Starting phenix.real_space_refine on Tue Aug 26 22:55:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jar_6351/08_2025/3jar_6351.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jar_6351/08_2025/3jar_6351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jar_6351/08_2025/3jar_6351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jar_6351/08_2025/3jar_6351.map" model { file = "/net/cci-nas-00/data/ceres_data/3jar_6351/08_2025/3jar_6351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jar_6351/08_2025/3jar_6351.cif" } resolution = 3.4 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= -0.008 sd= 0.921 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 290 5.16 5 C 27078 2.51 5 N 7340 2.21 5 O 8280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s 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: 43024 Number of models: 1 Model: "" Number of chains: 26 Chain: "E" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 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: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 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: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 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: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 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: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 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: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.38, per 1000 atoms: 0.19 Number of scatterers: 43024 At special positions: 0 Unit cell: (171.6, 113.52, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 290 16.00 P 30 15.00 Mg 6 11.99 O 8280 8.00 N 7340 7.00 C 27078 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: 3.25 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 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: 262 helices and 30 sheets defined 55.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.626A 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: 3.610A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.085A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.497A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 260 removed outlier: 4.186A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.667A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 298 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 384 through 400 Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.035A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.918A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.557A 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: 4.493A 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: 3.741A 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: 4.658A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.563A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.641A 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: 3.645A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.876A 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 287 through 297 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: 4.097A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 438 removed outlier: 3.765A 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: 3.557A 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: 3.866A 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: 3.999A 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 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.627A 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: 3.612A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.089A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.496A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 260 removed outlier: 4.185A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 removed outlier: 3.667A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 298 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 384 through 400 Processing helix chain 'J' and resid 404 through 411 removed outlier: 4.035A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.920A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 3.561A 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: 4.492A 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: 3.742A 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: 4.659A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.562A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.641A 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: 3.644A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.877A 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 287 through 297 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: 4.098A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 438 removed outlier: 3.765A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.627A 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: 3.611A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.084A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.496A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 4.186A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.666A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 384 through 400 Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.036A 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: 3.604A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.494A 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: 3.742A 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: 4.659A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.563A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.646A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.879A 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 287 through 297 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.097A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 438 removed outlier: 3.765A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.626A 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: 3.611A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.085A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 206 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.496A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 260 removed outlier: 4.186A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 282 removed outlier: 3.667A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 298 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 Processing helix chain 'L' and resid 384 through 400 Processing helix chain 'L' and resid 404 through 411 removed outlier: 4.035A 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: 3.603A pdb=" N SER L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 3.557A 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: 4.493A 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: 3.742A 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: 4.658A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS I 129 " --> pdb=" O GLU I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.562A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.645A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.878A 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 287 through 297 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: 4.099A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 438 removed outlier: 3.763A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.629A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.612A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.091A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.497A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 4.186A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.667A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 384 through 400 Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.036A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.919A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.562A 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: 4.492A 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: 3.740A 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: 4.658A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.563A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.646A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.878A 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 287 through 297 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: 3.765A 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: 3.557A 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: 3.865A 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: 3.999A 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 Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.625A 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: 3.611A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.084A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 196 through 198 No H-bonds generated for 'chain 'K' and resid 196 through 198' Processing helix chain 'K' and resid 206 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.498A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 260 removed outlier: 4.186A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 282 removed outlier: 3.667A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 298 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 384 through 400 Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.036A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.918A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.492A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.742A 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: 4.659A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.562A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.645A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.878A 