Starting phenix.real_space_refine on Sun Mar 24 07:57:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/03_2024/3jas_6353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/03_2024/3jas_6353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/03_2024/3jas_6353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/03_2024/3jas_6353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/03_2024/3jas_6353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/03_2024/3jas_6353.pdb" } resolution = 3.5 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= 0.028 sd= 0.918 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6924 2.21 5 O 7806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 64": "NH1" <-> "NH2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 386": "OE1" <-> "OE2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 71": "OE1" <-> "OE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 411": "OE1" <-> "OE2" Residue "J PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J GLU 433": "OE1" <-> "OE2" Residue "J GLU 434": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 345": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L GLU 71": "OE1" <-> "OE2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 386": "OE1" <-> "OE2" Residue "L GLU 411": "OE1" <-> "OE2" Residue "L PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L GLU 433": "OE1" <-> "OE2" Residue "L GLU 434": "OE1" <-> "OE2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 345": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 77": "OE1" <-> "OE2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 196": "OE1" <-> "OE2" Residue "K GLU 386": "OE1" <-> "OE2" Residue "K GLU 411": "OE1" <-> "OE2" Residue "K PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K GLU 433": "OE1" <-> "OE2" Residue "K GLU 434": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 183": "OE1" <-> "OE2" Residue "H GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40506 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "K" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.42, per 1000 atoms: 0.53 Number of scatterers: 40506 At special positions: 0 Unit cell: (170.28, 87.12, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 276 16.00 P 30 15.00 Mg 6 11.99 O 7806 8.00 N 6924 7.00 C 25464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 17.57 Conformation dependent library (CDL) restraints added in 7.5 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 30 sheets defined 55.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.628A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.592A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.098A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.608A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.008A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 283 removed outlier: 3.739A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.859A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.898A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.490A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.552A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.515A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.907A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 5.148A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 401 removed outlier: 3.633A pdb=" N ARG F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 436 removed outlier: 3.956A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 47 through 51 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.628A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.593A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.099A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.610A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 4.006A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 283 removed outlier: 3.737A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.860A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 removed outlier: 3.563A pdb=" N VAL J 328 " --> pdb=" O VAL J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 3.899A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.491A pdb=" N ARG G 48 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 71 through 81 removed outlier: 4.552A pdb=" N MET G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 129 removed outlier: 4.515A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.906A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 5.147A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 384 through 401 removed outlier: 3.632A pdb=" N ARG G 401 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 436 removed outlier: 3.957A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.629A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.592A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.098A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.607A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.007A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.737A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.858A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.899A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.493A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.551A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.515A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.907A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 