 (m-30) REVERT: L 210 TYR cc_start: 0.8647 (m-10) cc_final: 0.8003 (m-10) REVERT: L 285 GLN cc_start: 0.7625 (pm20) cc_final: 0.7230 (mp10) REVERT: L 339 ARG cc_start: 0.7117 (ptm160) cc_final: 0.6260 (tpt170) REVERT: I 413 MET cc_start: 0.8084 (ttm) cc_final: 0.7845 (ttp) REVERT: I 417 GLU cc_start: 0.7927 (mp0) cc_final: 0.7629 (mp0) REVERT: I 433 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8290 (tp40) REVERT: I 435 TYR cc_start: 0.8293 (m-80) cc_final: 0.7889 (m-10) REVERT: A 31 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7761 (mt0) REVERT: A 176 GLN cc_start: 0.8750 (mt0) cc_final: 0.8413 (mp10) REVERT: A 308 ARG cc_start: 0.8749 (mtm180) cc_final: 0.8347 (mtp180) REVERT: B 90 ASP cc_start: 0.8759 (t70) cc_final: 0.8495 (t0) REVERT: B 101 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8922 (m-40) REVERT: B 422 GLU cc_start: 0.8201 (tp30) cc_final: 0.7913 (tp30) REVERT: K 76 ASP cc_start: 0.8420 (m-30) cc_final: 0.8094 (t0) REVERT: K 172 TYR cc_start: 0.9033 (t80) cc_final: 0.8526 (t80) REVERT: K 176 GLN cc_start: 0.8879 (mt0) cc_final: 0.8534 (mt0) REVERT: K 203 MET cc_start: 0.8987 (mmm) cc_final: 0.8120 (mmm) REVERT: K 215 ARG cc_start: 0.8928 (ttp-110) cc_final: 0.8728 (mtm110) REVERT: K 313 MET cc_start: 0.9103 (mtm) cc_final: 0.8755 (mtp) REVERT: K 339 ARG cc_start: 0.7551 (ptm160) cc_final: 0.6876 (mmm160) REVERT: H 50 ASN cc_start: 0.8538 (p0) cc_final: 0.8197 (p0) REVERT: H 55 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7892 (tm-30) REVERT: H 323 MET cc_start: 0.8927 (ptp) cc_final: 0.8652 (ptm) REVERT: H 378 ILE cc_start: 0.9219 (mm) cc_final: 0.8917 (mt) REVERT: H 435 TYR cc_start: 0.8004 (m-80) cc_final: 0.7605 (m-10) outliers start: 54 outliers final: 27 residues processed: 688 average time/residue: 0.2242 time to fit residues: 257.4637 Evaluate side-chains 554 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 525 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 391 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 119 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 498 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 458 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 402 optimal weight: 7.9990 chunk 436 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 HIS E 88 HIS E 186 ASN E 283 HIS ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 258 ASN F 293 GLN F 349 ASN F 406 HIS J 8 HIS J 186 ASN J 283 HIS J 293 ASN C 8 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 258 ASN C 293 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 258 ASN D 385 GLN D 406 HIS D 433 GLN L 8 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN I 14 ASN I 247 GLN I 309 HIS A 8 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 258 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 406 HIS M 74 ASN ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 283 HIS H 247 GLN H 406 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085402 restraints weight = 70893.464| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.11 r_work: 0.3103 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 44052 Z= 0.271 Angle : 0.630 9.327 59830 Z= 0.331 Chirality : 0.047 0.163 6528 Planarity : 0.005 0.048 7782 Dihedral : 10.607 178.430 6066 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.35 % Allowed : 10.84 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.23 (0.11), residues: 5388 helix: 1.87 (0.10), residues: 2536 sheet: 0.21 (0.17), residues: 846 loop : -0.21 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 308 TYR 0.022 0.002 TYR J 172 PHE 0.024 0.002 PHE M 63 TRP 0.016 0.002 TRP J 388 HIS 0.018 0.002 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00635 (44052) covalent geometry : angle 0.62997 (59830) hydrogen bonds : bond 0.06135 ( 2194) hydrogen bonds : angle 5.01646 ( 6300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 560 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.8950 (mmm) cc_final: 0.8724 (mmm) REVERT: E 308 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7789 (mtm110) REVERT: E 357 TYR cc_start: 0.8619 (m-80) cc_final: 0.8268 (m-10) REVERT: E 392 ASP cc_start: 0.7828 (m-30) cc_final: 0.7078 (m-30) REVERT: E 429 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7749 (mp0) REVERT: F 229 HIS cc_start: 0.8447 (t70) cc_final: 0.8210 (t70) REVERT: N 50 MET cc_start: 0.7441 (ttm) cc_final: 0.7196 (ttm) REVERT: N 64 GLN cc_start: 0.6946 (mm-40) cc_final: 0.6637 (tm-30) REVERT: J 26 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8836 (mm) REVERT: J 76 ASP cc_start: 0.8580 (m-30) cc_final: 0.8258 (t0) REVERT: J 306 ASP cc_start: 0.8137 (t70) cc_final: 0.7632 (t0) REVERT: J 339 ARG cc_start: 0.7521 (ptm160) cc_final: 0.6317 (mmm160) REVERT: J 377 MET cc_start: 0.9367 (ttp) cc_final: 0.9034 (tmm) REVERT: J 413 MET cc_start: 0.8949 (ttm) cc_final: 0.8570 (ttm) REVERT: G 3 GLU cc_start: 0.8287 (mp0) cc_final: 0.8060 (mp0) REVERT: G 323 MET cc_start: 0.8992 (ptp) cc_final: 0.8756 (ptp) REVERT: C 172 TYR cc_start: 0.8599 (t80) cc_final: 0.8378 (t80) REVERT: C 313 MET cc_start: 0.8961 (mtm) cc_final: 0.8633 (mtm) REVERT: C 335 ILE cc_start: 0.9273 (mm) cc_final: 0.8828 (mm) REVERT: C 339 ARG cc_start: 0.8025 (ptt180) cc_final: 0.6601 (tpt170) REVERT: C 425 MET cc_start: 0.8482 (tpp) cc_final: 0.8039 (tpp) REVERT: C 433 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8280 (tm-30) REVERT: D 37 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.8107 (m-70) REVERT: D 101 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.9037 (t0) REVERT: D 213 CYS cc_start: 0.9065 (m) cc_final: 0.8602 (m) REVERT: D 373 MET cc_start: 0.8643 (ptp) cc_final: 0.8414 (ptp) REVERT: L 127 ASP cc_start: 0.8245 (m-30) cc_final: 0.7962 (m-30) REVERT: L 279 GLU cc_start: 0.7989 (pm20) cc_final: 0.7771 (pm20) REVERT: L 285 GLN cc_start: 0.7823 (pm20) cc_final: 