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 287 through 297 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: 4.098A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 438 removed outlier: 3.764A 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: 8.004A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.115A 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: 6.584A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.812A 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: 7.882A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.809A 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: 7.074A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.423A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.899A 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: 8.005A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.113A 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: 6.590A pdb=" N ASN J 380 " --> pdb=" O MET J 313 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N CYS J 315 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU J 378 " --> pdb=" O CYS J 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU J 317 " --> pdb=" O CYS J 376 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N CYS J 376 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR J 319 " --> pdb=" O ALA J 374 " (cutoff:3.500A) removed outlier: 6.813A 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: 7.881A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.846A 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: 7.174A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU G 137 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE G 7 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.422A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.900A 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: 8.004A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.116A 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: 6.586A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.811A 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: 7.881A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.694A 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: 7.511A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.423A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.899A 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: 8.004A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.113A 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: 6.587A pdb=" N ASN L 380 " --> pdb=" O MET L 313 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS L 315 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.525A pdb=" N CYS L 376 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR L 319 " --> pdb=" O ALA L 374 " (cutoff:3.500A) removed outlier: 6.813A 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: 7.881A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU I 137 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.696A 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: 7.075A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.421A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.899A 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: 8.005A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.115A 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: 6.591A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.813A 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: 7.882A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.846A 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: 7.172A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.424A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.898A 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: 8.004A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.113A 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: 6.586A pdb=" N ASN K 380 " --> pdb=" O MET K 313 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS K 315 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.522A pdb=" N CYS K 376 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR K 319 " --> pdb=" O ALA K 374 " (cutoff:3.500A) removed outlier: 6.813A 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: 7.881A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.423A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.898A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) 2158 hydrogen bonds defined for protein. 6246 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.66 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7468 1.32 - 1.44: 11796 1.44 - 1.57: 24244 1.57 - 1.69: 48 1.69 - 1.81: 454 Bond restraints: 44010 Sorted by residual: bond pdb=" C5 GTP L 501 " pdb=" C6 GTP L 501 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C5 GTP C 501 " pdb=" C6 GTP C 501 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C5 GTP J 501 " pdb=" C6 GTP J 501 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C5 GTP E 501 " pdb=" C6 GTP E 501 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C5 GTP K 501 " pdb=" C6 GTP K 501 " ideal model delta sigma weight residual 1.390 1.478 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 44005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 52197 2.07 - 4.15: 6900 4.15 - 6.22: 573 6.22 - 8.29: 59 8.29 - 10.37: 35 Bond angle restraints: 59764 Sorted by residual: angle pdb=" N LYS L 338 " pdb=" CA LYS L 338 " pdb=" C LYS L 338 " ideal model delta sigma weight residual 110.30 119.20 -8.90 1.50e+00 4.44e-01 3.52e+01 angle pdb=" N LYS C 338 " pdb=" CA LYS C 338 " pdb=" C LYS C 338 " ideal model delta sigma weight residual 110.30 119.17 -8.87 1.50e+00 4.44e-01 3.50e+01 angle pdb=" N LYS K 338 " pdb=" CA LYS K 338 " pdb=" C LYS K 338 " ideal model delta sigma weight residual 110.30 119.16 -8.86 1.50e+00 4.44e-01 3.49e+01 angle pdb=" N LYS E 338 " pdb=" CA LYS E 338 " pdb=" C LYS E 338 " ideal model delta sigma weight residual 110.30 119.14 -8.84 1.50e+00 4.44e-01 3.48e+01 angle pdb=" N LYS J 338 " pdb=" CA LYS J 338 " pdb=" C LYS J 338 " ideal model delta sigma weight residual 110.30 119.04 -8.74 1.50e+00 4.44e-01 3.39e+01 ... (remaining 59759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 25346 33.80 - 67.60: 736 67.60 - 101.40: 56 101.40 - 135.20: 6 135.20 - 169.00: 18 Dihedral angle restraints: 26162 sinusoidal: 10458 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 -121.73 -169.00 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 -121.78 -168.95 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.91 -168.82 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 26159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 5106 0.093 - 0.187: 1190 0.187 - 0.280: 193 0.280 - 0.373: 29 0.373 - 0.466: 10 Chirality restraints: 6528 Sorted by residual: 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 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA ASN D 167 " pdb=" N ASN D 167 " pdb=" C ASN D 167 " pdb=" CB ASN D 167 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA ASN F 167 " pdb=" N ASN F 167 " pdb=" C ASN F 167 " pdb=" CB ASN F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.47 2.00e-01 2.50e+01 5.41e+00 ... (remaining 6525 not shown) Planarity restraints: 7776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 88 " 0.051 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO C 89 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 89 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 89 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 88 " 0.051 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO E 89 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO E 89 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 89 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS L 88 " 0.051 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO L 89 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO L 89 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 89 " 0.043 5.00e-02 4.00e+02 ... (remaining 7773 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 63 2.52 - 3.11: 30628 3.11 - 3.71: 67201 3.71 - 4.30: 97426 4.30 - 4.90: 166510 Nonbonded interactions: 361828 Sorted by model distance: nonbonded pdb=" O3G GTP J 501 " pdb="MG MG J 502 " model vdw 1.923 2.170 nonbonded pdb=" O3G GTP K 501 " pdb="MG MG K 502 " model vdw 1.940 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.940 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.955 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.966 2.170 ... (remaining 361823 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: 0.11 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: 10.