5.148A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 401 removed outlier: 3.631A pdb=" N ARG D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.067A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 436 removed outlier: 3.957A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.630A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.592A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.101A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 206 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.609A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 4.004A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.736A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.860A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 removed outlier: 3.563A pdb=" N VAL L 328 " --> pdb=" O VAL L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 3.900A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.492A pdb=" N ARG I 48 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 71 through 81 removed outlier: 4.553A pdb=" N MET I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 109 through 129 removed outlier: 4.516A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.906A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 5.147A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG I 243 " --> pdb=" O THR I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 287 through 296 Processing helix chain 'I' and resid 297 through 301 Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 339 Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 384 through 401 removed outlier: 3.630A pdb=" N ARG I 401 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 436 removed outlier: 3.956A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.629A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.592A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.098A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.607A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.008A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.739A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.859A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.899A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.490A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.552A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.515A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.907A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 5.149A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.632A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 436 removed outlier: 3.957A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.629A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.592A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.100A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 196 through 198 No H-bonds generated for 'chain 'K' and resid 196 through 198' Processing helix chain 'K' and resid 206 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.608A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 4.005A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 283 removed outlier: 3.738A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.860A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 removed outlier: 3.563A pdb=" N VAL K 328 " --> pdb=" O VAL K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 401 removed outlier: 3.771A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 3.899A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.897A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.492A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.552A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.514A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.906A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 5.148A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG H 243 " --> pdb=" O THR H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 287 through 296 Processing helix chain 'H' and resid 297 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 401 removed outlier: 3.631A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.066A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 436 removed outlier: 3.957A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.210A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER J 165 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE J 171 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU G 137 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE G 7 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.210A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 53 through 55 Processing sheet with id= K, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER C 165 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 171 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.211A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 53 through 55 Processing sheet with id= P, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU L 3 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY L 134 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER L 165 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE L 171 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= R, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU I 137 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE I 7 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.209A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= U, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.212A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU K 3 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY K 134 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER K 165 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE K 171 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AB, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.210A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 53 through 55 2046 hydrogen bonds defined for protein. 5886 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.39 Time building geometry restraints manager: 18.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7360 1.32 - 1.45: 10850 1.45 - 1.57: 22746 1.57 - 1.69: 48 1.69 - 1.82: 432 Bond restraints: 41436 Sorted by residual: bond pdb=" C5 GTP E 501 " pdb=" C6 GTP E 501 " ideal model delta sigma weight residual 1.390 1.477 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CA PRO E 359 " pdb=" C PRO E 359 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.86e+01 bond pdb=" C5 GTP J 501 " pdb=" C6 GTP J 501 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CA PRO J 359 " pdb=" C PRO J 359 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.75e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 41431 not shown) Histogram of bond angle deviations from ideal: 95.01 - 103.40: 490 103.40 - 111.79: 16949 111.79 - 120.18: 21258 120.18 - 128.57: 17283 128.57 - 136.96: 324 Bond angle restraints: 56304 Sorted by residual: angle pdb=" N THR E 73 " pdb=" CA THR E 73 " pdb=" C THR E 73 " ideal model delta sigma weight residual 111.11 117.24 -6.13 1.20e+00 6.94e-01 2.61e+01 angle pdb=" N THR C 73 " pdb=" CA THR C 73 " pdb=" C THR C 73 " ideal model delta sigma weight residual 111.11 117.22 -6.11 1.20e+00 6.94e-01 2.59e+01 angle pdb=" N THR A 73 " pdb=" CA THR A 73 " pdb=" C THR A 73 " ideal model delta sigma weight residual 111.11 117.20 -6.09 1.20e+00 6.94e-01 2.58e+01 angle pdb=" N THR J 73 " pdb=" CA THR J 73 " pdb=" C THR J 73 " ideal model delta sigma weight residual 111.11 117.17 -6.06 1.20e+00 6.94e-01 2.55e+01 angle pdb=" N THR K 73 " pdb=" CA THR K 73 " pdb=" C THR K 73 " ideal model delta sigma weight residual 111.11 117.16 -6.05 1.20e+00 6.94e-01 2.55e+01 ... (remaining 56299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 23795 33.72 - 67.44: 757 67.44 - 101.16: 36 101.16 - 134.87: 6 134.87 - 168.59: 18 Dihedral angle restraints: 24612 sinusoidal: 9810 harmonic: 14802 Sorted by residual: dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.14 -168.59 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.34 -168.39 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.54 -168.19 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3714 0.064 - 0.127: 1671 0.127 - 0.191: 580 0.191 - 0.254: 149 0.254 - 0.318: 42 Chirality restraints: 6156 Sorted by residual: chirality pdb=" CA PHE I 83 " pdb=" N PHE I 83 " pdb=" C PHE I 83 " pdb=" CB PHE I 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA PHE F 83 " pdb=" N PHE F 83 " pdb=" C PHE F 83 " pdb=" CB PHE F 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA PHE B 83 " pdb=" N PHE B 83 " pdb=" C PHE B 83 " pdb=" CB PHE B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 6153 not shown) Planarity restraints: 7338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 288 " 0.048 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO F 289 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 288 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO G 289 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 289 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 288 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO H 289 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO H 289 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 289 " 0.041 5.00e-02 4.00e+02 ... (remaining 7335 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 51 2.46 - 3.07: 25244 3.07 - 3.68: 63912 3.68 - 4.29: 90901 4.29 - 4.90: 159585 Nonbonded interactions: 339693 Sorted by model distance: nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.846 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.857 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.857 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.884 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.926 2.170 ... (remaining 339688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 28.480 Check model and map are aligned: 0.700 Set scattering table: 0.410 Process input model: 111.290 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 41436 Z= 0.560 Angle : 1.458 9.437 56304 Z= 1.017 Chirality : 0.083 0.318 6156 Planarity : 0.006 0.074 7338 Dihedral : 16.413 168.593 15120 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 2.07 % Allowed : 8.44 % Favored : 89.49 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.11), residues: 5088 helix: 1.21 (0.10), residues: 2280 sheet: 0.70 (0.19), residues: 774 loop : -0.95 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 21 HIS 0.012 0.002 HIS C 8 PHE 0.024 0.003 PHE D 92 TYR 0.021 0.003 TYR F 224 ARG 0.025 0.001 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1009 time to evaluate : 4.