0.7309 (mp10) REVERT: L 339 ARG cc_start: 0.7501 (ptm160) cc_final: 0.6566 (tpt170) REVERT: L 425 MET cc_start: 0.8685 (tpt) cc_final: 0.8215 (tpt) REVERT: I 90 ASP cc_start: 0.8858 (t0) cc_final: 0.8559 (t70) REVERT: I 133 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8910 (tp40) REVERT: I 190 SER cc_start: 0.9240 (OUTLIER) cc_final: 0.9036 (t) REVERT: I 413 MET cc_start: 0.8568 (ttm) cc_final: 0.8215 (ttp) REVERT: I 417 GLU cc_start: 0.8290 (mp0) cc_final: 0.7923 (mp0) REVERT: I 433 GLN cc_start: 0.8525 (tp-100) cc_final: 0.8306 (tp40) REVERT: A 50 ASN cc_start: 0.8733 (t0) cc_final: 0.8491 (t0) REVERT: A 176 GLN cc_start: 0.8850 (mt0) cc_final: 0.8505 (mp10) REVERT: A 308 ARG cc_start: 0.8709 (mtm180) cc_final: 0.8484 (mtp180) REVERT: B 90 ASP cc_start: 0.8904 (t70) cc_final: 0.8646 (t70) REVERT: B 101 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8929 (m-40) REVERT: B 422 GLU cc_start: 0.8514 (tp30) cc_final: 0.8312 (tp30) REVERT: M 122 LYS cc_start: 0.6454 (mtpt) cc_final: 0.5997 (mmmm) REVERT: K 76 ASP cc_start: 0.8564 (m-30) cc_final: 0.8194 (t0) REVERT: K 215 ARG cc_start: 0.9041 (ttp-110) cc_final: 0.8772 (mtm110) REVERT: K 269 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8510 (pp) REVERT: K 290 GLU cc_start: 0.8224 (tt0) cc_final: 0.7813 (tm-30) REVERT: K 306 ASP cc_start: 0.7988 (t0) cc_final: 0.7502 (t0) REVERT: K 309 HIS cc_start: 0.7647 (m90) cc_final: 0.7385 (m90) REVERT: K 313 MET cc_start: 0.9054 (mtm) cc_final: 0.8731 (mtt) REVERT: K 339 ARG cc_start: 0.7842 (ptm160) cc_final: 0.7076 (tpt170) REVERT: H 323 MET cc_start: 0.8955 (ptp) cc_final: 0.8739 (ptm) outliers start: 109 outliers final: 60 residues processed: 645 average time/residue: 0.2292 time to fit residues: 244.5899 Evaluate side-chains 549 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 482 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 199 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 381 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 517 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 491 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN E 186 ASN F 293 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS D 37 HIS L 88 HIS I 8 GLN A 18 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087098 restraints weight = 69563.829| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.17 r_work: 0.3160 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 44052 Z= 0.130 Angle : 0.524 8.983 59830 Z= 0.270 Chirality : 0.042 0.151 6528 Planarity : 0.004 0.043 7782 Dihedral : 10.350 175.617 6065 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.07 % Allowed : 12.10 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 5388 helix: 2.03 (0.10), residues: 2536 sheet: 0.35 (0.17), residues: 828 loop : -0.17 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 308 TYR 0.015 0.001 TYR L 172 PHE 0.013 0.001 PHE E 169 TRP 0.014 0.001 TRP C 21 HIS 0.012 0.001 HIS D 37 Details of bonding type rmsd covalent geometry : bond 0.00285 (44052) covalent geometry : angle 0.52448 (59830) hydrogen bonds : bond 0.04773 ( 2194) hydrogen bonds : angle 4.65026 ( 6300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 571 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 136 LEU cc_start: 0.9181 (mt) cc_final: 0.8979 (mt) REVERT: E 203 MET cc_start: 0.9262 (mmp) cc_final: 0.9053 (mmt) REVERT: E 308 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7608 (mtm110) REVERT: E 357 TYR cc_start: 0.8586 (m-80) cc_final: 0.8328 (m-10) REVERT: E 382 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8875 (p) REVERT: E 429 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7723 (mp0) REVERT: F 229 HIS cc_start: 0.8406 (t70) cc_final: 0.8146 (t70) REVERT: F 334 ASN cc_start: 0.8247 (m110) cc_final: 0.7994 (m-40) REVERT: F 413 MET cc_start: 0.8925 (ttm) cc_final: 0.8513 (mtp) REVERT: F 422 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7871 (tp30) REVERT: N 64 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6592 (tm-30) REVERT: J 26 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8770 (mm) REVERT: J 76 ASP cc_start: 0.8687 (m-30) cc_final: 0.8251 (t0) REVERT: J 109 THR cc_start: 0.8830 (m) cc_final: 0.8593 (p) REVERT: J 203 MET cc_start: 0.9158 (mmm) cc_final: 0.8367 (mmm) REVERT: J 306 ASP cc_start: 0.8379 (t70) cc_final: 0.7972 (t0) REVERT: J 339 ARG cc_start: 0.7304 (ptm160) cc_final: 0.6275 (tpt170) REVERT: J 377 MET cc_start: 0.9333 (ttp) cc_final: 0.9067 (tmm) REVERT: J 413 MET cc_start: 0.8901 (ttm) cc_final: 0.8655 (ttm) REVERT: G 3 GLU cc_start: 0.8295 (mp0) cc_final: 0.7945 (mp0) REVERT: G 90 ASP cc_start: 0.8994 (t70) cc_final: 0.8698 (t0) REVERT: G 323 MET cc_start: 0.8905 (ptp) cc_final: 0.8654 (ptp) REVERT: C 172 TYR cc_start: 0.8498 (t80) cc_final: 0.8214 (t80) REVERT: C 335 ILE cc_start: 0.9171 (mm) cc_final: 0.8724 (mm) REVERT: C 339 ARG cc_start: 0.7907 (ptt180) cc_final: 0.6462 (tpt170) REVERT: C 425 MET cc_start: 0.8459 (tpp) cc_final: 0.7621 (tpp) REVERT: C 433 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 101 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.9033 (t0) REVERT: D 213 CYS cc_start: 0.9123 (m) cc_final: 0.8678 (m) REVERT: D 422 GLU cc_start: 0.8467 (tp30) cc_final: 0.8174 (tp30) REVERT: L 127 ASP cc_start: 0.8309 (m-30) cc_final: 0.8042 (m-30) REVERT: L 250 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.9024 (p) REVERT: L 285 GLN cc_start: 0.7827 (pm20) cc_final: 0.7218 (mp10) REVERT: L 339 ARG cc_start: 0.7304 (ptm160) cc_final: 0.6431 (tpt170) REVERT: L 425 MET cc_start: 0.8627 (tpt) cc_final: 0.8315 (tpp) REVERT: I 55 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7837 (tm-30) REVERT: I 90 ASP cc_start: 0.8810 (t0) cc_final: 0.8485 (t70) REVERT: I 133 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8680 (tp40) REVERT: I 190 SER cc_start: 0.9251 (t) cc_final: 0.9011 (t) REVERT: I 417 GLU cc_start: 0.8354 (mp0) cc_final: 0.7885 (mp0) REVERT: I 433 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8267 (tp40) REVERT: A 50 ASN cc_start: 0.8771 (t0) cc_final: 0.8448 (t0) REVERT: A 176 GLN cc_start: 0.8850 (mt0) cc_final: 0.8479 (mp10) REVERT: A 308 ARG cc_start: 0.8577 (mtm180) cc_final: 0.8224 (mtp180) REVERT: B 90 ASP cc_start: 0.8868 (t70) cc_final: 0.8604 (t70) REVERT: B 101 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8932 (m-40) REVERT: B 416 MET cc_start: 0.7855 (tpp) cc_final: 0.7525 (tpt) REVERT: B 422 GLU cc_start: 0.8451 (tp30) cc_final: 0.8206 (tp30) REVERT: M 50 MET cc_start: 0.7074 (ttm) cc_final: 0.6771 (mtp) REVERT: M 122 LYS cc_start: 0.6288 (mtpt) cc_final: 0.5840 (mmmm) REVERT: K 76 ASP cc_start: 0.8699 (m-30) cc_final: 0.8255 (t0) REVERT: K 215 ARG cc_start: 0.8969 (ttp-110) cc_final: 0.8704 (mtm110) REVERT: K 290 GLU cc_start: 0.8300 (tt0) cc_final: 0.7763 (tm-30) REVERT: K 306 ASP cc_start: 0.7910 (t0) cc_final: 0.7191 (t70) REVERT: K 309 HIS cc_start: 0.7665 (m90) cc_final: 0.7395 (m90) REVERT: K 313 MET cc_start: 0.9146 (mtm) cc_final: 0.8779 (mtt) REVERT: K 339 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7011 (tpt170) REVERT: K 377 MET cc_start: 0.9335 (ttp) cc_final: 0.8874 (tmm) REVERT: H 205 ASP cc_start: 0.8696 (m-30) cc_final: 0.8494 (m-30) REVERT: H 323 MET cc_start: 0.8967 (ptp) cc_final: 0.8755 (ptm) REVERT: H 357 ASP cc_start: 0.8430 (t0) cc_final: 0.8220 (t0) REVERT: H 393 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8643 (tp30) outliers start: 96 outliers final: 60 residues processed: 644 average time/residue: 0.2721 time to fit residues: 291.1669 Evaluate side-chains 574 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 508 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 327 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 263 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 273 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 473 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 305 optimal weight: 6.9990 chunk 482 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 ASN F 293 GLN F 349 ASN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN I 8 GLN I 258 ASN I 309 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086517 restraints weight = 69605.732| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.16 r_work: 0.3175 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 44052 Z= 0.139 Angle : 0.518 9.359 59830 Z= 0.265 Chirality : 0.042 0.150 6528 Planarity : 0.004 0.044 7782 Dihedral : 10.176 174.182 6064 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.46 % Allowed : 12.63 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.37 (0.12), residues: 5388 helix: 1.96 (0.10), residues: 2570 sheet: 0.35 (0.18), residues: 828 loop : -0.16 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 308 TYR 0.025 0.001 TYR D 435 PHE 0.025 0.001 PHE D 262 TRP 0.014 0.002 TRP K 388 HIS 0.005 0.001 HIS L 197 Details of bonding type rmsd covalent geometry : bond 0.00315 (44052) covalent geometry : angle 0.51791 (59830) hydrogen bonds : bond 0.04634 ( 2194) hydrogen bonds : angle 4.56931 ( 6300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 559 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 LEU cc_start: 0.9159 (mt) cc_final: 0.8956 (mt) REVERT: E 154 MET cc_start: 0.8914 (mmm) cc_final: 0.8651 (mmm) REVERT: E 308 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7564 (mtm110) REVERT: E 357 TYR cc_start: 0.8646 (m-80) cc_final: 0.8364 (m-10) REVERT: E 382 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8869 (p) REVERT: E 429 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7412 (mp0) REVERT: F 229 HIS cc_start: 0.8385 (t70) cc_final: 0.8134 (t70) REVERT: F 302 MET cc_start: 0.8572 (mtt) cc_final: 0.8302 (mtm) REVERT: F 384 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8587 (tt) REVERT: F 422 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7875 (tp30) REVERT: N 50 MET cc_start: 0.6786 (ttm) cc_final: 0.5731 (mtp) REVERT: N 64 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6826 (tm-30) REVERT: J 26 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8739 (mm) REVERT: J 109 THR cc_start: 0.8823 (m) cc_final: 0.8590 (p) REVERT: J 306 ASP cc_start: 0.8567 (t70) cc_final: 0.8313 (t0) REVERT: J 339 ARG cc_start: 0.7362 (ptm160) cc_final: 0.6289 (tpt170) REVERT: J 377 MET cc_start: 0.9301 (ttp) cc_final: 0.9049 (tmm) REVERT: J 413 MET cc_start: 0.8924 (ttm) cc_final: 0.8679 (ttm) REVERT: G 3 GLU cc_start: 0.8270 (mp0) cc_final: 0.7892 (mp0) REVERT: G 90 ASP cc_start: 0.8874 (t70) cc_final: 0.8605 (t0) REVERT: G 323 MET cc_start: 0.8975 (ptp) cc_final: 0.8724 (ptp) REVERT: C 172 TYR cc_start: 0.8492 (t80) cc_final: 0.8156 (t80) REVERT: C 308 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8257 (mtm-85) REVERT: C 335 ILE cc_start: 0.9146 (mm) cc_final: 0.8690 (mm) REVERT: C 339 ARG cc_start: 0.7898 (ptt180) cc_final: 0.6443 (tpt170) REVERT: C 425 MET cc_start: 0.8337 (tpp) cc_final: 0.7521 (tpp) REVERT: C 433 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 101 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.9079 (t0) REVERT: D 213 CYS cc_start: 0.9112 (m) cc_final: 0.8674 (m) REVERT: D 422 GLU cc_start: 0.8458 (tp30) cc_final: 0.8155 (tp30) REVERT: L 285 GLN cc_start: 0.7937 (pm20) cc_final: 0.7207 (mp10) REVERT: L 339 ARG cc_start: 0.7227 (ptm160) cc_final: 0.6489 (tpt170) REVERT: I 55 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7870 (tm-30) REVERT: I 90 ASP cc_start: 0.8797 (t0) cc_final: 0.8468 (t70) REVERT: I 133 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8642 (tp40) REVERT: I 190 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.9011 (t) REVERT: I 417 GLU cc_start: 0.8419 (mp0) cc_final: 0.7892 (mp0) REVERT: A 50 ASN cc_start: 