Starting phenix.real_space_refine on Sun Mar 24 17:36:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jar_6351/03_2024/3jar_6351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jar_6351/03_2024/3jar_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jar_6351/03_2024/3jar_6351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jar_6351/03_2024/3jar_6351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jar_6351/03_2024/3jar_6351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jar_6351/03_2024/3jar_6351.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "E ARG 64": "NH1" <-> "NH2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 279": "OE1" <-> "OE2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 13": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K GLU 279": "OE1" <-> "OE2" Residue "K ARG 390": "NH1" <-> "NH2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 21.50, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 17.06 Conformation dependent library (CDL) restraints added in 7.0 seconds 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: 4.70 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: 19.09 Time building geometry restraints manager: 17.96 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: 96.20 - 104.43: 909 104.43 - 112.66: 20677 112.66 - 120.89: 23031 120.89 - 129.12: 14823 129.12 - 137.35: 324 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 22.410 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: 0.000 Extract box with map and model: 23.490 Check model and map are aligned: 0.620 Set scattering table: 0.400 Process input model: 110.350 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.430 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: 0.020 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.200 ------------------------------------------------------------------------------- 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= 0.549 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP C 21 HIS 0.010 0.002 HIS L 8 PHE 0.026 0.003 PHE K 296 TYR 0.019 0.002 TYR D 224 ARG 0.023 0.001 ARG F 2 *********************** 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 fitting. rotamer outliers: 84 poor density : 915 time to evaluate : 4.817 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: 0.5822 (tpp) REVERT: N 48 MET cc_start: 0.6852 (tpt) cc_final: 0.6458 (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: 0.4891 (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: 0.8199 (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: 0.6899 (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: 0.8192 (mmm) REVERT: I 338 LYS cc_start: 0.9145 (ptpt) cc_final: 0.8937 (ptpp) REVERT: I 373 MET cc_start: 0.7882 (ptp) cc_final: 0.7657 (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: 0.8077 (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: 0.5746 time to fit residues: 906.4835 Evaluate side-chains 537 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 511 time to evaluate : 4.793 ------------------------------------------------------------------------------- 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 452 optimal weight: 0.9980 chunk 406 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 420 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 486 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS F 228 ASN F 336 GLN F 337 ASN F 349 ASN J 28 HIS ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 337 ASN G 339 ASN G 349 ASN C 28 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** 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 D 349 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** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 336 GLN B 337 ASN B 349 ASN M 118 ASN K 28 HIS K 88 HIS K 186 ASN K 197 HIS ** 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: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44010 Z= 0.204 Angle : 0.594 8.548 59764 Z= 0.313 Chirality : 0.042 0.149 6528 Planarity : 0.005 0.067 7776 Dihedral : 11.830 173.098 6075 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.47 % Allowed : 10.94 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.11), residues: 5388 helix: 2.15 (0.10), residues: 2480 sheet: 0.60 (0.18), residues: 792 loop : -0.52 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 346 HIS 0.008 0.001 HIS C 309 PHE 0.022 0.001 PHE M 114 TYR 0.023 0.001 TYR B 161 ARG 0.005 0.000 ARG F 322 *********************** 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 730 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 616 time to evaluate : 4.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8538 (m-30) cc_final: 0.8051 (m-30) REVERT: E 154 MET cc_start: 0.8596 (mmm) cc_final: 0.8329 (mmp) REVERT: F 284 ARG cc_start: 0.8469 (ptp-170) cc_final: 0.8196 (ptm-80) REVERT: N 20 MET cc_start: 0.5887 (ttp) cc_final: 0.5599 (tpp) REVERT: N 48 MET cc_start: 0.7034 (tpt) cc_final: 0.6724 (mmt) REVERT: N 113 LYS cc_start: 0.7369 (mmtm) cc_final: 0.7024 (mmtm) REVERT: J 221 ARG cc_start: 0.8665 (ptp90) cc_final: 0.8431 (mtm-85) REVERT: C 50 ASN cc_start: 0.8671 (t0) cc_final: 0.8383 (t0) REVERT: C 154 MET cc_start: 0.8493 (mmm) cc_final: 0.8106 (mmm) REVERT: C 168 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6839 (mt-10) REVERT: C 172 TYR cc_start: 0.8501 (t80) cc_final: 0.7929 (t80) REVERT: C 308 ARG cc_start: 0.8911 (mtm-85) cc_final: 0.8705 (mmm-85) REVERT: C 313 MET cc_start: 0.7920 (mtm) cc_final: 0.7516 (mtm) REVERT: D 254 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8668 (mtpp) REVERT: D 284 ARG cc_start: 0.8390 (ptp-170) cc_final: 0.8184 (ptm-80) REVERT: D 332 MET cc_start: 0.8562 (mmp) cc_final: 0.8347 (mmm) REVERT: D 373 MET cc_start: 0.8148 (ptp) cc_final: 0.7947 (mtm) REVERT: D 416 MET cc_start: 0.8428 (mmm) cc_final: 0.8198 (mmm) REVERT: L 172 TYR cc_start: 0.8598 (t80) cc_final: 0.8366 (t80) REVERT: L 361 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8848 (p) REVERT: I 254 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8548 (mtmt) REVERT: I 373 MET cc_start: 0.7913 (ptp) cc_final: 0.7433 (mtm) REVERT: A 50 ASN cc_start: 0.8386 (t0) cc_final: 0.8182 (t0) REVERT: A 172 TYR cc_start: 0.8593 (t80) cc_final: 0.7804 (t80) REVERT: A 279 GLU cc_start: 0.7950 (mp0) cc_final: 0.7669 (pm20) REVERT: B 254 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8668 (mtpt) REVERT: M 48 MET cc_start: 0.7142 (tpt) cc_final: 0.6810 (mmt) REVERT: K 154 MET cc_start: 0.8373 (mmm) cc_final: 0.8063 (mmt) REVERT: K 302 MET cc_start: 0.8219 (mtt) cc_final: 0.7875 (mtt) REVERT: K 390 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8180 (ttp-170) REVERT: H 384 ILE cc_start: 0.8994 (pp) cc_final: 0.8674 (mt) REVERT: H 389 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8784 (ptpt) outliers start: 114 outliers final: 59 residues processed: 702 average time/residue: 0.5497 time to fit residues: 631.8536 Evaluate side-chains 529 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 465 time to evaluate : 4.513 ------------------------------------------------------------------------------- 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 E residue 367 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 90 ASP 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 349 ASN Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 116 ASP 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 J residue 349 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 220 THR 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 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 C residue 367 ASP Chi-restraints excluded: chain C residue 417 GLU 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 349 ASN 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 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 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 147 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 254 LYS 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 270 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 331 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 487 optimal weight: 6.9990 chunk 526 optimal weight: 4.9990 chunk 434 optimal weight: 2.9990 chunk 483 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN J 8 HIS ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS C 35 GLN C 88 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN 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** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN K 8 HIS K 128 GLN K 206 ASN K 256 GLN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 44010 Z= 0.295 Angle : 0.571 8.025 59764 Z= 0.298 Chirality : 0.043 0.203 6528 Planarity : 0.004 0.058 7776 Dihedral : 11.176 173.118 6055 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.22 % Allowed : 12.31 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 5388 helix: 2.00 (0.10), residues: 2500 sheet: 0.61 (0.18), residues: 828 loop : -0.50 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 21 HIS 0.006 0.001 HIS K 266 PHE 0.018 0.002 PHE J 296 TYR 0.014 0.001 TYR N 32 ARG 0.004 0.000 ARG G 369 *********************** 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 647 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 498 time to evaluate : 5.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8553 (m-30) cc_final: 0.8344 (m-30) REVERT: E 154 MET cc_start: 0.8375 (mmm) cc_final: 0.8170 (mmp) REVERT: F 75 MET cc_start: 0.7989 (mmt) cc_final: 0.7706 (mmt) REVERT: F 284 ARG cc_start: 0.8474 (ptp-170) cc_final: 0.8184 (ptm-80) REVERT: N 20 MET cc_start: 0.5768 (OUTLIER) cc_final: 0.5551 (tpp) REVERT: N 48 MET cc_start: 0.7101 (tpt) cc_final: 0.6733 (mmt) REVERT: N 98 LYS cc_start: 0.7852 (mtmm) cc_final: 0.7512 (mtmm) REVERT: N 113 LYS cc_start: 0.7335 (mmtm) cc_final: 0.7023 (mmtm) REVERT: N 115 PHE cc_start: 0.5106 (t80) cc_final: 0.4537 (t80) REVERT: C 50 ASN cc_start: 0.8911 (t0) cc_final: 0.8489 (t0) REVERT: C 154 MET cc_start: 0.8408 (mmm) cc_final: 0.7999 (mmm) REVERT: C 168 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6778 (mt-10) REVERT: C 211 ASP cc_start: 0.8063 (m-30) cc_final: 0.7853 (m-30) REVERT: D 332 MET cc_start: 0.8722 (mmp) cc_final: 0.8327 (mmm) REVERT: L 361 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8853 (p) REVERT: I 133 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8869 (tp-100) REVERT: I 254 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8699 (mtmt) REVERT: I 259 MET cc_start: 0.8131 (mmm) cc_final: 0.7895 (mmm) REVERT: I 373 MET cc_start: 0.7992 (ptp) cc_final: 0.7505 (mtm) REVERT: A 127 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: A 172 TYR cc_start: 0.8505 (t80) cc_final: 0.8266 (t80) REVERT: B 254 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8658 (mtpt) REVERT: M 48 MET cc_start: 0.7026 (tpt) cc_final: 0.6696 (mmt) REVERT: K 154 MET cc_start: 0.8396 (mmm) cc_final: 0.8081 (mmt) REVERT: K 302 MET cc_start: 0.8380 (mtt) cc_final: 0.8015 (mtt) REVERT: H 389 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8815 (ptpt) outliers start: 149 outliers final: 98 residues processed: 615 average time/residue: 0.5337 time to fit residues: 544.0804 Evaluate side-chains 544 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 439 time to evaluate : 4.647 ------------------------------------------------------------------------------- 