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 36.680 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 44010 Z= 0.600 Angle : 1.383 10.366 59764 Z= 0.966 Chirality : 0.083 0.466 6528 Planarity : 0.007 0.079 7776 Dihedral : 16.190 169.000 16082 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.56 % Favored : 97.22 % Rotamer: Outliers : 1.82 % Allowed : 6.51 % Favored : 91.67 % Cbeta Deviations : 0.12 % 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: 1.00 (0.10), residues: 2438 sheet: 0.46 (0.18), residues: 780 loop : -0.81 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 2 TYR 0.019 0.002 TYR D 224 PHE 0.026 0.003 PHE K 296 TRP 0.018 0.002 TRP C 21 HIS 0.010 0.002 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00830 (44010) covalent geometry : angle 1.38321 (59764) hydrogen bonds : bond 0.18865 ( 2158) hydrogen bonds : angle 7.18003 ( 6246) *********************** 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 999 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 915 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.8470 (mmm) cc_final: 0.8194 (mmp) REVERT: F 284 ARG cc_start: 0.8423 (ptp-170) cc_final: 0.8209 (ptm-80) REVERT: N 20 MET cc_start: 0.6307 (ttp) cc_final: 0.5821 (tpp) REVERT: N 48 MET cc_start: 0.6852 (tpt) cc_final: 0.6457 (mmt) REVERT: N 105 PHE cc_start: 0.7358 (t80) cc_final: 0.7120 (t80) REVERT: N 115 PHE cc_start: 0.5099 (t80) cc_final: 0.4892 (t80) REVERT: J 154 MET cc_start: 0.8208 (mmm) cc_final: 0.7892 (mmt) REVERT: J 172 TYR cc_start: 0.8580 (t80) cc_final: 0.8273 (t80) REVERT: G 129 CYS cc_start: 0.8026 (m) cc_final: 0.7822 (m) REVERT: G 130 ASP cc_start: 0.8350 (t70) cc_final: 0.8000 (t70) REVERT: C 154 MET cc_start: 0.8509 (mmm) cc_final: 0.8200 (mmm) REVERT: C 168 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6885 (mt-10) REVERT: C 205 ASP cc_start: 0.7195 (t0) cc_final: 0.6900 (t0) REVERT: C 313 MET cc_start: 0.8110 (mtm) cc_final: 0.7680 (mtm) REVERT: C 349 THR cc_start: 0.8320 (p) cc_final: 0.8103 (p) REVERT: D 284 ARG cc_start: 0.8281 (ptp-170) cc_final: 0.8051 (ptm-80) REVERT: D 302 MET cc_start: 0.8611 (mtt) cc_final: 0.8372 (mtt) REVERT: D 373 MET cc_start: 0.7964 (ptp) cc_final: 0.7753 (ptp) REVERT: L 172 TYR cc_start: 0.8632 (t80) cc_final: 0.8197 (t80) REVERT: L 361 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8824 (p) REVERT: L 398 MET cc_start: 0.8720 (mtp) cc_final: 0.8511 (mtp) REVERT: I 332 MET cc_start: 0.8549 (mmp) cc_final: 0.8193 (mmm) REVERT: I 338 LYS cc_start: 0.9145 (ptpt) cc_final: 0.8938 (ptpp) REVERT: I 373 MET cc_start: 0.7882 (ptp) cc_final: 0.7656 (ptp) REVERT: I 422 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 172 TYR cc_start: 0.8659 (t80) cc_final: 0.8073 (t80) REVERT: A 313 MET cc_start: 0.8126 (mtm) cc_final: 0.7888 (mtm) REVERT: B 302 MET cc_start: 0.8284 (mtt) cc_final: 0.8076 (mtt) REVERT: B 313 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8942 (mt) REVERT: M 48 MET cc_start: 0.7153 (tpt) cc_final: 0.6803 (tpt) REVERT: M 85 MET cc_start: 0.5126 (mmp) cc_final: 0.4619 (mmt) REVERT: M 122 LYS cc_start: 0.6387 (mtpt) cc_final: 0.5775 (tmmt) REVERT: K 154 MET cc_start: 0.8388 (mmm) cc_final: 0.8131 (mmt) REVERT: K 302 MET cc_start: 0.8108 (mtt) cc_final: 0.7753 (mtt) REVERT: H 149 MET cc_start: 0.7817 (tpt) cc_final: 0.7510 (tpt) outliers start: 84 outliers final: 24 residues processed: 989 average time/residue: 0.2817 time to fit residues: 447.5946 Evaluate side-chains 536 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 510 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 295 CYS Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 0.0370 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 206 ASN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN F 139 HIS F 228 ASN F 336 GLN F 337 ASN J 28 HIS J 88 HIS J 186 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN J 293 ASN G 37 HIS G 139 HIS G 228 ASN G 336 GLN G 337 ASN G 339 ASN G 349 ASN C 28 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 206 ASN C 283 HIS C 342 GLN D 139 HIS D 228 ASN D 337 ASN L 28 HIS L 88 HIS L 186 ASN L 283 HIS I 139 HIS I 228 ASN I 229 HIS I 349 ASN A 18 ASN A 28 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 206 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 336 GLN B 337 ASN M 118 ASN K 28 HIS K 88 HIS K 186 ASN K 197 HIS K 206 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 GLN H 139 HIS H 228 ASN H 229 HIS H 293 GLN H 349 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.076323 restraints weight = 77239.315| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.71 r_work: 0.3061 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44010 Z= 0.160 Angle : 0.596 8.329 59764 Z= 0.316 Chirality : 0.043 0.149 6528 Planarity : 0.005 0.071 7776 Dihedral : 11.756 170.844 6075 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 10.79 % Favored : 87.05 % 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: 1.33 (0.11), residues: 5388 helix: 2.14 (0.10), residues: 2480 sheet: 0.53 (0.18), residues: 792 loop : -0.49 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 390 TYR 0.024 0.001 TYR B 161 PHE 0.022 0.002 PHE G 94 TRP 0.014 0.002 TRP H 346 HIS 0.009 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00327 (44010) covalent geometry : angle 0.59638 (59764) hydrogen bonds : bond 0.05700 ( 2158) hydrogen bonds : angle 5.00392 ( 6246) *********************** 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 716 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 616 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8760 (m-30) cc_final: 0.8139 (m-30) REVERT: E 154 MET cc_start: 0.9207 (mmm) cc_final: 0.8880 (mmp) REVERT: E 313 MET cc_start: 0.9211 (mtm) cc_final: 0.8904 (mtm) REVERT: F 50 ASN cc_start: 0.8768 (p0) cc_final: 0.8420 (p0) REVERT: F 76 ASP cc_start: 0.8632 (m-30) cc_final: 0.8391 (m-30) REVERT: F 118 VAL cc_start: 0.9509 (t) cc_final: 0.9265 (p) REVERT: N 20 MET cc_start: 0.5453 (ttp) cc_final: 0.5238 (tpp) REVERT: N 113 LYS cc_start: 0.7103 (mmtm) cc_final: 0.6802 (mmtm) REVERT: N 115 PHE cc_start: 0.4501 (t80) cc_final: 0.4109 (t80) REVERT: J 154 MET cc_start: 0.9051 (mmm) cc_final: 0.8752 (mmm) REVERT: J 221 ARG cc_start: 0.8708 (ptp90) cc_final: 0.8330 (mtm-85) REVERT: J 377 MET cc_start: 0.9008 (ttp) cc_final: 0.8755 (ttp) REVERT: G 199 ASP cc_start: 0.8205 (m-30) cc_final: 0.7835 (m-30) REVERT: G 254 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8594 (mtpt) REVERT: C 50 ASN cc_start: 0.8742 (t0) cc_final: 0.8435 (t0) REVERT: C 154 MET cc_start: 0.9259 (mmm) cc_final: 0.8957 (mmm) REVERT: C 168 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8092 (mt-10) REVERT: C 172 TYR cc_start: 0.8825 (t80) cc_final: 0.8190 (t80) REVERT: C 196 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: C 254 GLU cc_start: 0.8463 (mp0) cc_final: 0.8121 (mp0) REVERT: C 308 ARG cc_start: 0.9143 (mtm-85) cc_final: 0.8874 (mmm-85) REVERT: C 313 MET cc_start: 0.9053 (mtm) cc_final: 0.8568 (mtm) REVERT: C 349 THR cc_start: 0.8551 (p) cc_final: 0.8344 (p) REVERT: D 138 THR cc_start: 0.9255 (m) cc_final: 0.8987 (p) REVERT: D 200 GLU cc_start: 0.8516 (pm20) cc_final: 0.8305 (pm20) REVERT: D 254 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8309 (mtpp) REVERT: D 284 ARG cc_start: 0.8496 (ptp-170) cc_final: 0.8038 (ptm-80) REVERT: D 323 MET cc_start: 0.9007 (ptp) cc_final: 0.8792 (ptp) REVERT: D 332 MET cc_start: 0.9142 (mmp) cc_final: 0.8783 (mmm) REVERT: L 361 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8744 (p) REVERT: L 367 ASP cc_start: 0.7603 (t70) cc_final: 0.7287 (t0) REVERT: I 33 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8941 (p) REVERT: I 55 GLU cc_start: 0.8862 (tt0) cc_final: 0.8347 (tm-30) REVERT: I 116 ASP cc_start: 0.8425 (p0) cc_final: 0.8132 (t0) REVERT: I 200 GLU cc_start: 0.8191 (pt0) cc_final: 0.7844 (pt0) REVERT: I 213 CYS cc_start: 0.9024 (m) cc_final: 0.8605 (m) REVERT: I 254 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8113 (mtmt) REVERT: I 301 MET cc_start: 0.9143 (mmp) cc_final: 0.8854 (mmm) REVERT: I 373 MET cc_start: 0.8795 (ptp) cc_final: 0.8360 (mtm) REVERT: I 422 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8212 (tm-30) REVERT: A 50 ASN cc_start: 0.8591 (t0) cc_final: 0.8363 (t0) REVERT: A 127 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8374 (m-30) REVERT: A 172 TYR cc_start: 0.8868 (t80) cc_final: 0.7867 (t80) REVERT: A 196 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: A 313 MET cc_start: 0.9035 (mtm) cc_final: 0.8816 (mtm) REVERT: A 339 ARG cc_start: 0.9042 (ptt180) cc_final: 0.8835 (tmm-80) REVERT: B 71 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: B 149 MET cc_start: 0.8632 (tpt) cc_final: 0.8293 (tpt) REVERT: B 176 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8818 (mtpt) REVERT: K 122 ILE cc_start: 0.9369 (mt) cc_final: 0.9082 (mp) REVERT: K 154 MET cc_start: 0.9069 (mmm) cc_final: 0.8794 (mmt) REVERT: K 302 MET cc_start: 0.8845 (mtt) cc_final: 0.8365 (mtt) REVERT: K 390 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8022 (ttp-170) REVERT: H 55 GLU cc_start: 0.8649 (tt0) cc_final: 0.8318 (tm-30) REVERT: H 384 ILE cc_start: 0.8910 (pp) cc_final: 0.8693 (mt) REVERT: H 389 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8814 (ptpt) REVERT: H 422 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8009 (tm-30) outliers start: 100 outliers final: 48 residues processed: 693 average time/residue: 0.2559 time to fit residues: 291.5024 Evaluate side-chains 556 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 498 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 302 MET Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 389 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 341 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 372 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 462 optimal weight: 2.9990 chunk 491 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 515 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN J 8 HIS J 206 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS C 8 HIS C 35 GLN C 88 HIS L 8 HIS L 206 ASN I 133 GLN I 339 ASN A 35 GLN A 88 HIS A 101 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 HIS K 107 HIS K 256 GLN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN H 247 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.074245 restraints weight = 78860.003| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.73 r_work: 0.3022 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 44010 Z= 0.175 Angle : 0.556 7.490 59764 Z= 0.290 Chirality : 0.043 0.160 6528 Planarity : 0.004 0.062 7776 Dihedral : 11.044 170.489 6055 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.07 % Allowed : 11.63 % Favored : 85.29 % 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: 1.31 (0.11), residues: 5388 helix: 2.00 (0.10), residues: 2506 sheet: 0.54 (0.18), residues: 828 loop : -0.39 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 390 TYR 0.017 0.001 TYR L 24 PHE 0.016 0.001 PHE M 115 TRP 0.012 0.002 TRP J 21 HIS 