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8200 (tt) REVERT: F 329 ASP cc_start: 0.7856 (m-30) cc_final: 0.7570 (m-30) REVERT: J 50 ASN cc_start: 0.7924 (t0) cc_final: 0.7701 (t0) REVERT: J 203 MET cc_start: 0.7088 (mtt) cc_final: 0.6716 (mtm) REVERT: J 424 ASP cc_start: 0.7628 (t70) cc_final: 0.7222 (t0) REVERT: G 44 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8277 (tt) REVERT: G 301 MET cc_start: 0.8499 (mmp) cc_final: 0.7966 (mmt) REVERT: G 323 MET cc_start: 0.7702 (mtp) cc_final: 0.7485 (mtm) REVERT: G 325 MET cc_start: 0.8361 (tpp) cc_final: 0.7977 (mmm) REVERT: G 356 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7661 (m) REVERT: G 373 MET cc_start: 0.7945 (ttp) cc_final: 0.7484 (ttp) REVERT: G 398 MET cc_start: 0.8161 (mtt) cc_final: 0.7926 (mtp) REVERT: G 408 TYR cc_start: 0.8598 (m-80) cc_final: 0.8225 (m-80) REVERT: G 415 GLU cc_start: 0.7980 (tt0) cc_final: 0.7528 (tm-30) REVERT: C 50 ASN cc_start: 0.7720 (t0) cc_final: 0.7503 (m-40) REVERT: C 209 ILE cc_start: 0.8959 (mt) cc_final: 0.8492 (mt) REVERT: C 425 MET cc_start: 0.8132 (tpp) cc_final: 0.7878 (mmp) REVERT: D 240 THR cc_start: 0.8869 (t) cc_final: 0.8484 (t) REVERT: D 329 ASP cc_start: 0.7993 (m-30) cc_final: 0.7518 (m-30) REVERT: D 356 CYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7472 (t) REVERT: D 373 MET cc_start: 0.7431 (ttp) cc_final: 0.7225 (ttm) REVERT: D 413 MET cc_start: 0.7629 (ttp) cc_final: 0.7182 (ttm) REVERT: L 172 TYR cc_start: 0.8422 (t80) cc_final: 0.7989 (t80) REVERT: L 391 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8421 (tt) REVERT: L 424 ASP cc_start: 0.7322 (t70) cc_final: 0.7064 (t0) REVERT: I 44 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8485 (tt) REVERT: I 214 PHE cc_start: 0.8828 (t80) cc_final: 0.8512 (t80) REVERT: I 332 MET cc_start: 0.9011 (mmp) cc_final: 0.8301 (mmm) REVERT: I 356 CYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8056 (m) REVERT: I 413 MET cc_start: 0.7889 (ttp) cc_final: 0.7420 (ttm) REVERT: B 44 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7807 (tt) REVERT: B 108 TYR cc_start: 0.7576 (m-80) cc_final: 0.7281 (m-80) REVERT: B 214 PHE cc_start: 0.7984 (t80) cc_final: 0.7777 (t80) REVERT: B 332 MET cc_start: 0.8324 (mmp) cc_final: 0.8098 (mmp) REVERT: B 356 CYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7588 (t) REVERT: B 411 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7140 (tp30) REVERT: K 50 ASN cc_start: 0.7808 (t0) cc_final: 0.7492 (m-40) REVERT: K 154 MET cc_start: 0.8329 (mmp) cc_final: 0.8077 (mmt) REVERT: K 172 TYR cc_start: 0.8216 (t80) cc_final: 0.7905 (t80) REVERT: K 178 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.8012 (p) REVERT: H 44 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8260 (tt) REVERT: H 211 ASP cc_start: 0.7942 (m-30) cc_final: 0.7556 (m-30) REVERT: H 301 MET cc_start: 0.8577 (mmp) cc_final: 0.8163 (mmt) REVERT: H 325 MET cc_start: 0.8050 (tpp) cc_final: 0.7656 (tpt) REVERT: H 373 MET cc_start: 0.7998 (ttp) cc_final: 0.7689 (ttm) REVERT: H 398 MET cc_start: 0.8204 (mtt) cc_final: 0.7838 (mtt) outliers start: 90 outliers final: 33 residues processed: 1086 average time/residue: 0.5319 time to fit residues: 924.4135 Evaluate side-chains 602 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 558 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 382 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 382 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 395 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 294 optimal weight: 7.9990 chunk 457 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN E 15 GLN E 88 HIS E 101 ASN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 91 ASN F 350 ASN F 406 HIS J 8 HIS J 15 GLN J 35 GLN J 88 HIS J 101 ASN J 176 GLN J 266 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN G 349 ASN C 8 HIS C 11 GLN C 15 GLN C 88 HIS C 101 ASN C 283 HIS D 14 ASN D 91 ASN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 349 ASN D 350 ASN D 406 HIS L 8 HIS L 15 GLN L 28 HIS L 31 GLN L 88 HIS L 101 ASN L 300 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 91 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 349 ASN I 350 ASN I 385 GLN I 433 GLN I 436 GLN A 8 HIS A 15 GLN A 18 ASN A 31 GLN A 88 HIS A 101 ASN A 256 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS A 342 GLN B 14 ASN B 91 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN B 406 HIS K 8 HIS K 15 GLN K 31 GLN K 88 HIS K 101 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN K 358 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 ASN H 349 ASN H 406 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 41436 Z= 0.278 Angle : 0.644 7.151 56304 Z= 0.338 Chirality : 0.046 0.173 6156 Planarity : 0.005 0.067 7338 Dihedral : 12.444 173.011 5781 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.09 % Allowed : 15.17 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.27 (0.12), residues: 5088 helix: 2.01 (0.10), residues: 2334 sheet: 1.05 (0.17), residues: 822 loop : -0.72 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 346 HIS 0.008 0.001 HIS A 107 PHE 0.016 0.002 PHE H 135 TYR 0.020 0.002 TYR I 408 ARG 0.008 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 614 time to evaluate : 5.