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 223 THR Chi-restraints excluded: chain E residue 250 VAL 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 E residue 367 ASP Chi-restraints excluded: chain E residue 390 ARG Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 170 SER 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 305 CYS 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 20 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 116 ASP 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 250 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 337 ASN 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 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 295 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 367 ASP 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 314 THR 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 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 302 MET Chi-restraints excluded: chain L residue 361 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain I residue 133 GLN 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 398 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 147 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 349 ASN 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 367 ASP 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 179 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 327 optimal weight: 1.9990 chunk 489 optimal weight: 7.9990 chunk 518 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 chunk 463 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 256 GLN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN L 35 GLN L 101 ASN I 133 GLN A 101 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN B 349 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3205 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= 0.200 Angle : 0.526 8.534 59764 Z= 0.271 Chirality : 0.041 0.166 6528 Planarity : 0.004 0.053 7776 Dihedral : 10.747 168.342 6052 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.09 % Allowed : 13.02 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.11), residues: 5388 helix: 1.98 (0.10), residues: 2512 sheet: 0.63 (0.18), residues: 834 loop : -0.47 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.006 0.001 HIS A 309 PHE 0.020 0.001 PHE M 115 TYR 0.019 0.001 TYR B 161 ARG 0.011 0.000 ARG K 390 *********************** 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 640 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 497 time to evaluate : 5.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: F 75 MET cc_start: 0.7954 (mmt) cc_final: 0.7714 (mmt) REVERT: F 284 ARG cc_start: 0.8417 (ptp-170) cc_final: 0.8078 (ttm170) REVERT: N 20 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5782 (tpp) REVERT: N 48 MET cc_start: 0.7030 (tpt) cc_final: 0.6608 (mmt) REVERT: N 98 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7454 (mtmm) REVERT: N 113 LYS cc_start: 0.7413 (mmtm) cc_final: 0.7148 (mmtm) REVERT: N 115 PHE cc_start: 0.5028 (t80) cc_final: 0.4671 (t80) REVERT: J 221 ARG cc_start: 0.8722 (ptp90) cc_final: 0.8454 (ptp90) REVERT: J 363 VAL cc_start: 0.9457 (OUTLIER) cc_final: 0.9105 (t) REVERT: C 50 ASN cc_start: 0.8945 (t0) cc_final: 0.8632 (t0) REVERT: C 154 MET cc_start: 0.8348 (mmm) cc_final: 0.7935 (mmm) REVERT: C 168 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6743 (mt-10) REVERT: C 211 ASP cc_start: 0.8032 (m-30) cc_final: 0.7814 (m-30) REVERT: D 332 MET cc_start: 0.8698 (mmp) cc_final: 0.8244 (mmm) REVERT: L 361 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8862 (p) REVERT: L 363 VAL cc_start: 0.9475 (OUTLIER) cc_final: 0.9227 (m) REVERT: I 254 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8601 (mtmt) REVERT: I 373 MET cc_start: 0.8044 (ptp) cc_final: 0.7534 (mtm) REVERT: A 127 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: A 172 TYR cc_start: 0.8623 (t80) cc_final: 0.8342 (t80) REVERT: B 254 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8630 (mtpt) REVERT: M 48 MET cc_start: 0.6938 (tpt) cc_final: 0.6684 (mmt) REVERT: M 50 MET cc_start: 0.4307 (mtp) cc_final: 0.3934 (mmm) REVERT: K 154 MET cc_start: 0.8347 (mmm) cc_final: 0.8096 (mmp) REVERT: K 302 MET cc_start: 0.8345 (mtt) cc_final: 0.8014 (mtt) REVERT: H 110 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: H 389 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8815 (ptpt) outliers start: 143 outliers final: 98 residues processed: 598 average time/residue: 0.5285 time to fit residues: 526.6314 Evaluate side-chains 567 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 459 time to evaluate : 5.540 ------------------------------------------------------------------------------- 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 223 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 252 LEU 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 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 20 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 125 LEU 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 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 387 LEU 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 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 345 ASP Chi-restraints excluded: chain C residue 367 ASP 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 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 223 THR 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 L residue 363 VAL Chi-restraints excluded: chain I residue 41 ASP 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 147 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 345 ASP 