0.8789 (t0) cc_final: 0.8440 (t0) REVERT: A 176 GLN cc_start: 0.8834 (mt0) cc_final: 0.8482 (mp10) REVERT: A 275 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8880 (m) REVERT: A 308 ARG cc_start: 0.8582 (mtm180) cc_final: 0.8174 (mtp180) REVERT: B 3 GLU cc_start: 0.8352 (mp0) cc_final: 0.8130 (mp0) REVERT: B 90 ASP cc_start: 0.8884 (t70) cc_final: 0.8580 (t0) REVERT: B 101 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8940 (m-40) REVERT: B 416 MET cc_start: 0.7904 (tpp) cc_final: 0.7618 (tpt) REVERT: B 422 GLU cc_start: 0.8425 (tp30) cc_final: 0.8181 (tp30) REVERT: B 435 TYR cc_start: 0.8234 (m-10) cc_final: 0.8000 (m-10) REVERT: M 64 GLN cc_start: 0.7364 (tm-30) cc_final: 0.7135 (tm-30) REVERT: M 122 LYS cc_start: 0.6307 (mtpt) cc_final: 0.5864 (mmmm) REVERT: K 76 ASP cc_start: 0.8744 (m-30) cc_final: 0.8295 (t0) REVERT: K 215 ARG cc_start: 0.8921 (ttp-110) cc_final: 0.8681 (mtm110) REVERT: K 269 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8295 (pp) REVERT: K 290 GLU cc_start: 0.8331 (tt0) cc_final: 0.7899 (tm-30) REVERT: K 306 ASP cc_start: 0.7872 (t0) cc_final: 0.7670 (t0) REVERT: K 309 HIS cc_start: 0.7743 (m90) cc_final: 0.7454 (m90) REVERT: K 313 MET cc_start: 0.9149 (mtm) cc_final: 0.8774 (mtt) REVERT: K 339 ARG cc_start: 0.7758 (ptm160) cc_final: 0.7054 (tpt170) REVERT: H 205 ASP cc_start: 0.8691 (m-30) cc_final: 0.8482 (m-30) REVERT: H 332 MET cc_start: 0.8939 (mmm) cc_final: 0.8650 (mmm) REVERT: H 384 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8426 (pp) outliers start: 114 outliers final: 77 residues processed: 640 average time/residue: 0.2674 time to fit residues: 285.3290 Evaluate side-chains 606 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 519 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 384 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 455 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 460 optimal weight: 0.8980 chunk 383 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 522 optimal weight: 7.9990 chunk 279 optimal weight: 3.9990 chunk 387 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 435 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 293 GLN F 334 ASN F 349 ASN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 309 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086092 restraints weight = 69964.154| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.17 r_work: 0.3168 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 44052 Z= 0.145 Angle : 0.518 8.729 59830 Z= 0.265 Chirality : 0.042 0.177 6528 Planarity : 0.004 0.046 7782 Dihedral : 10.017 172.108 6064 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.59 % Allowed : 12.63 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.35 (0.12), residues: 5388 helix: 1.95 (0.10), residues: 2582 sheet: 0.33 (0.18), residues: 828 loop : -0.20 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 308 TYR 0.016 0.001 TYR M 32 PHE 0.017 0.001 PHE D 262 TRP 0.012 0.002 TRP C 21 HIS 0.004 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00333 (44052) covalent geometry : angle 0.51797 (59830) hydrogen bonds : bond 0.04583 ( 2194) hydrogen bonds : angle 4.52466 ( 6300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 552 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.8937 (mmm) cc_final: 0.8644 (mmm) REVERT: E 221 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7384 (mtt90) REVERT: E 308 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7569 (mtm110) REVERT: E 357 TYR cc_start: 0.8691 (m-80) cc_final: 0.8368 (m-10) REVERT: F 229 HIS cc_start: 0.8382 (t70) cc_final: 0.8137 (t70) REVERT: F 384 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8529 (tt) REVERT: N 50 MET cc_start: 0.6796 (ttm) cc_final: 0.5764 (mtp) REVERT: N 64 GLN cc_start: 0.7389 (mm-40) cc_final: 0.6860 (tm-30) REVERT: J 26 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8777 (mm) REVERT: J 203 MET cc_start: 0.9136 (mmm) cc_final: 0.8540 (mmm) REVERT: J 215 ARG cc_start: 0.8781 (ttp-110) cc_final: 0.8413 (mtm110) REVERT: J 306 ASP cc_start: 0.8688 (t70) cc_final: 0.8394 (t0) REVERT: J 339 ARG cc_start: 0.7534 (ptm160) cc_final: 0.6511 (tpt170) REVERT: J 377 MET cc_start: 0.9284 (ttp) cc_final: 0.8982 (tmm) REVERT: J 413 MET cc_start: 0.8926 (ttm) cc_final: 0.8700 (ttm) REVERT: G 3 GLU cc_start: 0.8287 (mp0) cc_final: 0.7898 (mp0) REVERT: G 323 MET cc_start: 0.9007 (ptp) cc_final: 0.8727 (ptp) REVERT: G 384 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8366 (pp) REVERT: C 172 TYR cc_start: 0.8501 (t80) cc_final: 0.8123 (t80) REVERT: C 308 ARG cc_start: 0.8649 (mtm110) cc_final: 0.8294 (mtm-85) REVERT: C 335 ILE cc_start: 0.9115 (mm) cc_final: 0.8644 (mm) REVERT: C 339 ARG cc_start: 0.7923 (ptt180) cc_final: 0.6507 (tpt170) REVERT: C 425 MET cc_start: 0.8376 (tpp) cc_final: 0.7817 (tpp) REVERT: C 433 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8260 (tm-30) REVERT: D 213 CYS cc_start: 0.9136 (m) cc_final: 0.8694 (m) REVERT: D 422 GLU cc_start: 0.8457 (tp30) cc_final: 0.8104 (tp30) REVERT: L 285 GLN cc_start: 0.7961 (pm20) cc_final: 0.7192 (mp10) REVERT: L 339 ARG cc_start: 0.7281 (ptm160) cc_final: 0.6511 (tpt170) REVERT: I 133 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8634 (tp40) REVERT: I 190 SER cc_start: 0.9248 (OUTLIER) cc_final: 0.9016 (t) REVERT: A 24 TYR cc_start: 0.9185 (m-10) cc_final: 0.8594 (m-10) REVERT: A 176 GLN cc_start: 0.8855 (mt0) cc_final: 0.8478 (mp10) REVERT: A 275 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8856 (m) REVERT: A 308 ARG cc_start: 0.8515 (mtm180) cc_final: 0.8278 (mtp180) REVERT: B 3 GLU cc_start: 0.8384 (mp0) cc_final: 0.8093 (mp0) REVERT: B 90 ASP cc_start: 0.8861 (t70) cc_final: 0.8544 (t0) REVERT: B 101 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8868 (t0) REVERT: B 416 MET cc_start: 0.7865 (tpp) cc_final: 0.7624 (tpt) REVERT: B 422 GLU cc_start: 0.8430 (tp30) cc_final: 0.8228 (tp30) REVERT: M 64 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7262 (tm-30) REVERT: M 85 MET cc_start: 0.7632 (mmp) cc_final: 0.7340 (mmp) REVERT: M 122 LYS cc_start: 0.6223 (mtpt) cc_final: 0.5862 (mmmm) REVERT: K 76 ASP cc_start: 0.8780 (m-30) cc_final: 0.8305 (t0) REVERT: K 203 MET cc_start: 0.9107 (mmm) cc_final: 0.8028 (mmm) REVERT: K 215 ARG cc_start: 0.8945 (ttp-110) cc_final: 0.8725 (mtm110) REVERT: K 269 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8339 (pp) REVERT: K 290 GLU cc_start: 0.8320 (tt0) cc_final: 0.7885 (tm-30) REVERT: K 309 HIS cc_start: 0.7844 (m90) cc_final: 0.7483 (m90) REVERT: K 313 MET cc_start: 0.9140 (mtm) cc_final: 0.8760 (mtt) REVERT: K 339 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7024 (tpt170) REVERT: K 377 MET cc_start: 0.9327 (ttp) cc_final: 0.8887 (tmm) REVERT: H 384 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8335 (pp) REVERT: H 413 MET cc_start: 0.9062 (ttm) cc_final: 0.8497 (ttm) outliers start: 120 outliers final: 89 residues processed: 630 average time/residue: 0.2678 time to fit residues: 280.4956 Evaluate side-chains 612 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 514 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR 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 223 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 413 MET Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 384 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 193 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 424 optimal weight: 0.0970 chunk 9 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 426 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 chunk 522 optimal weight: 0.9990 chunk 398 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 293 GLN F 334 ASN F 349 ASN N 69 HIS ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN I 8 GLN I 309 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.101464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086825 restraints weight = 69455.833| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.15 r_work: 0.3177 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 44052 Z= 0.127 Angle : 0.505 9.344 59830 Z= 0.258 Chirality : 0.042 0.160 6528 Planarity : 0.004 0.043 7782 Dihedral : 9.836 169.700 6061 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.57 % Allowed : 13.05 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.41 (0.12), residues: 5388 helix: 2.00 (0.10), residues: 2576 sheet: 0.34 (0.18), residues: 810 loop : -0.16 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 221 TYR 0.015 0.001 TYR M 32 PHE 0.014 0.001 PHE B 262 TRP 0.013 0.002 TRP C 21 HIS 0.006 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00286 (44052) covalent geometry : angle 0.50493 (59830) hydrogen bonds : bond 0.04342 ( 2194) hydrogen bonds : angle 4.46766 ( 6300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 551 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 308 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7546 (mtm110) REVERT: E 357 TYR cc_start: 0.8694 (m-80) cc_final: 0.8377 (m-10) REVERT: F 229 HIS cc_start: 0.8372 (t70) cc_final: 0.8123 (t70) REVERT: F 302 MET cc_start: 0.8491 (mtt) cc_final: 0.8223 (mtm) REVERT: F 334 ASN cc_start: 0.8355 (m-40) cc_final: 0.7889 (m-40) REVERT: F 384 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8502 (tt) REVERT: N 50 MET cc_start: 0.6990 (ttm) cc_final: 0.5928 (mtp) REVERT: N 64 GLN cc_start: 0.7509 (mm-40) cc_final: 0.6932 (tm-30) REVERT: J 26 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8753 (mm) REVERT: J 203 MET cc_start: 0.9061 (mmm) cc_final: 0.8475 (mmm) REVERT: J 215 ARG cc_start: 0.8768 (ttp-110) cc_final: 0.8419 (mtm110) REVERT: J 306 ASP cc_start: 0.8718 (t70) cc_final: 0.8403 (t0) REVERT: J 339 ARG cc_start: 0.7605 (ptm160) cc_final: 0.6562 (tpt170) REVERT: J 377 MET cc_start: 0.9217 (ttp) cc_final: 0.8858 (tmm) REVERT: J 413 MET cc_start: 0.8903 (ttm) cc_final: 0.8679 (ttm) REVERT: G 3 GLU cc_start: 0.8265 (mp0) cc_final: 0.7863 (mp0) REVERT: G 284 ARG cc_start: 0.8595 (ptt180) cc_final: 0.8245 (ptt90) REVERT: G 323 MET cc_start: 0.8921 (ptp) cc_final: 0.8618 (ptp) REVERT: G 384 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8339 (pp) REVERT: C 172 TYR cc_start: 0.8485 (t80) cc_final: 0.8090 (t80) REVERT: C 308 ARG cc_start: 0.8665 (mtm110) cc_final: 0.8280 (mtm-85) REVERT: C 335 ILE cc_start: 0.9135 (mm) cc_final: 0.8640 (mm) REVERT: C 339 ARG cc_start: 0.7921 (ptt180) cc_final: 0.6490 (tpt170) REVERT: C 425 MET cc_start: 0.8447 (tpp) cc_final: 0.7984 (tpp) REVERT: C 433 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8217 (tm-30) REVERT: D 213 CYS cc_start: 0.9124 (m) cc_final: 0.8684 (m) REVERT: D 422 GLU cc_start: 0.8422 (tp30) cc_final: 0.8060 (tp30) REVERT: L 285 GLN cc_start: 0.7964 (pm20) cc_final: 0.7178 (mp10) REVERT: L 339 ARG cc_start: 0.7244 (ptm160) cc_final: 0.6488 (tpt170) REVERT: I 90 ASP cc_start: 0.8857 (t0) cc_final: 0.8593 (t70) REVERT: I 133 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8657 (tp40) REVERT: A 24 TYR cc_start: 0.9161 (m-10) cc_final: 0.8551 (m-10) REVERT: A 176 GLN cc_start: 0.8874 (mt0) cc_final: 0.8607 (mp10) REVERT: A 275 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8824 (m) REVERT: A 308 ARG cc_start: 0.8491 (mtm180) cc_final: 0.8194 (mtp180) REVERT: B 90 ASP cc_start: 0.8867 (t70) cc_final: 0.8545 (t0) REVERT: B 101 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8868 (t0) REVERT: B 130 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8576 (t0) REVERT: B 416 MET cc_start: 0.7892 (tpp) cc_final: 0.7590 (tpt) REVERT: B 422 GLU cc_start: 0.8459 (tp30) cc_final: 0.8247 (tp30) REVERT: M 64 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7263 (tm-30) REVERT: M 85 MET cc_start: 0.7838 (mmp) cc_final: 0.7541 (mmp) REVERT: M 122 LYS cc_start: 0.6222 (mtpt) cc_final: 0.5858 (mmmm) REVERT: K 203 MET cc_start: 0.9129 (mmm) cc_final: 0.7964 (mmm) REVERT: K 215 ARG cc_start: 0.8943 (ttp-110) cc_final: 0.8640 (mtm110) REVERT: K 269 LEU cc_start: 0.8583 (pp) cc_final: 0.8342 (pp) REVERT: K 290 GLU cc_start: 0.8299 (tt0) cc_final: 0.7859 (tm-30) REVERT: K 313 MET cc_start: 0.9153 (mtm) cc_final: 0.8788 (mtt) REVERT: K 339 ARG cc_start: 0.7795 (ptm160) cc_final: 0.7063 (tpt170) REVERT: K 377 MET cc_start: 0.9332 (ttp) cc_final: 0.8862 (tmm) REVERT: H 332 MET cc_start: 0.8891 (mmm) cc_final: 0.8623 (mmm) REVERT: H 384 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8329 (pp) REVERT: H 393 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8627 (tp30) REVERT: H 413 MET cc_start: 0.9086 (ttm) cc_final: 0.8562 (ttm) outliers start: 119 outliers final: 95 residues processed: 627 average time/residue: 0.2663 time to fit residues: 278.5379 Evaluate side-chains 624 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 521 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 381 SER Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 384 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 404 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 263 optimal weight: 4.9990 chunk 531 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 338 optimal weight: 0.9990 chunk 458 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN F 349 ASN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 HIS ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN I 8 GLN I 229 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS K 18 ASN K 31 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083223 restraints weight = 71229.751| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.16 r_work: 0.3113 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 44052 Z= 0.255 Angle : 0.597 10.378 59830 Z= 0.307 Chirality : 0.045 0.154 6528 Planarity : 0.004 0.084 7782 Dihedral : 9.874 169.533 6061 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.57 % Allowed : 13.33 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.14 (0.11), residues: 5388 helix: 1.81 (0.10), residues: 2570 sheet: 0.02 (0.17), residues: 828 loop : -0.23 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 284 TYR 0.019 0.002 TYR B 435 PHE 0.021 0.002 PHE D 262 TRP 0.012 0.002 TRP D 346 HIS 0.011 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00596 (44052) covalent geometry : angle 0.59682 (59830) hydrogen bonds : bond 0.05422 ( 2194) hydrogen bonds : angle 4.70939 ( 6300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 511 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.8866 (mmm) cc_final: 0.8664 (mmm) REVERT: E 357 TYR cc_start: 0.8818 (m-80) cc_final: 0.8486 (m-10) REVERT: E 392 ASP cc_start: 0.8187 (m-30) cc_final: 0.7909 (m-30) REVERT: F 229 HIS cc_start: 0.8470 (t70) cc_final: 0.8258 (t70) REVERT: F 235 MET cc_start: 0.8710 (mtm) cc_final: 0.8507 (mtm) REVERT: F 416 MET cc_start: 0.8387 (tpp) cc_final: 0.8124 (tpp) REVERT: N 50 MET cc_start: 0.6932 (ttm) cc_final: 0.6666 (ttm) REVERT: N 64 GLN cc_start: 0.7714 (mm-40) cc_final: 0.6992 (tm-30) REVERT: N 83 LYS cc_start: 0.8152 (tttt) cc_final: 0.7565 (tptp) REVERT: J 26 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8764 (mm) REVERT: J 76 ASP cc_start: 0.8747 (m-30) cc_final: 0.8136 (t0) REVERT: J 306 ASP cc_start: 0.8752 (t70) cc_final: 0.8427 (t0) REVERT: J 339 ARG cc_start: 0.7885 (ptm160) cc_final: 0.6914 (tpt170) REVERT: J 377 MET cc_start: 0.9290 (ttp) cc_final: 0.8963 (tmm) REVERT: J 413 MET cc_start: 0.8900 (ttm) cc_final: 0.8646 (ttm) REVERT: G 3 GLU cc_start: 0.8299 (mp0) cc_final: 0.7904 (mp0) REVERT: G 323 MET cc_start: 0.8897 (ptp) cc_final: 0.7685 (ptp) REVERT: C 172 TYR cc_start: 0.8550 (t80) cc_final: 0.8128 (t80) REVERT: C 308 ARG cc_start: 0.8645 (mtm110) cc_final: 0.8273 (mtm-85) REVERT: C 339 ARG cc_start: 0.8089 (ptt180) cc_final: 0.6517 (tpt170) REVERT: C 425 MET cc_start: 0.8492 (tpp) cc_final: 0.8105 (tpp) REVERT: C 433 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8422 (tm-30) REVERT: D 213 CYS cc_start: 0.9145 (m) cc_final: 0.8698 (m) REVERT: D 422 GLU cc_start: 0.8499 (tp30) cc_final: 0.8151 (tp30) REVERT: L 285 GLN cc_start: 0.8087 (pm20) cc_final: 0.7376 (mp10) REVERT: L 339 ARG cc_start: 0.7854 (ptm160) cc_final: 0.7168 (tpt170) REVERT: L 425 MET cc_start: 0.8498 (tpt) cc_final: 0.8214 (tpp) REVERT: A 176 GLN cc_start: 0.8888 (mt0) cc_final: 0.8609 (mp10) REVERT: A 275 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8882 (m) REVERT: A 308 ARG cc_start: 0.8436 (mtm180) cc_final: 0.8187 (mtp180) REVERT: B 90 ASP cc_start: 0.8873 (t70) cc_final: 0.8498 (t0) REVERT: B 101 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.8909 (t0) REVERT: B 179 ASP cc_start: 0.8726 (t70) cc_final: 0.8295 (t0) REVERT: B 422 GLU cc_start: 0.8526 (tp30) cc_final: 0.8313 (tp30) REVERT: M 64 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7327 (tm-30) REVERT: M 122 LYS cc_start: 0.5938 (mtpt) cc_final: 0.5642 (mmmm) REVERT: K 2 ARG cc_start: 0.4230 (mtt90) cc_final: 0.3823 (mpt90) REVERT: K 76 ASP cc_start: 0.8780 (m-30) cc_final: 0.8300 (t0) REVERT: K 203 MET cc_start: 0.9139 (mmm) cc_final: 0.7942 (mmm) REVERT: K 215 ARG cc_start: 0.8969 (ttp-110) cc_final: 0.8648 (mtm110) REVERT: K 290 GLU cc_start: 0.8161 (tt0) cc_final: 0.7802 (tm-30) REVERT: K 313 MET cc_start: 0.9126 (mtm) cc_final: 0.8756 (mtt) REVERT: K 339 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7094 (tpt170) REVERT: K 377 MET cc_start: 0.9380 (ttp) cc_final: 0.8940 (tmm) REVERT: H 384 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8500 (pp) REVERT: H 393 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8610 (tp30) REVERT: H 413 MET cc_start: 0.9171 (ttm) cc_final: 0.8649 (ttm) outliers start: 119 