0.007 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00394 (44010) covalent geometry : angle 0.55620 (59764) hydrogen bonds : bond 0.05170 ( 2158) hydrogen bonds : angle 4.72781 ( 6246) *********************** 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 665 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 523 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8510 (m-30) REVERT: E 154 MET cc_start: 0.9127 (mmm) cc_final: 0.8870 (mmp) REVERT: E 279 GLU cc_start: 0.7983 (mp0) cc_final: 0.7579 (pm20) REVERT: E 313 MET cc_start: 0.9252 (mtm) cc_final: 0.8919 (mtm) REVERT: E 377 MET cc_start: 0.8754 (ttp) cc_final: 0.8147 (tmm) REVERT: F 50 ASN cc_start: 0.8829 (p0) cc_final: 0.8444 (p0) REVERT: F 75 MET cc_start: 0.8714 (mmt) cc_final: 0.8482 (mmt) REVERT: F 76 ASP cc_start: 0.8683 (m-30) cc_final: 0.8393 (m-30) REVERT: F 118 VAL cc_start: 0.9465 (t) cc_final: 0.9225 (p) REVERT: N 98 LYS cc_start: 0.7182 (mtmm) cc_final: 0.6867 (mtmm) REVERT: N 113 LYS cc_start: 0.7110 (mmtm) cc_final: 0.6807 (mmtm) REVERT: N 115 PHE cc_start: 0.4555 (t80) cc_final: 0.4238 (t80) REVERT: J 377 MET cc_start: 0.9098 (ttp) cc_final: 0.8853 (ttp) REVERT: G 199 ASP cc_start: 0.8185 (m-30) cc_final: 0.7846 (m-30) REVERT: G 254 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.7760 (mtmm) REVERT: G 301 MET cc_start: 0.9103 (mmp) cc_final: 0.8830 (mmp) REVERT: G 389 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8920 (ptpt) REVERT: C 24 TYR cc_start: 0.9167 (m-10) cc_final: 0.8966 (m-80) REVERT: C 50 ASN cc_start: 0.9154 (t0) cc_final: 0.8716 (t0) REVERT: C 154 MET cc_start: 0.9161 (mmm) cc_final: 0.8811 (mmm) REVERT: C 168 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7945 (mt-10) REVERT: C 196 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: C 254 GLU cc_start: 0.8596 (mp0) cc_final: 0.8284 (mp0) REVERT: D 75 MET cc_start: 0.8935 (mmt) cc_final: 0.8726 (mmt) REVERT: D 254 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8339 (mtpp) REVERT: D 259 MET cc_start: 0.8889 (mmm) cc_final: 0.8406 (mmm) REVERT: D 284 ARG cc_start: 0.8654 (ptp-170) cc_final: 0.8291 (ptm160) REVERT: D 323 MET cc_start: 0.9059 (ptp) cc_final: 0.8684 (ptp) REVERT: D 332 MET cc_start: 0.9233 (mmp) cc_final: 0.8713 (mmm) REVERT: D 416 MET cc_start: 0.8807 (mmm) cc_final: 0.8560 (mmm) REVERT: L 313 MET cc_start: 0.9193 (mtm) cc_final: 0.8858 (mtt) REVERT: L 361 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8741 (p) REVERT: L 367 ASP cc_start: 0.7647 (t70) cc_final: 0.7195 (t0) REVERT: I 33 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8746 (p) REVERT: I 37 HIS cc_start: 0.8056 (m-70) cc_final: 0.7686 (m-70) REVERT: I 145 THR cc_start: 0.9142 (m) cc_final: 0.8802 (p) REVERT: I 149 MET cc_start: 0.8826 (tpt) cc_final: 0.8625 (tpt) REVERT: I 196 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: I 200 GLU cc_start: 0.7949 (pt0) cc_final: 0.7683 (pt0) REVERT: I 213 CYS cc_start: 0.9099 (m) cc_final: 0.8695 (m) REVERT: I 254 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8252 (mtmt) REVERT: I 373 MET cc_start: 0.8846 (ptp) cc_final: 0.8431 (mtm) REVERT: I 422 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8246 (tm-30) REVERT: A 127 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: A 172 TYR cc_start: 0.8782 (t80) cc_final: 0.8334 (t80) REVERT: A 196 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: A 313 MET cc_start: 0.9056 (mtm) cc_final: 0.8808 (mtm) REVERT: A 382 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9100 (p) REVERT: B 149 MET cc_start: 0.8853 (tpt) cc_final: 0.8461 (tpt) REVERT: B 161 TYR cc_start: 0.8979 (m-80) cc_final: 0.8744 (m-80) REVERT: B 176 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8922 (mtpt) REVERT: B 334 ASN cc_start: 0.9230 (t0) cc_final: 0.8993 (t0) REVERT: M 98 LYS cc_start: 0.7178 (ttmm) cc_final: 0.6957 (mtmm) REVERT: K 36 MET cc_start: 0.8862 (ptm) cc_final: 0.8507 (ttp) REVERT: K 122 ILE cc_start: 0.9412 (mt) cc_final: 0.9134 (mp) REVERT: K 154 MET cc_start: 0.9070 (mmm) cc_final: 0.8803 (mmt) REVERT: K 302 MET cc_start: 0.8951 (mtt) cc_final: 0.8444 (mtt) REVERT: K 390 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8385 (ttp-110) REVERT: H 301 MET cc_start: 0.9016 (mmp) cc_final: 0.8747 (mmp) REVERT: H 373 MET cc_start: 0.8960 (ptp) cc_final: 0.8637 (ptp) REVERT: H 389 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8761 (ptpt) REVERT: H 422 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8027 (tm-30) REVERT: H 425 MET cc_start: 0.8601 (ttm) cc_final: 0.8396 (ttm) outliers start: 142 outliers final: 82 residues processed: 637 average time/residue: 0.2504 time to fit residues: 266.4198 Evaluate side-chains 554 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 459 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 389 LYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 285 GLN Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 389 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 454 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 475 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 chunk 158 optimal weight: 0.0020 chunk 322 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 107 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 GLN A 101 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074932 restraints weight = 77932.917| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.76 r_work: 0.3038 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44010 Z= 0.126 Angle : 0.520 7.964 59764 Z= 0.268 Chirality : 0.042 0.149 6528 Planarity : 0.004 0.057 7776 Dihedral : 10.702 166.981 6053 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.60 % Allowed : 12.69 % Favored : 84.71 % 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: 1.28 (0.11), residues: 5388 helix: 1.92 (0.10), residues: 2544 sheet: 0.58 (0.18), residues: 834 loop : -0.39 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.015 0.001 TYR M 124 PHE 0.023 0.001 PHE M 52 TRP 0.011 0.001 TRP J 21 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00274 (44010) covalent geometry : angle 0.51981 (59764) hydrogen bonds : bond 0.04571 ( 2158) hydrogen bonds : angle 4.55712 ( 6246) *********************** 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 622 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 502 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8482 (m-30) REVERT: E 154 MET cc_start: 0.9087 (mmm) cc_final: 0.8838 (mmp) REVERT: E 377 MET cc_start: 0.8846 (ttp) cc_final: 0.8323 (tmm) REVERT: F 50 ASN cc_start: 0.8760 (p0) cc_final: 0.8386 (p0) REVERT: F 71 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: F 75 MET cc_start: 0.8734 (mmt) cc_final: 0.8512 (mmt) REVERT: F 76 ASP cc_start: 0.8587 (m-30) cc_final: 0.8242 (m-30) REVERT: F 118 VAL cc_start: 0.9441 (t) cc_final: 0.9222 (p) REVERT: N 98 LYS cc_start: 0.7034 (mtmm) cc_final: 0.6740 (mtmm) REVERT: N 113 LYS cc_start: 0.7093 (mmtm) cc_final: 0.6784 (mmtm) REVERT: N 115 PHE cc_start: 0.4185 (t80) cc_final: 0.3861 (t80) REVERT: J 221 ARG cc_start: 0.8706 (ptp90) cc_final: 0.8346 (ptp90) REVERT: J 319 TYR cc_start: 0.9421 (m-80) cc_final: 0.9082 (m-80) REVERT: J 363 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9117 (t) REVERT: J 377 MET cc_start: 0.9089 (ttp) cc_final: 0.8842 (ttp) REVERT: G 254 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.7705 (mtmm) REVERT: G 301 MET cc_start: 0.9096 (mmp) cc_final: 0.8843 (mmp) REVERT: C 36 MET cc_start: 0.8566 (ptm) cc_final: 0.8359 (ptm) REVERT: C 50 ASN cc_start: 0.9132 (t0) cc_final: 0.8706 (t0) REVERT: C 127 ASP cc_start: 0.8646 (m-30) cc_final: 0.8124 (m-30) REVERT: C 154 MET cc_start: 0.9152 (mmm) cc_final: 0.8799 (mmm) REVERT: C 168 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 196 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: C 211 ASP cc_start: 0.9136 (m-30) cc_final: 0.8658 (m-30) REVERT: C 254 GLU cc_start: 0.8605 (mp0) cc_final: 0.7929 (mp0) REVERT: D 71 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7215 (pp20) REVERT: D 75 MET cc_start: 0.8946 (mmt) cc_final: 0.8731 (mmt) REVERT: D 200 GLU cc_start: 0.8503 (pm20) cc_final: 0.8171 (pm20) REVERT: D 254 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8451 (mtpp) REVERT: D 259 MET cc_start: 0.8749 (mmm) cc_final: 0.8426 (mmm) REVERT: D 284 ARG cc_start: 0.8613 (ptp-170) cc_final: 0.8280 (ptm160) REVERT: D 323 MET cc_start: 0.8991 (ptp) cc_final: 0.8643 (ptp) REVERT: D 332 MET cc_start: 0.9247 (mmp) cc_final: 0.8683 (mmm) REVERT: L 361 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8755 (p) REVERT: L 367 ASP cc_start: 0.7652 (t70) cc_final: 0.7106 (t0) REVERT: I 33 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8792 (p) REVERT: I 37 HIS cc_start: 0.8020 (m-70) cc_final: 0.7624 (m-70) REVERT: I 127 GLU cc_start: 0.8072 (mp0) cc_final: 0.7822 (mm-30) REVERT: I 145 THR cc_start: 0.8991 (m) cc_final: 0.8723 (p) REVERT: I 200 GLU cc_start: 0.8087 (pt0) cc_final: 0.7778 (pt0) REVERT: I 213 CYS cc_start: 0.9090 (m) cc_final: 0.8637 (m) REVERT: I 254 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8240 (mtmt) REVERT: I 373 MET cc_start: 0.8795 (ptp) cc_final: 0.8420 (mtm) REVERT: I 422 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 50 ASN cc_start: 0.8972 (t0) cc_final: 0.8606 (t0) REVERT: A 127 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: A 172 TYR cc_start: 0.8851 (t80) cc_final: 0.8340 (t80) REVERT: A 196 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: A 313 MET cc_start: 0.8938 (mtm) cc_final: 0.8738 (mtm) REVERT: A 392 ASP cc_start: 0.8508 (m-30) cc_final: 0.8090 (m-30) REVERT: A 396 ASP cc_start: 0.8456 (m-30) cc_final: 0.8253 (m-30) REVERT: B 161 TYR cc_start: 0.8976 (m-80) cc_final: 0.8770 (m-80) REVERT: B 176 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8883 (mtpt) REVERT: M 98 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6859 (mtmm) REVERT: K 36 MET