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 71 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 166 MET 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 254 LYS Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 349 ASN 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 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 367 ASP Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 241 CYS 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 431 optimal weight: 6.9990 chunk 294 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 385 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 442 optimal weight: 20.0000 chunk 358 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 465 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN ** I 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN B 349 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 44010 Z= 0.251 Angle : 0.530 7.577 59764 Z= 0.272 Chirality : 0.042 0.173 6528 Planarity : 0.004 0.052 7776 Dihedral : 10.384 165.796 6047 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.24 % Allowed : 13.19 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.11), residues: 5388 helix: 1.86 (0.10), residues: 2554 sheet: 0.69 (0.18), residues: 828 loop : -0.57 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 21 HIS 0.006 0.001 HIS K 309 PHE 0.021 0.001 PHE M 115 TYR 0.014 0.001 TYR B 161 ARG 0.005 0.000 ARG B 369 *********************** 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 627 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 477 time to evaluate : 5.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: F 75 MET cc_start: 0.7986 (mmt) cc_final: 0.7751 (mmt) REVERT: F 149 MET cc_start: 0.8588 (mmm) cc_final: 0.8367 (mmm) REVERT: F 284 ARG cc_start: 0.8404 (ptp-170) cc_final: 0.8067 (ttm170) REVERT: N 20 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5764 (tpp) REVERT: N 48 MET cc_start: 0.6868 (tpt) cc_final: 0.6457 (mmt) REVERT: N 98 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7360 (mtmm) REVERT: N 113 LYS cc_start: 0.7425 (mmtm) cc_final: 0.7153 (mmtm) REVERT: N 115 PHE cc_start: 0.5022 (t80) cc_final: 0.4717 (t80) REVERT: J 221 ARG cc_start: 0.8719 (ptp90) cc_final: 0.8475 (ptp90) REVERT: J 363 VAL cc_start: 0.9456 (OUTLIER) cc_final: 0.9090 (t) REVERT: J 413 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8096 (ttm) REVERT: C 24 TYR cc_start: 0.8882 (m-10) cc_final: 0.8504 (m-80) REVERT: C 127 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: C 154 MET cc_start: 0.8420 (mmm) cc_final: 0.8018 (mmm) REVERT: C 168 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6703 (mt-10) REVERT: C 211 ASP cc_start: 0.8043 (m-30) cc_final: 0.7828 (m-30) REVERT: L 363 VAL cc_start: 0.9413 (OUTLIER) cc_final: 0.9171 (m) REVERT: I 254 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8564 (mtmt) REVERT: I 373 MET cc_start: 0.8036 (ptp) cc_final: 0.7484 (mtm) REVERT: A 172 TYR cc_start: 0.8695 (t80) cc_final: 0.8388 (t80) REVERT: B 254 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8569 (mtpt) REVERT: M 20 MET cc_start: 0.5247 (tpp) cc_final: 0.4990 (tpp) REVERT: M 48 MET cc_start: 0.6937 (tpt) cc_final: 0.6695 (mmt) REVERT: M 50 MET cc_start: 0.4222 (mtp) cc_final: 0.3745 (mmm) REVERT: K 154 MET cc_start: 0.8235 (mmm) cc_final: 0.7967 (mmp) REVERT: K 302 MET cc_start: 0.8391 (mtt) cc_final: 0.8043 (mtt) REVERT: H 110 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8171 (mm-30) outliers start: 150 outliers final: 99 residues processed: 587 average time/residue: 0.5391 time to fit residues: 527.8447 Evaluate side-chains 554 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 446 time to evaluate : 4.870 ------------------------------------------------------------------------------- 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 223 THR 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 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 20 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 116 ASP 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 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 J residue 413 MET Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 179 THR 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 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 33 THR 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 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 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 302 MET Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain I residue 145 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 33 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 166 MET 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 254 LYS Chi-restraints excluded: chain B residue 290 GLU 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 165 SER 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 285 GLN Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP 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 97 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 241 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 7.9990 chunk 466 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 127 optimal weight: 0.5980 chunk 518 optimal weight: 5.9990 chunk 430 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN F 349 ASN N 104 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN C 226 ASN C 256 GLN L 293 ASN ** I 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 44010 Z= 0.283 Angle : 0.544 7.563 59764 Z= 0.279 Chirality : 0.042 0.150 6528 Planarity : 0.004 0.052 7776 Dihedral : 10.052 162.816 6045 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.07 % Allowed : 13.60 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.11), residues: 5388 helix: 1.79 (0.10), residues: 2560 sheet: 0.60 (0.18), residues: 828 loop : -0.62 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 21 HIS 0.007 0.001 HIS A 309 PHE 0.023 0.001 PHE M 115 TYR 0.012 0.001 TYR B 161 ARG 0.008 0.000 ARG K 390 *********************** 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 605 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 463 time to evaluate : 4.