outliers final: 97 residues processed: 590 average time/residue: 0.2672 time to fit residues: 262.2869 Evaluate side-chains 602 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 501 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 381 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 384 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 188 optimal weight: 0.0980 chunk 245 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 497 optimal weight: 0.9980 chunk 308 optimal weight: 4.9990 chunk 530 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 293 GLN F 349 ASN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 309 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087280 restraints weight = 69218.944| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.15 r_work: 0.3175 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 44052 Z= 0.107 Angle : 0.507 11.110 59830 Z= 0.257 Chirality : 0.041 0.154 6528 Planarity : 0.004 0.057 7782 Dihedral : 9.572 165.552 6061 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.86 % Allowed : 14.02 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 5388 helix: 1.87 (0.10), residues: 2600 sheet: 0.21 (0.18), residues: 828 loop : -0.20 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 284 TYR 0.014 0.001 TYR M 32 PHE 0.013 0.001 PHE I 94 TRP 0.017 0.002 TRP C 21 HIS 0.005 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00230 (44052) covalent geometry : angle 0.50652 (59830) hydrogen bonds : bond 0.04112 ( 2194) hydrogen bonds : angle 4.44335 ( 6300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 562 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.8857 (mmm) cc_final: 0.8605 (mmm) REVERT: E 357 TYR cc_start: 0.8716 (m-80) cc_final: 0.8377 (m-10) REVERT: F 229 HIS cc_start: 0.8368 (t70) cc_final: 0.8129 (t70) REVERT: F 293 GLN cc_start: 0.8419 (tt0) cc_final: 0.7793 (mm110) REVERT: F 384 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8471 (tt) REVERT: N 50 MET cc_start: 0.7056 (ttm) cc_final: 0.6018 (mtp) REVERT: N 64 GLN cc_start: 0.7714 (mm-40) cc_final: 0.6971 (tm-30) REVERT: J 26 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8766 (mm) REVERT: J 215 ARG cc_start: 0.8842 (ttp-110) cc_final: 0.8458 (mtm110) REVERT: J 306 ASP cc_start: 0.8768 (t70) cc_final: 0.8475 (t0) REVERT: J 339 ARG cc_start: 0.7637 (ptm160) cc_final: 0.6653 (tpt170) REVERT: J 377 MET cc_start: 0.9179 (ttp) cc_final: 0.8877 (tmm) REVERT: J 413 MET cc_start: 0.8890 (ttm) cc_final: 0.8661 (ttm) REVERT: G 3 GLU cc_start: 0.8233 (mp0) cc_final: 0.7819 (mp0) REVERT: G 301 MET cc_start: 0.8358 (mmt) cc_final: 0.7981 (mmm) REVERT: G 323 MET cc_start: 0.8731 (ptp) cc_final: 0.8231 (ptp) REVERT: G 384 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8362 (pp) REVERT: C 172 TYR cc_start: 0.8485 (t80) cc_final: 0.8093 (t80) REVERT: C 308 ARG cc_start: 0.8653 (mtm110) cc_final: 0.8272 (mtm-85) REVERT: C 335 ILE cc_start: 0.9138 (mm) cc_final: 0.8629 (mm) REVERT: C 339 ARG cc_start: 0.7907 (ptt180) cc_final: 0.6446 (tpt170) REVERT: C 425 MET cc_start: 0.8432 (tpp) cc_final: 0.8055 (tpp) REVERT: C 433 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 213 CYS cc_start: 0.9147 (m) cc_final: 0.8742 (m) REVERT: D 422 GLU cc_start: 0.8382 (tp30) cc_final: 0.8016 (tp30) REVERT: L 285 GLN cc_start: 0.8052 (pm20) cc_final: 0.7270 (mp10) REVERT: L 339 ARG cc_start: 0.7385 (ptm160) cc_final: 0.6573 (tpt170) REVERT: I 90 ASP cc_start: 0.8846 (t0) cc_final: 0.8620 (t70) REVERT: A 24 TYR cc_start: 0.9163 (m-10) cc_final: 0.8535 (m-10) REVERT: A 31 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8028 (mp10) REVERT: A 176 GLN cc_start: 0.8838 (mt0) cc_final: 0.8615 (mp10) REVERT: A 275 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8820 (m) REVERT: B 90 ASP cc_start: 0.8833 (t70) cc_final: 0.8497 (t0) REVERT: B 101 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.8869 (t0) REVERT: B 179 ASP cc_start: 0.8563 (t70) cc_final: 0.8157 (t0) REVERT: B 299 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8126 (ttpt) REVERT: B 422 GLU cc_start: 0.8365 (tp30) cc_final: 0.8165 (tp30) REVERT: M 64 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7280 (tm-30) REVERT: M 122 LYS cc_start: 0.6139 (mtpt) cc_final: 0.5915 (mmmm) REVERT: K 203 MET cc_start: 0.9088 (mmm) cc_final: 0.8059 (mmm) REVERT: K 215 ARG cc_start: 0.8956 (ttp-110) cc_final: 0.8683 (mtm110) REVERT: K 290 GLU cc_start: 0.8195 (tt0) cc_final: 0.7796 (tm-30) REVERT: K 313 MET cc_start: 0.9141 (mtm) cc_final: 0.8778 (mtt) REVERT: K 339 ARG cc_start: 0.7749 (ptm160) cc_final: 0.7061 (tpt170) REVERT: K 377 MET cc_start: 0.9223 (ttp) cc_final: 0.8825 (tmm) REVERT: H 384 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8354 (pp) REVERT: H 393 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8629 (tp30) REVERT: H 413 MET cc_start: 0.9069 (ttm) cc_final: 0.8589 (ttm) REVERT: H 435 TYR cc_start: 0.7730 (m-80) cc_final: 0.7502 (m-10) outliers start: 86 outliers final: 69 residues processed: 615 average time/residue: 0.2664 time to fit residues: 273.1660 Evaluate side-chains 602 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 526 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 384 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 288 optimal weight: 6.9990 chunk 510 optimal weight: 3.9990 chunk 521 optimal weight: 7.9990 chunk 309 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 405 optimal weight: 5.9990 chunk 52 optimal weight: 0.0030 chunk 340 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 349 ASN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 309 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.101267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.086616 restraints weight = 70059.777| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.16 r_work: 0.3155 