cc_start: 0.8853 (ptm) cc_final: 0.8461 (ttp) REVERT: K 122 ILE cc_start: 0.9401 (mt) cc_final: 0.9113 (mp) REVERT: K 125 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9077 (mm) REVERT: K 154 MET cc_start: 0.9067 (mmm) cc_final: 0.8796 (mmp) REVERT: K 269 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8464 (pp) REVERT: K 302 MET cc_start: 0.8892 (mtt) cc_final: 0.8381 (mtt) REVERT: K 390 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8406 (ttp-110) REVERT: K 434 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7925 (pt0) REVERT: H 71 GLU cc_start: 0.7257 (pp20) cc_final: 0.6705 (pp20) REVERT: H 149 MET cc_start: 0.8496 (tpt) cc_final: 0.8268 (tpt) REVERT: H 386 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8480 (pp20) REVERT: H 389 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8777 (ptpt) REVERT: H 422 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7935 (tm-30) REVERT: H 425 MET cc_start: 0.8552 (ttm) cc_final: 0.8289 (ttm) outliers start: 120 outliers final: 72 residues processed: 590 average time/residue: 0.2694 time to fit residues: 265.3829 Evaluate side-chains 546 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 458 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 252 LEU 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 71 GLU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 177 VAL 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 417 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 302 MET Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 389 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 289 optimal weight: 1.9990 chunk 260 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 323 optimal weight: 0.0970 chunk 261 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 421 optimal weight: 3.9990 chunk 223 optimal weight: 0.0870 chunk 298 optimal weight: 9.9990 chunk 460 optimal weight: 5.9990 chunk 428 optimal weight: 5.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 256 GLN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS L 226 ASN I 337 ASN A 285 GLN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074431 restraints weight = 78410.020| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.74 r_work: 0.3031 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 44010 Z= 0.142 Angle : 0.514 7.790 59764 Z= 0.265 Chirality : 0.042 0.151 6528 Planarity : 0.004 0.053 7776 Dihedral : 10.388 163.577 6048 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.64 % Allowed : 13.00 % Favored : 84.36 % 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: 1.25 (0.11), residues: 5388 helix: 1.90 (0.10), residues: 2554 sheet: 0.60 (0.18), residues: 828 loop : -0.45 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.012 0.001 TYR C 24 PHE 0.017 0.001 PHE M 115 TRP 0.012 0.001 TRP J 21 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00317 (44010) covalent geometry : angle 0.51449 (59764) hydrogen bonds : bond 0.04451 ( 2158) hydrogen bonds : angle 4.51095 ( 6246) *********************** 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 622 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 500 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8463 (m-30) REVERT: E 154 MET cc_start: 0.9072 (mmm) cc_final: 0.8834 (mmp) REVERT: E 279 GLU cc_start: 0.8171 (mp0) cc_final: 0.7761 (pm20) REVERT: F 50 ASN cc_start: 0.8702 (p0) cc_final: 0.8420 (p0) REVERT: F 71 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7104 (pp20) REVERT: F 75 MET cc_start: 0.8790 (mmt) cc_final: 0.8562 (mmt) REVERT: F 118 VAL cc_start: 0.9450 (t) cc_final: 0.9209 (p) REVERT: F 149 MET cc_start: 0.9416 (mmm) cc_final: 0.9196 (mmm) REVERT: F 269 MET cc_start: 0.8986 (mtm) cc_final: 0.8613 (mtp) REVERT: F 323 MET cc_start: 0.9069 (ptp) cc_final: 0.8778 (ptp) REVERT: N 98 LYS cc_start: 0.7050 (mtmm) cc_final: 0.6728 (mtmm) REVERT: N 113 LYS cc_start: 0.7133 (mmtm) cc_final: 0.6824 (mmtm) REVERT: J 90 GLU cc_start: 0.8006 (mp0) cc_final: 0.7696 (mp0) REVERT: J 221 ARG cc_start: 0.8703 (ptp90) cc_final: 0.8395 (ptp90) REVERT: J 363 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9135 (t) REVERT: J 377 MET cc_start: 0.9107 (ttp) cc_final: 0.8834 (ttp) REVERT: G 200 GLU cc_start: 0.8430 (pt0) cc_final: 0.8123 (pt0) REVERT: G 254 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.7729 (mtmm) REVERT: C 127 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: C 154 MET cc_start: 0.9112 (mmm) cc_final: 0.8763 (mmm) REVERT: C 168 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7856 (mt-10) REVERT: C 196 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: C 211 ASP cc_start: 0.9155 (m-30) cc_final: 0.8707 (m-30) REVERT: C 254 GLU cc_start: 0.8602 (mp0) cc_final: 0.7890 (mp0) REVERT: D 75 MET cc_start: 0.9063 (mmt) cc_final: 0.8863 (mmt) REVERT: D 240 THR cc_start: 0.9479 (t) cc_final: 0.8934 (m) REVERT: D 254 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8415 (mtpp) REVERT: D 259 MET cc_start: 0.8617 (mmm) cc_final: 0.8132 (mmm) REVERT: D 284 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.8314 (ptm160) REVERT: D 323 MET cc_start: 0.8985 (ptp) cc_final: 0.8704 (ptp) REVERT: D 413 MET cc_start: 0.8882 (mtp) cc_final: 0.8480 (mtp) REVERT: L 361 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8808 (p) REVERT: L 367 ASP cc_start: 0.7777 (t70) cc_final: 0.7179 (t0) REVERT: I 33 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8867 (p) REVERT: I 37 HIS cc_start: 0.8027 (m-70) cc_final: 0.7621 (m-70) REVERT: I 127 GLU cc_start: 0.8047 (mp0) cc_final: 0.7784 (mm-30) REVERT: I 145 THR cc_start: 0.8855 (m) cc_final: 0.8634 (p) REVERT: I 200 GLU cc_start: 0.7970 (pt0) cc_final: 0.7650 (pt0) REVERT: I 213 CYS cc_start: 0.9129 (m) cc_final: 0.8640 (m) REVERT: I 337 ASN cc_start: 0.8614 (m110) cc_final: 0.8399 (p0) REVERT: I 373 MET cc_start: 0.8783 (ptp) cc_final: 0.8401 (mtm) REVERT: I 422 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8227 (tm-30) REVERT: A 127 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8277 (m-30) REVERT: A 129 CYS cc_start: 0.8275 (m) cc_final: 0.7949 (m) REVERT: A 172 TYR cc_start: 0.8902 (t80) cc_final: 0.8473 (t80) REVERT: A 196 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: A 254 GLU cc_start: 0.8553 (mp0) cc_final: 0.8287 (mp0) REVERT: A 382 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9108 (p) REVERT: A 434 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 176 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8911 (mtpt) REVERT: M 20 MET cc_start: 0.4878 (tpp) cc_final: 0.4662 (tpp) REVERT: M 98 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6913 (mtmm) REVERT: K 36 MET cc_start: 0.8865 (ptm) cc_final: 0.8653 (ttp) REVERT: K 122 ILE cc_start: 0.9418 (mt) cc_final: 0.9127 (mp) REVERT: K 125 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9083 (mm) REVERT: K 127 ASP cc_start: 0.8661 (m-30) cc_final: 0.8352 (m-30) REVERT: K 154 MET cc_start: 0.9062 (mmm) cc_final: 0.8768 (mmp) REVERT: K 302 MET cc_start: 0.8944 (mtt) cc_final: 0.8420 (mtt) REVERT: H 71 GLU cc_start: 0.7405 (pp20) cc_final: 0.6815 (pp20) REVERT: H 193 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8808 (mm-40) REVERT: H 301 MET cc_start: 0.9013 (mmp) cc_final: 0.8755 (mmp) REVERT: H 422 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8066 (tm-30) REVERT: H 425 MET cc_start: 0.8542 (ttm) cc_final: 0.8284 (ttm) outliers start: 122 outliers final: 82 residues processed: 590 average time/residue: 0.2679 time to fit residues: 264.2080 Evaluate side-chains 552 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 456 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 127 ASP 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 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 177 VAL 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 314 THR Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 302 MET Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 285 GLN Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 387 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 68 optimal weight: 3.9990 chunk 480 optimal weight: 7.9990 chunk 395 optimal weight: 8.9990 chunk 528 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 chunk 383 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 366 optimal weight: 6.9990 chunk 443 optimal weight: 20.0000 chunk 478 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 GLN G 107 HIS C 50 ASN C 226 ASN C 256 GLN L 293 ASN I 336 GLN A 8 HIS A 256 GLN M 104 ASN K 285 GLN H 107 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.070942 restraints weight = 80091.010| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.76 r_work: 0.2965 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 44010 Z= 0.277 Angle : 0.607 7.452 59764 Z= 0.314 Chirality : 0.045 0.158 6528 Planarity : 0.004 0.055 7776 Dihedral : 10.323 162.076 6045 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.72 % Allowed : 13.80 % Favored : 83.48 % 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: 0.94 (0.11), residues: 5388 helix: 1.67 (0.10), residues: 2560 sheet: 0.47 (0.18), residues: 798 loop : -0.65 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 339 TYR 0.016 0.001 TYR B 161 PHE 0.018 0.002 PHE A 395 TRP 0.011 0.002 TRP J 21 HIS 0.007 0.001 HIS J 266 Details of bonding type rmsd covalent geometry : bond 0.00639 (44010) covalent geometry : angle 0.60714 (59764) hydrogen bonds : bond 0.05340 ( 2158) hydrogen bonds : angle 4.74667 ( 6246) *********************** 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 578 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 452 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8798 (m-30) cc_final: 0.8465 (m-30) REVERT: F 75 MET cc_start: 0.8787 (mmt) cc_final: 0.8450 (mmt) REVERT: F 118 VAL cc_start: 0.9475 (t) cc_final: 0.9230 (p) REVERT: N 85 MET cc_start: 0.3592 (mmm) cc_final: 0.3310 (mmm) REVERT: N 98 LYS cc_start: 0.7140 (mtmm) cc_final: 0.6815 (mtmm) REVERT: N 113 LYS cc_start: 0.7279 (mmtm) cc_final: 0.6979 (mmtm) REVERT: J 363 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9071 (t) REVERT: J 377 MET cc_start: 0.9149 (ttp) cc_final: 0.8908 (ttp) REVERT: G 200 GLU cc_start: 0.8495 (pt0) cc_final: 0.8230 (pt0) REVERT: G 254 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.7782 (mtmm) REVERT: G 337 ASN cc_start: 0.9414 (OUTLIER) cc_final: 0.8881 (p0) REVERT: G 422 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 24 TYR cc_start: 0.9210 (m-80) cc_final: 0.8719 (m-80) REVERT: C 127 ASP cc_start: 0.8683 (m-30) cc_final: 0.8149 (m-30) REVERT: C 154 MET cc_start: 0.9087 (mmm) cc_final: 0.8779 (mmm) REVERT: C 168 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7761 (mt-10) REVERT: C 211 ASP cc_start: 0.9138 (m-30) cc_final: 0.8711 (m-30) REVERT: C 254 GLU cc_start: 0.8654 (mp0) cc_final: 0.8119 (mp0) REVERT: D 75 MET cc_start: 0.9004 (mmt) cc_final: 0.8751 (mmt) REVERT: D 254 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8649 (mtpp) REVERT: D 259 MET cc_start: 0.8653 (mmm) cc_final: 0.8190 (mmm) REVERT: D 284 ARG cc_start: 0.8731 (ptp-170) cc_final: 0.8362 (ptm160) REVERT: D 323 MET cc_start: 0.9049 (ptp) cc_final: 0.8799 (ptp) REVERT: D 413 MET cc_start: 0.9009 (mtp) cc_final: 0.8608 (mtp) REVERT: L 361 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8827 (p) REVERT: L 367 ASP cc_start: 0.7923 (t70) cc_final: 0.7300 (t0) REVERT: I 37 HIS cc_start: 0.8054 (m-70) cc_final: 0.7821 (m-70) REVERT: I 127 GLU cc_start: 0.7940 (mp0) cc_final: 0.7728 (mm-30) REVERT: I 145 THR cc_start: 0.8894 (m) cc_final: 0.8622 (p) REVERT: I 200 GLU cc_start: 0.8133 (pt0) cc_final: 0.7933 (pt0) REVERT: I 213 CYS cc_start: 0.9325 (m) cc_final: 0.8882 (m) REVERT: I 337 ASN cc_start: 0.8653 (m110) cc_final: 0.8340 (m110) REVERT: I 373 MET cc_start: 0.8943 (ptp) cc_final: 0.8390 (ptp) REVERT: I 422 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8347 (tm-30) REVERT: A 36 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8315 (ptm) REVERT: A 127 ASP cc_start: 0.8609 (m-30) cc_final: 0.8269 (m-30) REVERT: A 172 TYR cc_start: 0.9058 (t80) cc_final: 0.8618 (t80) REVERT: A 196 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: A 434 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 337 ASN cc_start: 0.8694 (p0) cc_final: 0.8477 (p0) REVERT: M 85 MET cc_start: 0.4253 (tpp) cc_final: 0.3633 (mmm) REVERT: M 98 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6979 (mtmm) REVERT: K 122 ILE cc_start: 0.9436 (mt) cc_final: 0.9165 (mp) REVERT: K 154 MET cc_start: 0.9018 (mmm) cc_final: 0.8668 (mmt) REVERT: K 377 MET cc_start: 0.9083 (ttp) cc_final: 0.8829 (tmm) REVERT: H 71 GLU cc_start: 0.7387 (pp20) cc_final: 0.6804 (pp20) REVERT: H 149 MET cc_start: 0.8685 (tpt) cc_final: 0.8325 (tpt) REVERT: H 422 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7925 (tm-30) outliers start: 126 outliers final: 91 residues processed: 547 average time/residue: 0.2504 time to fit residues: 230.6864 Evaluate side-chains 525 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 426 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 252 LEU 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 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 177 VAL 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 417 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 302 MET Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 302 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 317 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 519 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 340 optimal weight: 2.9990 chunk 399 optimal weight: 1.9990 chunk 372 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 360 optimal weight: 3.9990 chunk 353 optimal weight: 6.9990 chunk 342 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN L 128 GLN I 433 GLN B 139 HIS ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074087 restraints weight = 78428.520| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.75 r_work: 0.3025 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44010 Z= 0.123 Angle : 0.521 9.094 59764 Z= 0.267 Chirality : 0.041 0.147 6528 Planarity : 0.004 0.054 7776 Dihedral : 10.018 159.570 6045 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.14 % Allowed : 14.73 % Favored : 83.13 % 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: 1.12 (0.11), residues: 5388 helix: 1.83 (0.10), residues: 2560 sheet: 0.52 (0.18), residues: 798 loop : -0.54 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 369 TYR 0.017 0.001 TYR B 161 PHE 0.024 0.001 PHE N 47 TRP 0.012 0.001 TRP E 21 HIS 0.006 0.001 HIS L 309 Details of bonding type rmsd covalent geometry : bond 0.00271 (44010) covalent geometry : angle 0.52094 (59764) hydrogen bonds : bond 0.04281 ( 2158) hydrogen bonds : angle 4.49689 ( 6246) *********************** 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 582 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 483 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 TYR cc_start: 0.9164 (m-10) cc_final: 0.8785 (m-10) REVERT: E 36 MET cc_start: 0.8643 (ptp) cc_final: 0.7822 (ptm) REVERT: E 127 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8400 (m-30) REVERT: E 154 MET cc_start: 0.9242 (mmp) cc_final: 0.9038 (mmp) REVERT: E 279 GLU cc_start: 0.8115 (mp0) cc_final: 0.7687 (pm20) REVERT: F 71 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7154 (pp20) REVERT: F 75 MET cc_start: 0.8720 (mmt) cc_final: 0.8457 (mmt) REVERT: F 118 VAL cc_start: 0.9440 (t) cc_final: 0.9202 (p) REVERT: F 149 MET cc_start: 0.9380 (mmm) cc_final: 0.9158 (mmm) REVERT: F 269 MET cc_start: 0.8953 (mtm) cc_final: 0.8624 (mtp) REVERT: F 349 ASN cc_start: 0.8477 (p0) cc_final: 0.8134 (p0) REVERT: N 85 MET cc_start: 0.3893 (mmm) cc_final: 0.3627 (mmm) REVERT: N 98 LYS cc_start: 0.7221 (mtmm) cc_final: 0.6906 (mtmm) REVERT: N 113 LYS cc_start: 0.7257 (mmtm) cc_final: 0.6941 (mmtm) REVERT: N 115 PHE cc_start: 0.4259 (t80) cc_final: 0.3973 (t80) REVERT: J 90 GLU cc_start: 0.7873 (mp0) cc_final: 0.7473 (mp0) REVERT: J 363 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9149 (t) REVERT: G 200 GLU cc_start: 0.8388 (pt0) cc_final: 0.8137 (pt0) REVERT: G 254 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.7711 (mtmm) REVERT: G 422 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 24 TYR cc_start: 0.9177 (m-10) cc_final: 0.8696 (m-80) REVERT: C 127 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: C 154 MET cc_start: 0.9070 (mmm) cc_final: 0.8743 (mmm) REVERT: C 168 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7858 (mt-10) REVERT: C 211 ASP cc_start: 0.9143 (m-30) cc_final: 0.8709 (m-30) REVERT: C 254 GLU cc_start: 0.8638 (mp0) cc_final: 0.7919 (mp0) REVERT: C 377 MET cc_start: 0.9107 (ttp) cc_final: 0.8643 (tmm) REVERT: D 71 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7129 (pp20) REVERT: D 75 MET cc_start: 0.9066 (mmt) cc_final: 0.8846 (mmt) REVERT: D 200 GLU cc_start: 0.8414 (pm20) cc_final: 0.8149 (pm20) REVERT: D 254 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8395 (mtpp) REVERT: D 259 MET cc_start: 0.8593 (mmm) cc_final: 0.8183 (mmm) REVERT: D 284 ARG cc_start: 0.8682 (ptp-170) cc_final: 0.8333 (ptm160) REVERT: D 413 MET cc_start: 0.8938 (mtp) cc_final: 0.8724 (mtp) REVERT: L 361 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8833 (p) REVERT: L 367 ASP cc_start: 0.7836 (t70) cc_final: 0.7199 (t0) REVERT: I 33 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9005 (p) REVERT: I 37 HIS cc_start: 0.8090 (m-70) cc_final: 0.7844 (m-70) REVERT: I 193 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8777 (mp10) REVERT: I 200 GLU cc_start: 0.8027 (pt0) cc_final: 0.7720 (pt0) REVERT: I 213 CYS cc_start: 0.9235 (m) cc_final: 0.8723 (m) REVERT: I 337 ASN cc_start: 0.8663 (m110) cc_final: 0.8410 (p0) REVERT: I 373 MET cc_start: 0.8917 (ptp) cc_final: 0.8350 (ptp) REVERT: I 422 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8229 (tm-30) REVERT: A 127 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: A 172 TYR cc_start: 0.9042 (t80) cc_final: 0.8571 (t80) REVERT: A 279 GLU cc_start: 0.8381 (mp0) cc_final: 0.7787 (pm20) REVERT: A 377 MET cc_start: 0.9150 (ttp) cc_final: 0.8844 (tmm) REVERT: A 396 ASP cc_start: 0.8538 (m-30) cc_final: 0.8262 (m-30) REVERT: A 434 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8068 (tm-30) REVERT: B 176 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8886 (mtpt) REVERT: B 337 ASN cc_start: 0.8628 (p0) cc_final: 0.8242 (p0) REVERT: M 85 MET cc_start: 0.3872 (tpp) cc_final: 0.3467 (mmm) REVERT: M 98 LYS cc_start: 0.7309 (ttmm) cc_final: 0.7095 (mtmm) REVERT: K 154 MET cc_start: 0.8986 (mmm) cc_final: 0.8733 (mmp) REVERT: K 269 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8523 (pp) REVERT: K 377 MET cc_start: 0.9031 (ttp) cc_final: 0.8742 (tmm) REVERT: K 430 LYS cc_start: 0.8972 (pttp) cc_final: 0.8690 (mttm) REVERT: K 434 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8342 (tt0) REVERT: H 71 GLU cc_start: 0.7457 (pp20) cc_final: 0.6856 (pp20) REVERT: H 145 THR cc_start: 0.8753 (m) cc_final: 0.8521 (p) REVERT: H 149 MET cc_start: 0.8653 (tpt) cc_final: 0.8359 (tpt) REVERT: H 193 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8844 (mm-40) REVERT: H 422 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8075 (tm-30) outliers start: 99 outliers final: 69 residues processed: 556 average time/residue: 0.2611 time to fit residues: 242.7559 Evaluate side-chains 523 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 443 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 127 ASP 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 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 177 VAL 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 417 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 