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8327 (m-30) REVERT: E 398 MET cc_start: 0.8276 (mtp) cc_final: 0.7912 (mtp) REVERT: F 75 MET cc_start: 0.8012 (mmt) cc_final: 0.7738 (mmt) REVERT: N 20 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.5694 (tpp) REVERT: N 48 MET cc_start: 0.7066 (tpt) cc_final: 0.6665 (mmt) REVERT: N 85 MET cc_start: 0.4673 (mmm) cc_final: 0.4312 (mmm) REVERT: N 98 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7488 (mtmm) REVERT: N 113 LYS cc_start: 0.7429 (mmtm) cc_final: 0.7142 (mmtm) REVERT: J 363 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9093 (t) REVERT: C 24 TYR cc_start: 0.8874 (m-10) cc_final: 0.8587 (m-80) REVERT: C 127 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: C 154 MET cc_start: 0.8323 (mmm) cc_final: 0.7914 (mmm) REVERT: C 168 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6641 (mt-10) REVERT: C 211 ASP cc_start: 0.8048 (m-30) cc_final: 0.7829 (m-30) REVERT: D 75 MET cc_start: 0.8431 (mmt) cc_final: 0.8033 (mmt) REVERT: L 363 VAL cc_start: 0.9397 (OUTLIER) cc_final: 0.9194 (m) REVERT: I 254 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8742 (mtpt) REVERT: I 373 MET cc_start: 0.8100 (ptp) cc_final: 0.7835 (ptp) REVERT: A 127 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: A 172 TYR cc_start: 0.8758 (t80) cc_final: 0.8467 (t80) REVERT: B 254 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8590 (mtpt) REVERT: M 48 MET cc_start: 0.6974 (tpt) cc_final: 0.6738 (mmt) REVERT: M 50 MET cc_start: 0.4338 (mtp) cc_final: 0.3750 (mmm) REVERT: M 85 MET cc_start: 0.4964 (tpp) cc_final: 0.4226 (mmm) REVERT: K 154 MET cc_start: 0.8270 (mmm) cc_final: 0.8051 (mmp) REVERT: K 302 MET cc_start: 0.8414 (mtt) cc_final: 0.8056 (mtt) REVERT: H 110 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8232 (mm-30) outliers start: 142 outliers final: 101 residues processed: 561 average time/residue: 0.5110 time to fit residues: 481.9214 Evaluate side-chains 536 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 426 time to evaluate : 4.753 ------------------------------------------------------------------------------- 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 223 THR 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 344 VAL 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 314 THR Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 116 ASP 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 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 145 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 179 THR 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 C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 33 THR 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 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 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 363 VAL Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain I residue 145 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 A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 ASN 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 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 166 MET 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 254 LYS Chi-restraints excluded: chain B residue 290 GLU 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 165 SER 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 367 ASP 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 165 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 241 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 295 optimal weight: 6.9990 chunk 378 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 436 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 516 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 chunk 314 optimal weight: 0.0870 chunk 238 optimal weight: 1.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN C 50 ASN D 433 GLN I 206 ASN ** I 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 433 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN B 139 HIS B 349 ASN B 433 GLN M 104 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 GLN H 133 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 44010 Z= 0.152 Angle : 0.509 11.464 59764 Z= 0.258 Chirality : 0.041 0.154 6528 Planarity : 0.004 0.051 7776 Dihedral : 9.755 158.131 6045 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.51 % Allowed : 14.77 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.11), residues: 5388 helix: 1.91 (0.10), residues: 2560 sheet: 0.62 (0.18), residues: 828 loop : -0.50 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 21 HIS 0.007 0.001 HIS A 309 PHE 0.025 0.001 PHE N 47 TYR 0.014 0.001 TYR B 161 ARG 0.005 0.000 ARG B 369 *********************** 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 605 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 489 time to evaluate : 4.795 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: 0.8574 (OUTLIER) cc_final: 0.8304 (m-30) REVERT: F 75 MET cc_start: 0.7884 (mmt) cc_final: 0.7653 (mmt) REVERT: F 284 ARG cc_start: 0.8357 (ptp-170) cc_final: 0.8014 (ttm170) REVERT: N 20 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5631 (tpp) REVERT: N 48 MET cc_start: 