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44052 Z= 0.139 Angle : 0.523 11.656 59830 Z= 0.266 Chirality : 0.042 0.148 6528 Planarity : 0.004 0.045 7782 Dihedral : 9.414 162.142 6061 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.75 % Allowed : 14.34 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 5388 helix: 1.90 (0.10), residues: 2600 sheet: 0.18 (0.18), residues: 828 loop : -0.20 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 308 TYR 0.014 0.001 TYR I 108 PHE 0.013 0.001 PHE I 94 TRP 0.013 0.002 TRP J 346 HIS 0.006 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00320 (44052) covalent geometry : angle 0.52263 (59830) hydrogen bonds : bond 0.04354 ( 2194) hydrogen bonds : angle 4.45836 ( 6300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 539 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.8860 (mmm) cc_final: 0.8644 (mmm) REVERT: E 203 MET cc_start: 0.9013 (mmm) cc_final: 0.8327 (mmm) REVERT: E 357 TYR cc_start: 0.8741 (m-80) cc_final: 0.8385 (m-10) REVERT: F 172 VAL cc_start: 0.9317 (t) cc_final: 0.9016 (m) REVERT: F 229 HIS cc_start: 0.8336 (t70) cc_final: 0.8097 (t70) REVERT: F 293 GLN cc_start: 0.8454 (tt0) cc_final: 0.7826 (mm110) REVERT: F 384 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8485 (tt) REVERT: N 50 MET cc_start: 0.7101 (ttm) cc_final: 0.6897 (ttm) REVERT: N 64 GLN cc_start: 0.7758 (mm-40) cc_final: 0.6987 (tm-30) REVERT: N 83 LYS cc_start: 0.8184 (tttt) cc_final: 0.7591 (tptp) REVERT: J 26 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8772 (mm) REVERT: J 76 ASP cc_start: 0.8692 (m-30) cc_final: 0.8037 (t0) REVERT: J 215 ARG cc_start: 0.8847 (ttp-110) cc_final: 0.8452 (mtm110) REVERT: J 306 ASP cc_start: 0.8766 (t70) cc_final: 0.8463 (t0) REVERT: J 339 ARG cc_start: 0.7716 (ptm160) cc_final: 0.6874 (tpt170) REVERT: J 377 MET cc_start: 0.9211 (ttp) cc_final: 0.8922 (tmm) REVERT: J 413 MET cc_start: 0.8919 (ttm) cc_final: 0.8689 (ttm) REVERT: G 3 GLU cc_start: 0.8241 (mp0) cc_final: 0.7831 (mp0) REVERT: G 301 MET cc_start: 0.8418 (mmt) cc_final: 0.8092 (mmm) REVERT: G 323 MET cc_start: 0.8735 (ptp) cc_final: 0.8294 (ptp) REVERT: G 384 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8394 (pp) REVERT: C 172 TYR cc_start: 0.8509 (t80) cc_final: 0.8112 (t80) REVERT: C 308 ARG cc_start: 0.8627 (mtm110) cc_final: 0.8258 (mtm-85) REVERT: C 339 ARG cc_start: 0.7926 (ptt180) cc_final: 0.6442 (tpt170) REVERT: C 425 MET cc_start: 0.8442 (tpp) cc_final: 0.8092 (tpp) REVERT: C 433 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D 213 CYS cc_start: 0.9165 (m) cc_final: 0.8756 (m) REVERT: D 422 GLU cc_start: 0.8360 (tp30) cc_final: 0.7982 (tp30) REVERT: L 285 GLN cc_start: 0.8058 (pm20) cc_final: 0.7395 (mp10) REVERT: L 339 ARG cc_start: 0.7638 (ptm160) cc_final: 0.6977 (tpt170) REVERT: I 90 ASP cc_start: 0.8846 (t0) cc_final: 0.8621 (t70) REVERT: A 24 TYR cc_start: 0.9191 (m-10) cc_final: 0.8613 (m-10) REVERT: A 176 GLN cc_start: 0.8827 (mt0) cc_final: 0.8598 (mp10) REVERT: A 275 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8804 (m) REVERT: B 90 ASP cc_start: 0.8795 (t70) cc_final: 0.8450 (t0) REVERT: B 101 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.8913 (t0) REVERT: B 179 ASP cc_start: 0.8614 (t70) cc_final: 0.8208 (t0) REVERT: B 201 THR cc_start: 0.9185 (m) cc_final: 0.8968 (m) REVERT: B 299 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8114 (ttpt) REVERT: M 64 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7341 (tm-30) REVERT: M 122 LYS cc_start: 0.6113 (mtpt) cc_final: 0.5897 (mmmm) REVERT: K 2 ARG cc_start: 0.4269 (mtt90) cc_final: 0.3744 (mpt90) REVERT: K 203 MET cc_start: 0.9103 (mmm) cc_final: 0.8003 (mmm) REVERT: K 215 ARG cc_start: 0.8958 (ttp-110) cc_final: 0.8677 (mtm110) REVERT: K 290 GLU cc_start: 0.8246 (tt0) cc_final: 0.7849 (tm-30) REVERT: K 313 MET cc_start: 0.9132 (mtm) cc_final: 0.8785 (mtt) REVERT: K 338 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7936 (mmtm) REVERT: K 339 ARG cc_start: 0.7745 (ptm160) cc_final: 0.7089 (tpt170) REVERT: K 377 MET cc_start: 0.9267 (ttp) cc_final: 0.8877 (tmm) REVERT: H 332 MET cc_start: 0.8854 (mmm) cc_final: 0.8625 (mmm) REVERT: H 384 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8405 (pp) REVERT: H 393 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8657 (tp30) REVERT: H 413 MET cc_start: 0.8945 (ttm) cc_final: 0.8454 (ttm) outliers start: 81 outliers final: 70 residues processed: 590 average time/residue: 0.2667 time to fit residues: 261.7745 Evaluate side-chains 607 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 530 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 384 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 322 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 334 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 ASN K 31 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083129 restraints weight = 71317.770| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.15 r_work: 0.3116 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 44052 Z= 0.270 Angle : 0.613 11.646 59830 Z= 0.315 Chirality : 0.045 0.159 6528 Planarity : 0.004 0.047 7782 Dihedral : 9.459 161.948 6061 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.12 % Allowed : 14.02 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.12), residues: 5388 helix: 1.78 (0.10), residues: 2570 sheet: -0.12 (0.17), residues: 828 loop : -0.26 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 308 TYR 0.017 0.002 TYR B 435 PHE 0.019 0.002 PHE H 92 TRP 0.014 0.002 TRP D 346 HIS 0.008 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00631 (44052) covalent geometry : angle 0.61294 (59830) hydrogen bonds : bond 0.05381 ( 2194) hydrogen bonds : angle 4.70101 ( 6300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10643.43 seconds wall clock time: 184 minutes 5.60 seconds (11045.60 seconds total)