241 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 216 optimal weight: 1.9990 chunk 381 optimal weight: 0.6980 chunk 254 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 410 optimal weight: 6.9990 chunk 532 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 chunk 301 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 308 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 GLN E 226 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074382 restraints weight = 78762.052| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.76 r_work: 0.3035 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44010 Z= 0.125 Angle : 0.524 14.330 59764 Z= 0.265 Chirality : 0.041 0.151 6528 Planarity : 0.004 0.054 7776 Dihedral : 9.788 155.251 6045 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.12 % Allowed : 15.01 % Favored : 82.87 % 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: 1.18 (0.11), residues: 5388 helix: 1.88 (0.10), residues: 2560 sheet: 0.46 (0.18), residues: 804 loop : -0.48 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 369 TYR 0.016 0.001 TYR B 161 PHE 0.022 0.001 PHE M 115 TRP 0.013 0.001 TRP E 21 HIS 0.005 0.001 HIS L 309 Details of bonding type rmsd covalent geometry : bond 0.00277 (44010) covalent geometry : angle 0.52437 (59764) hydrogen bonds : bond 0.04160 ( 2158) hydrogen bonds : angle 4.47467 ( 6246) *********************** 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 568 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 470 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 TYR cc_start: 0.9160 (m-10) cc_final: 0.8775 (m-10) REVERT: E 36 MET cc_start: 0.8608 (ptp) cc_final: 0.7861 (ptm) REVERT: E 127 ASP cc_start: 0.8730 (m-30) cc_final: 0.8382 (m-30) REVERT: E 279 GLU cc_start: 0.8006 (mp0) cc_final: 0.7642 (pm20) REVERT: E 377 MET cc_start: 0.8723 (ttp) cc_final: 0.7933 (tmm) REVERT: F 71 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7156 (pp20) REVERT: F 75 MET cc_start: 0.8707 (mmt) cc_final: 0.8430 (mmt) REVERT: F 118 VAL cc_start: 0.9436 (t) cc_final: 0.9201 (p) REVERT: F 149 MET cc_start: 0.9350 (mmm) cc_final: 0.9100 (mmm) REVERT: F 259 MET cc_start: 0.9122 (mmm) cc_final: 0.8916 (mmm) REVERT: F 349 ASN cc_start: 0.8501 (p0) cc_final: 0.8142 (p0) REVERT: N 85 MET cc_start: 0.3503 (mmm) cc_final: 0.3181 (mmm) REVERT: N 98 LYS cc_start: 0.7242 (mtmm) cc_final: 0.6923 (mtmm) REVERT: N 113 LYS cc_start: 0.7245 (mmtm) cc_final: 0.6931 (mmtm) REVERT: J 90 GLU cc_start: 0.7919 (mp0) cc_final: 0.7672 (mp0) REVERT: J 154 MET cc_start: 0.9142 (mmm) cc_final: 0.8569 (mmp) REVERT: J 168 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8208 (mt-10) REVERT: G 127 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8031 (mm-30) REVERT: G 193 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8749 (mm-40) REVERT: G 200 GLU cc_start: 0.8420 (pt0) cc_final: 0.8178 (pt0) REVERT: G 254 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.7716 (mtmm) REVERT: C 24 TYR cc_start: 0.9101 (m-10) cc_final: 0.8705 (m-80) REVERT: C 127 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: C 154 MET cc_start: 0.9061 (mmm) cc_final: 0.8737 (mmm) REVERT: C 168 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7884 (mt-10) REVERT: C 211 ASP cc_start: 0.9154 (m-30) cc_final: 0.8580 (m-30) REVERT: C 254 GLU cc_start: 0.8625 (mp0) cc_final: 0.7944 (mp0) REVERT: D 71 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7081 (pp20) REVERT: D 75 MET cc_start: 0.9073 (mmt) cc_final: 0.8855 (mmt) REVERT: D 254 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8541 (mtpp) REVERT: D 259 MET cc_start: 0.8556 (mmm) cc_final: 0.8148 (mmm) REVERT: D 284 ARG cc_start: 0.8646 (ptp-170) cc_final: 0.8306 (ptm160) REVERT: D 413 MET cc_start: 0.8916 (mtp) cc_final: 0.8703 (mtp) REVERT: L 361 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8846 (p) REVERT: L 367 ASP cc_start: 0.7798 (t70) cc_final: 0.7262 (t0) REVERT: L 430 LYS cc_start: 0.9047 (pttp) cc_final: 0.8812 (mmmt) REVERT: I 33 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9023 (p) REVERT: I 193 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8719 (mp10) REVERT: I 200 GLU cc_start: 0.8101 (pt0) cc_final: 0.7807 (pt0) REVERT: I 209 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8706 (mt) REVERT: I 213 CYS cc_start: 0.9224 (m) cc_final: 0.8727 (m) REVERT: I 337 ASN cc_start: 0.8640 (m110) cc_final: 0.8379 (p0) REVERT: I 373 MET cc_start: 0.8902 (ptp) cc_final: 0.8368 (ptp) REVERT: I 422 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8125 (tm-30) REVERT: A 127 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: A 172 TYR cc_start: 0.8949 (t80) cc_final: 0.8481 (t80) REVERT: A 279 GLU cc_start: 0.8375 (mp0) cc_final: 0.7729 (pm20) REVERT: A 396 ASP cc_start: 0.8562 (m-30) cc_final: 0.8278 (m-30) REVERT: A 434 GLU cc_start: 0.8265 (tm-30) cc_final: 0.8006 (tm-30) REVERT: B 176 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8876 (mtpt) REVERT: B 337 ASN cc_start: 0.8576 (p0) cc_final: 0.8208 (p0) REVERT: M 98 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6998 (mtmm) REVERT: K 125 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8942 (mm) REVERT: K 154 MET cc_start: 0.8989 (mmm) cc_final: 0.8739 (mmp) REVERT: K 269 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8566 (pp) REVERT: K 430 LYS cc_start: 0.8963 (pttp) cc_final: 0.8695 (mttm) REVERT: H 71 GLU cc_start: 0.7448 (pp20) cc_final: 0.6862 (pp20) REVERT: H 193 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8842 (mm-40) REVERT: H 422 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8072 (tm-30) outliers start: 98 outliers final: 72 residues processed: 543 average time/residue: 0.2683 time to fit residues: 244.2976 Evaluate side-chains 531 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 447 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 252 LEU 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 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 177 VAL 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 J residue 26 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 367 ASP 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 254 LYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 241 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 381 optimal weight: 0.7980 chunk 490 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 394 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 299 optimal weight: 0.9990 chunk 321 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN D 107 HIS D 331 GLN I 107 HIS A 226 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.075644 restraints weight = 78152.961| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.77 r_work: 0.3058 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 44010 Z= 0.108 Angle : 0.518 13.396 59764 Z= 0.260 Chirality : 0.041 0.147 6528 Planarity : 0.004 0.055 7776 Dihedral : 9.566 150.208 6045 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.90 % Allowed : 15.33 % Favored : 82.76 % 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 (0.11), residues: 5388 helix: 1.95 (0.10), residues: 2560 sheet: 0.61 (0.18), residues: 798 loop : -0.41 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 369 TYR 0.016 0.001 TYR B 161 PHE 0.022 0.001 PHE M 115 TRP 0.014 0.001 TRP D 346 HIS 0.005 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00234 (44010) covalent geometry : angle 0.51848 (59764) hydrogen bonds : bond 0.03881 ( 2158) hydrogen bonds : angle 4.40457 ( 6246) *********************** 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 574 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 486 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 TYR cc_start: 0.9149 (m-10) cc_final: 0.8818 (m-10) REVERT: E 36 MET cc_start: 0.8564 (ptp) cc_final: 0.7997 (ptm) REVERT: E 127 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: E 279 GLU cc_start: 0.7981 (mp0) cc_final: 0.7667 (pm20) REVERT: F 71 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7135 (pp20) REVERT: F 75 MET cc_start: 0.8685 (mmt) cc_final: 0.8418 (mmt) REVERT: F 118 VAL cc_start: 0.9422 (t) cc_final: 0.9202 (p) REVERT: F 149 MET cc_start: 0.9330 (mmm) cc_final: 0.9108 (mmm) REVERT: F 259 MET cc_start: 0.9037 (mmm) cc_final: 0.8821 (mmm) REVERT: F 346 TRP cc_start: 0.9024 (p-90) cc_final: 0.8675 (p-90) REVERT: F 349 ASN cc_start: 0.8453 (p0) cc_final: 0.8058 (p0) REVERT: N 85 MET cc_start: 0.3438 (mmm) cc_final: 0.2989 (mmm) REVERT: N 98 LYS cc_start: 0.7282 (mtmm) cc_final: 0.7009 (mtmm) REVERT: N 113 LYS cc_start: 0.7248 (mmtm) cc_final: 0.6930 (mmtm) REVERT: J 154 MET cc_start: 0.9124 (mmm) cc_final: 0.8534 (mmp) REVERT: G 127 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7975 (mm-30) REVERT: G 193 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8839 (mm-40) REVERT: G 200 GLU cc_start: 0.8382 (pt0) cc_final: 0.8149 (pt0) REVERT: G 369 ARG cc_start: 0.8077 (tpp80) cc_final: 0.7834 (mtp85) REVERT: C 24 TYR cc_start: 0.9014 (m-10) cc_final: 0.8674 (m-80) REVERT: C 127 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: C 154 MET cc_start: 0.9043 (mmm) cc_final: 0.8724 (mmm) REVERT: C 168 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7814 (mt-10) REVERT: C 211 ASP cc_start: 0.9168 (m-30) cc_final: 0.8587 (m-30) REVERT: C 254 GLU cc_start: 0.8639 (mp0) cc_final: 0.7980 (mp0) REVERT: C 377 MET cc_start: 0.9087 (ttp) cc_final: 0.8749 (tmm) REVERT: D 71 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6949 (pp20) REVERT: D 254 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8479 (mtpp) REVERT: D 259 MET cc_start: 0.8555 (mmm) cc_final: 0.8016 (mmm) REVERT: D 269 MET cc_start: 0.8787 (ptp) cc_final: 0.8503 (ptm) REVERT: D 284 ARG cc_start: 0.8670 (ptp-170) cc_final: 0.8349 (ptm160) REVERT: D 347 ILE cc_start: 0.8956 (mm) cc_final: 0.8724 (tt) REVERT: D 413 MET cc_start: 0.8889 (mtp) cc_final: 