0.7079 (tpt) cc_final: 0.6692 (mmt) REVERT: N 85 MET cc_start: 0.4236 (mmm) cc_final: 0.3909 (mmm) REVERT: N 98 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7519 (mtmm) REVERT: N 113 LYS cc_start: 0.7447 (mmtm) cc_final: 0.7158 (mmtm) REVERT: J 363 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9110 (t) REVERT: G 428 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8839 (tt) REVERT: C 127 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: C 154 MET cc_start: 0.8303 (mmm) cc_final: 0.7900 (mmm) REVERT: C 168 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6716 (mt-10) REVERT: C 211 ASP cc_start: 0.8003 (m-30) cc_final: 0.7778 (m-30) REVERT: L 363 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.9090 (m) REVERT: I 254 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8669 (mtmt) REVERT: I 373 MET cc_start: 0.8057 (ptp) cc_final: 0.7798 (ptp) REVERT: A 127 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: A 172 TYR cc_start: 0.8750 (t80) cc_final: 0.8437 (t80) REVERT: B 254 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8611 (mtpt) REVERT: M 20 MET cc_start: 0.5289 (tpp) cc_final: 0.5008 (tpp) REVERT: M 48 MET cc_start: 0.6935 (tpt) cc_final: 0.6699 (mmt) REVERT: M 50 MET cc_start: 0.4198 (mtp) cc_final: 0.3732 (mmm) REVERT: K 154 MET cc_start: 0.8224 (mmm) cc_final: 0.8021 (mmp) REVERT: K 302 MET cc_start: 0.8321 (mtt) cc_final: 0.8025 (mtt) REVERT: H 110 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8250 (mm-30) outliers start: 116 outliers final: 84 residues processed: 571 average time/residue: 0.5293 time to fit residues: 503.8437 Evaluate side-chains 552 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 458 time to evaluate : 4.935 ------------------------------------------------------------------------------- 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 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 N residue 20 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 116 ASP 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 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 41 ASP 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 428 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 SER 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 C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP 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 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 223 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 335 ILE Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain I residue 145 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 A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP 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 204 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 166 MET 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 254 LYS Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 349 ASN 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 165 SER Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP 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 179 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 319 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 328 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 406 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** I 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44010 Z= 0.191 Angle : 0.522 12.882 59764 Z= 0.263 Chirality : 0.041 0.149 6528 Planarity : 0.004 0.051 7776 Dihedral : 9.540 154.738 6045 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.47 % Allowed : 14.94 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.11), residues: 5388 helix: 1.90 (0.10), residues: 2560 sheet: 0.61 (0.18), residues: 828 loop : -0.47 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 346 HIS 0.006 0.001 HIS K 309 PHE 0.021 0.001 PHE G 94 TYR 0.016 0.001 TYR C 24 ARG 0.006 0.000 ARG B 369 *********************** 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 582 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 468 time to evaluate : 4.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: F 149 MET cc_start: 0.8620 (mmm) cc_final: 0.8400 (tpp) REVERT: F 284 ARG cc_start: 0.8369 (ptp-170) cc_final: 0.8045 (ttm170) REVERT: N 20 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.5337 (tpp) REVERT: N 48 MET cc_start: 0.6980 (tpt) cc_final: 0.6606 (mmt) REVERT: N 98 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7467 (mtmm) REVERT: N 113 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7144 (mmtm) REVERT: J 363 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9114 (t) REVERT: G 428 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8938 (tt) REVERT: C 127 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: C 154 MET cc_start: 0.8325 (mmm) cc_final: 0.7942 (mmm) REVERT: C 168 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6754 (mt-10) REVERT: C 211 ASP cc_start: 0.8011 (m-30) cc_final: 0.7789 (m-30) REVERT: D 413 MET cc_start: 0.8570 (mtp) cc_final: 0.8321 (mtp) REVERT: L 363 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9078 (m) REVERT: I 373 MET cc_start: 0.8080 (ptp) cc_final: 0.7818 (ptp) REVERT: A 127 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: A 172 TYR cc_start: 0.8770 (t80) cc_final: 0.8464 (t80) REVERT: A 377 MET cc_start: 0.8338 (tmm) cc_final: 0.7717 (tmm) REVERT: B 254 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8699 (mtpt) REVERT: M 48 MET cc_start: 0.6946 (tpt) cc_final: 0.6716 (mmt) REVERT: M 50 MET cc_start: 0.4230 (mtp) cc_final: 0.3735 (mmm) REVERT: M 85 MET cc_start: 0.4043 (mmm) cc_final: 0.3518 (mmm) REVERT: K 125 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9080 (mm) REVERT: K 302 MET cc_start: 0.8401 (mtt) cc_final: 0.8068 (mtt) REVERT: H 110 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8133 (mm-30) outliers start: 114 outliers final: 91 residues processed: 546 average time/residue: 0.5216 time to fit residues: 476.6715 Evaluate side-chains 548 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 447 time to evaluate : 4.376 ------------------------------------------------------------------------------- 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 275 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 344 VAL 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 313 LEU Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 116 ASP 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 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 41 ASP 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 428 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 SER 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 C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP 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 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 223 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 302 MET Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP 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 204 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 166 MET 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 254 LYS 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 165 SER 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 363 VAL Chi-restraints excluded: chain K residue 367 ASP 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 179 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 469 optimal weight: 5.9990 chunk 494 optimal weight: 0.9980 chunk 451 optimal weight: 10.0000 chunk 481 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 378 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 435 optimal weight: 0.9980 chunk 455 optimal weight: 3.9990 chunk 479 optimal weight: 10.0000 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN D 206 ASN ** I 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 44010 Z= 0.200 Angle : 0.530 11.255 59764 Z= 0.266 Chirality : 0.041 0.149 6528 Planarity : 0.004 0.051 7776 Dihedral : 9.379 152.930 6045 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.47 % Allowed : 15.29 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 5388 helix: 1.90 (0.10), residues: 2560 sheet: 0.63 (0.18), residues: 828 loop : -0.46 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 346 HIS 0.006 0.001 HIS E 61 PHE 0.019 0.001 PHE G 94 TYR 0.012 0.001 TYR B 161 ARG 0.006 0.000 ARG B 369 *********************** 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 575 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 461 time to evaluate : 4.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: F 149 MET cc_start: 0.8620 (mmm) cc_final: 0.8382 (mmm) REVERT: F 284 ARG cc_start: 0.8346 (ptp-170) cc_final: 0.8016 (ttm170) REVERT: N 20 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.5320 (tpp) REVERT: N 48 MET cc_start: 0.7009 (tpt) cc_final: 0.6642 (mmt) REVERT: N 85 MET cc_start: 0.3834 (mmm) cc_final: 0.3352 (mmm) REVERT: N 98 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7466 (mtmm) REVERT: N 113 LYS cc_start: 0.7372 (mmtm) cc_final: 0.7070 (mmtm) REVERT: J 363 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9123 (t) REVERT: G 428 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8931 (tt) REVERT: C 127 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: C 154 MET cc_start: 0.8317 (mmm) cc_final: 0.7929 (mmm) REVERT: C 168 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6681 (mt-10) REVERT: C 211 ASP cc_start: 0.8003 (m-30) cc_final: 0.7782 (m-30) REVERT: D 413 MET cc_start: 0.8572 (mtp) cc_final: 0.8330 (mtp) REVERT: L 363 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.9073 (m) REVERT: I 373 MET cc_start: 0.8095 (ptp) cc_final: 0.7841 (ptp) REVERT: A 127 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: A 172 TYR cc_start: 0.8780 (t80) cc_final: 0.8473 (t80) REVERT: A 279 GLU cc_start: 0.8176 (mp0) cc_final: 0.7957 (pm20) REVERT: A 377 MET cc_start: 0.8362 (tmm) cc_final: 0.7744 (tmm) REVERT: B 254 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8706 (mtpt) REVERT: M 48 MET cc_start: 0.6947 (tpt) cc_final: 0.6723 (mmt) REVERT: M 50 MET cc_start: 0.4228 (mtp) cc_final: 0.3735 (mmm) REVERT: M 85 MET cc_start: 0.3688 (mmm) cc_final: 0.3212 (mmm) REVERT: K 125 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8985 (mm) REVERT: K 154 MET cc_start: 0.8342 (mmp) cc_final: 0.8097 (mmt) REVERT: K 302 MET cc_start: 0.8399 (mtt) cc_final: 0.8057 (mtt) outliers start: 114 outliers final: 92 residues processed: 543 average time/residue: 0.5251 time to fit residues: 479.8884 Evaluate side-chains 554 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 453 time to evaluate : 5.020 ------------------------------------------------------------------------------- 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 179 THR 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 344 VAL 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 313 LEU Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 116 ASP 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 363 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 428 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 LEU 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 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL 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 223 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 