0.8685 (mtp) REVERT: L 24 TYR cc_start: 0.9197 (m-80) cc_final: 0.8869 (m-80) REVERT: L 430 LYS cc_start: 0.9016 (pttp) cc_final: 0.8785 (mmmt) REVERT: I 33 THR cc_start: 0.9381 (m) cc_final: 0.9036 (p) REVERT: I 69 ASP cc_start: 0.8672 (t0) cc_final: 0.8471 (t0) REVERT: I 193 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8714 (mp10) REVERT: I 200 GLU cc_start: 0.8176 (pt0) cc_final: 0.7893 (pt0) REVERT: I 209 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8702 (mt) REVERT: I 213 CYS cc_start: 0.9233 (m) cc_final: 0.8766 (m) REVERT: I 337 ASN cc_start: 0.8632 (m110) cc_final: 0.8358 (p0) REVERT: I 373 MET cc_start: 0.8883 (ptp) cc_final: 0.8347 (ptp) REVERT: I 422 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8068 (tm-30) REVERT: A 127 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: A 172 TYR cc_start: 0.8955 (t80) cc_final: 0.8503 (t80) REVERT: A 279 GLU cc_start: 0.8315 (mp0) cc_final: 0.7701 (pm20) REVERT: B 176 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8890 (mtpt) REVERT: B 337 ASN cc_start: 0.8538 (p0) cc_final: 0.8192 (p0) REVERT: M 85 MET cc_start: 0.3137 (mmm) cc_final: 0.2804 (mmm) REVERT: M 98 LYS cc_start: 0.7324 (ttmm) cc_final: 0.7002 (mtmm) REVERT: K 24 TYR cc_start: 0.9126 (m-10) cc_final: 0.8860 (m-10) REVERT: K 125 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8817 (mm) REVERT: K 127 ASP cc_start: 0.8642 (m-30) cc_final: 0.8367 (m-30) REVERT: K 154 MET cc_start: 0.8991 (mmm) cc_final: 0.8755 (mmp) REVERT: K 269 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8558 (pp) REVERT: K 377 MET cc_start: 0.8834 (ttp) cc_final: 0.8555 (tmm) REVERT: K 430 LYS cc_start: 0.8950 (pttp) cc_final: 0.8570 (mtpp) REVERT: K 434 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8262 (pt0) REVERT: H 71 GLU cc_start: 0.7489 (pp20) cc_final: 0.6894 (pp20) REVERT: H 193 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8888 (mp10) REVERT: H 422 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8058 (tm-30) outliers start: 88 outliers final: 59 residues processed: 554 average time/residue: 0.2618 time to fit residues: 243.0534 Evaluate side-chains 537 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 469 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 252 LEU 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 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 177 VAL 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 47 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 367 ASP 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 337 ASN Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 18 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 416 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 432 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 255 optimal weight: 0.4980 chunk 429 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 509 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.074798 restraints weight = 78860.680| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.76 r_work: 0.3043 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 44010 Z= 0.133 Angle : 0.538 13.909 59764 Z= 0.268 Chirality : 0.041 0.150 6528 Planarity : 0.004 0.056 7776 Dihedral : 9.447 147.593 6040 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.69 % Allowed : 15.90 % Favored : 82.42 % 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: 1.88 (0.10), residues: 2596 sheet: 0.58 (0.18), residues: 798 loop : -0.46 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 369 TYR 0.015 0.001 TYR B 161 PHE 0.021 0.001 PHE M 115 TRP 0.012 0.001 TRP D 346 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00302 (44010) covalent geometry : angle 0.53818 (59764) hydrogen bonds : bond 0.04034 ( 2158) hydrogen bonds : angle 4.43011 ( 6246) ********************** 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 552 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 474 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 TYR cc_start: 0.9168 (m-10) cc_final: 0.8819 (m-10) REVERT: E 36 MET cc_start: 0.8574 (ptp) cc_final: 0.8007 (ptm) REVERT: E 127 ASP cc_start: 0.8732 (m-30) cc_final: 0.8367 (m-30) REVERT: E 279 GLU cc_start: 0.7985 (mp0) cc_final: 0.7680 (pm20) REVERT: E 377 MET cc_start: 0.8690 (ttp) cc_final: 0.8292 (tmm) REVERT: F 71 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7070 (pp20) REVERT: F 75 MET cc_start: 0.8705 (mmt) cc_final: 0.8418 (mmt) REVERT: F 118 VAL cc_start: 0.9439 (t) cc_final: 0.9201 (p) REVERT: F 127 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8174 (mm-30) REVERT: F 149 MET cc_start: 0.9235 (mmm) cc_final: 0.8995 (mmm) REVERT: F 259 MET cc_start: 0.9020 (mmm) cc_final: 0.8819 (mmm) REVERT: F 346 TRP cc_start: 0.9058 (p-90) cc_final: 0.8589 (p-90) REVERT: F 349 ASN cc_start: 0.8461 (p0) cc_final: 0.8107 (p0) REVERT: N 85 MET cc_start: 0.3355 (mmm) cc_final: 0.2905 (mmm) REVERT: N 98 LYS cc_start: 0.7165 (mtmm) cc_final: 0.6868 (mtmm) REVERT: N 113 LYS cc_start: 0.7248 (mmtm) cc_final: 0.6932 (mmtm) REVERT: J 6 SER cc_start: 0.9198 (m) cc_final: 0.8895 (p) REVERT: J 90 GLU cc_start: 0.7889 (mp0) cc_final: 0.7465 (mp0) REVERT: J 154 MET cc_start: 0.9032 (mmm) cc_final: 0.8500 (mmp) REVERT: G 127 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7977 (mm-30) REVERT: G 193 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8854 (mm-40) REVERT: G 200 GLU cc_start: 0.8346 (pt0) cc_final: 0.8122 (pt0) REVERT: G 369 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7839 (mtp85) REVERT: G 428 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8580 (tt) REVERT: C 24 TYR cc_start: 0.9072 (m-10) cc_final: 0.8781 (m-80) REVERT: C 127 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: C 154 MET cc_start: 0.9044 (mmm) cc_final: 0.8747 (mmm) REVERT: C 168 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7832 (mt-10) REVERT: C 211 ASP cc_start: 0.9167 (m-30) cc_final: 0.8594 (m-30) REVERT: C 254 GLU cc_start: 0.8638 (mp0) cc_final: 0.7981 (mp0) REVERT: C 377 MET cc_start: 0.9160 (ttp) cc_final: 0.8716 (tmm) REVERT: D 71 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7057 (pp20) REVERT: D 200 GLU cc_start: 0.8325 (pm20) cc_final: 0.7992 (pm20) REVERT: D 254 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8456 (mtpp) REVERT: D 259 MET cc_start: 0.8555 (mmm) cc_final: 0.8033 (mmm) REVERT: D 269 MET cc_start: 0.8772 (ptp) cc_final: 0.8562 (ptm) REVERT: D 284 ARG cc_start: 0.8685 (ptp-170) cc_final: 0.8310 (ptm160) REVERT: D 347 ILE cc_start: 0.8944 (mm) cc_final: 0.8727 (tt) REVERT: D 413 MET cc_start: 0.8924 (mtp) cc_final: 0.8705 (mtp) REVERT: L 24 TYR cc_start: 0.9157 (m-80) cc_final: 0.8883 (m-80) REVERT: L 430 LYS cc_start: 0.9033 (pttp) cc_final: 0.8777 (mmmt) REVERT: I 33 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9052 (p) REVERT: I 193 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8718 (mp10) REVERT: I 200 GLU cc_start: 0.8203 (pt0) cc_final: 0.7927 (pt0) REVERT: I 209 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8751 (mt) REVERT: I 213 CYS cc_start: 0.9271 (m) cc_final: 0.8850 (m) REVERT: I 337 ASN cc_start: 0.8663 (m110) cc_final: 0.8362 (p0) REVERT: I 422 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 127 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: A 172 TYR cc_start: 0.8948 (t80) cc_final: 0.8486 (t80) REVERT: A 279 GLU cc_start: 0.8288 (mp0) cc_final: 0.7695 (pm20) REVERT: B 176 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8909 (mtpt) REVERT: M 85 MET cc_start: 0.3177 (mmm) cc_final: 0.2871 (mmt) REVERT: K 24 TYR cc_start: 0.9187 (m-10) cc_final: 0.8929 (m-10) REVERT: K 125 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8787 (mm) REVERT: K 127 ASP cc_start: 0.8629 (m-30) cc_final: 0.8365 (m-30) REVERT: K 154 MET cc_start: 0.8976 (mmm) cc_final: 0.8741 (mmp) REVERT: K 205 ASP cc_start: 0.8136 (t0) cc_final: 0.7848 (t0) REVERT: K 269 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8559 (pp) REVERT: K 430 LYS cc_start: 0.8959 (pttp) cc_final: 0.8579 (mtpp) REVERT: K 434 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8274 (pt0) REVERT: H 71 GLU cc_start: 0.7514 (pp20) cc_final: 0.6938 (pp20) REVERT: H 193 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8878 (mp10) REVERT: H 422 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8066 (tm-30) outliers start: 78 outliers final: 64 residues processed: 532 average time/residue: 0.2730 time to fit residues: 242.8219 Evaluate side-chains 535 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 461 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 334 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 274 optimal weight: 0.1980 chunk 299 optimal weight: 0.8980 chunk 436 optimal weight: 3.9990 chunk 425 optimal weight: 0.7980 chunk 448 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN L 216 ASN I 167 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076748 restraints weight = 78313.730| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.72 r_work: 0.3080 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 44010 Z= 0.102 Angle : 0.527 13.881 59764 Z= 0.263 Chirality : 0.041 0.187 6528 Planarity : 0.004 0.055 7776 Dihedral : 9.241 142.200 6040 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.82 % Allowed : 15.87 % Favored : 82.31 % 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: 1.32 (0.12), residues: 5388 helix: 1.93 (0.10), residues: 2596 sheet: 0.61 (0.18), residues: 798 loop : -0.39 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 369 TYR 0.016 0.001 TYR B 161 PHE 0.026 0.001 PHE F 94 TRP 0.014 0.001 TRP D 346 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00220 (44010) covalent geometry : angle 0.52717 (59764) hydrogen bonds : bond 0.03693 ( 2158) hydrogen bonds : angle 4.35755 ( 6246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9466.35 seconds wall clock time: 163 minutes 52.97 seconds (9832.97 seconds total)