302 MET Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP 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 204 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 166 MET 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 254 LYS 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 54 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 179 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 316 optimal weight: 0.7980 chunk 509 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 353 optimal weight: 8.9990 chunk 533 optimal weight: 7.9990 chunk 491 optimal weight: 0.0010 chunk 425 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** I 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 44010 Z= 0.198 Angle : 0.529 12.128 59764 Z= 0.265 Chirality : 0.041 0.150 6528 Planarity : 0.004 0.051 7776 Dihedral : 9.209 151.870 6045 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.27 % Allowed : 15.53 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.11), residues: 5388 helix: 1.83 (0.10), residues: 2596 sheet: 0.60 (0.18), residues: 828 loop : -0.45 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP F 346 HIS 0.007 0.001 HIS A 309 PHE 0.018 0.001 PHE G 94 TYR 0.012 0.001 TYR L 172 ARG 0.006 0.000 ARG B 369 ********************** 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 572 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 467 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: F 284 ARG cc_start: 0.8334 (ptp-170) cc_final: 0.8008 (ttm170) REVERT: N 20 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5307 (tpp) REVERT: N 48 MET cc_start: 0.7009 (tpt) cc_final: 0.6642 (mmt) REVERT: N 85 MET cc_start: 0.3924 (mmm) cc_final: 0.3275 (mmm) REVERT: N 98 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7426 (mtmm) REVERT: N 113 LYS cc_start: 0.7347 (mmtm) cc_final: 0.7038 (mmtm) REVERT: J 363 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9114 (t) REVERT: G 428 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8921 (tt) REVERT: C 127 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: C 154 MET cc_start: 0.8311 (mmm) cc_final: 0.7924 (mmm) REVERT: C 168 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6678 (mt-10) REVERT: C 172 TYR cc_start: 0.8553 (t80) cc_final: 0.8338 (t80) REVERT: C 211 ASP cc_start: 0.8002 (m-30) cc_final: 0.7784 (m-30) REVERT: C 279 GLU cc_start: 0.8437 (mp0) cc_final: 0.8145 (pm20) REVERT: D 413 MET cc_start: 0.8542 (mtp) cc_final: 0.8284 (mtp) REVERT: L 363 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.9069 (m) REVERT: I 373 MET cc_start: 0.8042 (ptp) cc_final: 0.7794 (ptp) REVERT: A 127 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: A 172 TYR cc_start: 0.8771 (t80) cc_final: 0.8436 (t80) REVERT: A 377 MET cc_start: 0.8369 (tmm) cc_final: 0.8093 (tmm) REVERT: B 254 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8717 (mtpt) REVERT: M 48 MET cc_start: 0.6948 (tpt) cc_final: 0.6737 (mmt) REVERT: M 50 MET cc_start: 0.4228 (mtp) cc_final: 0.3739 (mmm) REVERT: M 85 MET cc_start: 0.3594 (mmm) cc_final: 0.3169 (mmm) REVERT: K 154 MET cc_start: 0.8371 (mmp) cc_final: 0.8122 (mmt) REVERT: K 302 MET cc_start: 0.8410 (mtt) cc_final: 0.8146 (mtt) REVERT: K 363 VAL cc_start: 0.9498 (OUTLIER) cc_final: 0.9237 (t) outliers start: 105 outliers final: 89 residues processed: 540 average time/residue: 0.5209 time to fit residues: 470.9022 Evaluate side-chains 552 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 454 time to evaluate : 4.797 ------------------------------------------------------------------------------- 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 179 THR 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 344 VAL Chi-restraints excluded: chain E residue 363 VAL 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 349 ASN Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 116 ASP 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 363 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 428 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 VAL 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 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 302 MET Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP 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 204 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 166 MET 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 254 LYS Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 179 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 337 optimal weight: 1.9990 chunk 452 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 392 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 425 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 437 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** I 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074846 restraints weight = 78891.223| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.73 r_work: 0.3042 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 44010 Z= 0.228 Angle : 0.614 59.108 59764 Z= 0.333 Chirality : 0.043 0.896 6528 Planarity : 0.004 0.073 7776 Dihedral : 9.195 151.869 6043 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.23 % Allowed : 15.81 % Favored : 81.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.11), residues: 5388 helix: 1.82 (0.10), residues: 2596 sheet: 0.60 (0.18), residues: 828 loop : -0.45 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 346 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.001 PHE N 47 TYR 0.012 0.001 TYR L 172 ARG 0.005 0.000 ARG B 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10384.43 seconds wall clock time: 188 minutes 58.81 seconds (11338.81 seconds total)