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.8743 (mmm) cc_final: 0.8066 (mmp) REVERT: E 388 TRP cc_start: 0.8980 (m100) cc_final: 0.8769 (m100) REVERT: F 269 MET cc_start: 0.7610 (mtt) cc_final: 0.7312 (mtp) REVERT: J 50 ASN cc_start: 0.8046 (t0) cc_final: 0.7578 (m-40) REVERT: J 424 ASP cc_start: 0.7808 (t70) cc_final: 0.7476 (t0) REVERT: G 269 MET cc_start: 0.7569 (mtt) cc_final: 0.7318 (mtp) REVERT: G 301 MET cc_start: 0.8301 (mmp) cc_final: 0.7894 (mmt) REVERT: G 373 MET cc_start: 0.7910 (ttp) cc_final: 0.7624 (ttp) REVERT: G 398 MET cc_start: 0.8236 (mtt) cc_final: 0.8026 (mtp) REVERT: G 408 TYR cc_start: 0.8558 (m-80) cc_final: 0.8167 (m-80) REVERT: G 415 GLU cc_start: 0.7942 (tt0) cc_final: 0.7231 (tm-30) REVERT: D 295 MET cc_start: 0.8257 (mtm) cc_final: 0.8044 (mtp) REVERT: D 325 MET cc_start: 0.7705 (mmm) cc_final: 0.7114 (mmm) REVERT: D 356 CYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7564 (t) REVERT: D 373 MET cc_start: 0.7372 (ttp) cc_final: 0.7168 (ttm) REVERT: D 413 MET cc_start: 0.7765 (ttp) cc_final: 0.7312 (ttp) REVERT: L 424 ASP cc_start: 0.7675 (t70) cc_final: 0.7275 (t0) REVERT: I 214 PHE cc_start: 0.8724 (t80) cc_final: 0.8438 (t80) REVERT: I 217 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8391 (tt) REVERT: I 269 MET cc_start: 0.7891 (mpp) cc_final: 0.7647 (mtp) REVERT: I 332 MET cc_start: 0.8950 (mmp) cc_final: 0.8623 (mmm) REVERT: I 413 MET cc_start: 0.8070 (ttp) cc_final: 0.7634 (ttm) REVERT: I 415 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 44 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8320 (tp) REVERT: B 332 MET cc_start: 0.8290 (mmp) cc_final: 0.8016 (mmp) REVERT: B 356 CYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7682 (t) REVERT: B 416 MET cc_start: 0.8234 (mmm) cc_final: 0.7808 (mmm) REVERT: H 86 ILE cc_start: 0.8930 (mt) cc_final: 0.8728 (tt) REVERT: H 269 MET cc_start: 0.7658 (mtt) cc_final: 0.7408 (mtp) REVERT: H 325 MET cc_start: 0.7933 (tpp) cc_final: 0.7673 (tpt) outliers start: 134 outliers final: 68 residues processed: 716 average time/residue: 0.5364 time to fit residues: 640.7703 Evaluate side-chains 555 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 483 time to evaluate : 4.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 417 GLU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 380 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 458 optimal weight: 4.9990 chunk 495 optimal weight: 9.9990 chunk 408 optimal weight: 3.9990 chunk 454 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 367 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN E 31 GLN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN J 31 GLN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 GLN G 349 ASN C 11 GLN C 31 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS L 358 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS I 309 HIS A 256 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 336 GLN H 350 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 41436 Z= 0.302 Angle : 0.605 9.524 56304 Z= 0.315 Chirality : 0.044 0.157 6156 Planarity : 0.005 0.062 7338 Dihedral : 11.948 176.640 5740 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.95 % Allowed : 16.67 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.37 (0.12), residues: 5088 helix: 2.02 (0.11), residues: 2334 sheet: 1.31 (0.18), residues: 786 loop : -0.63 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 346 HIS 0.008 0.001 HIS C 88 PHE 0.026 0.002 PHE A 49 TYR 0.019 0.001 TYR F 435 ARG 0.009 0.001 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 540 time to evaluate : 4.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 33 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7580 (p0) REVERT: E 302 MET cc_start: 0.8154 (mmm) cc_final: 0.7769 (mtt) REVERT: F 269 MET cc_start: 0.7588 (mtt) cc_final: 0.7278 (mtp) REVERT: J 50 ASN cc_start: 0.8379 (t0) cc_final: 0.8142 (t0) REVERT: J 203 MET cc_start: 0.8328 (mmm) cc_final: 0.7947 (mmp) REVERT: G 269 MET cc_start: 0.7747 (mtt) cc_final: 0.7398 (mtp) REVERT: G 301 MET cc_start: 0.8501 (mmp) cc_final: 0.8238 (mmt) REVERT: G 323 MET cc_start: 0.7290 (mtm) cc_final: 0.7076 (mtm) REVERT: G 373 MET cc_start: 0.7972 (ttp) cc_final: 0.7635 (ttm) REVERT: G 408 TYR cc_start: 0.8479 (m-80) cc_final: 0.8273 (m-80) REVERT: G 415 GLU cc_start: 0.8015 (tt0) cc_final: 0.7309 (tm-30) REVERT: D 356 CYS cc_start: 0.8092 (m) cc_final: 0.7608 (t) REVERT: D 413 MET cc_start: 0.7782 (ttp) cc_final: 0.7308 (ttp) REVERT: L 424 ASP cc_start: 0.7691 (t70) cc_final: 0.7327 (t0) REVERT: I 214 PHE cc_start: 0.8761 (t80) cc_final: 0.8462 (t80) REVERT: I 217 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8614 (tt) REVERT: I 332 MET cc_start: 0.8999 (mmp) cc_final: 0.8636 (mmm) REVERT: I 413 MET cc_start: 0.8049 (ttp) cc_final: 0.7681 (ttm) REVERT: I 415 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6676 (tm-30) REVERT: A 108 TYR cc_start: 0.8024 (m-80) cc_final: 0.7778 (m-10) REVERT: B 44 LEU cc_start: 0.8703 (tt) cc_final: 0.8420 (tp) REVERT: B 332 MET cc_start: 0.8306 (mmp) cc_final: 0.8095 (mmp) REVERT: B 356 CYS cc_start: 0.8261 (m) cc_final: 0.8056 (t) REVERT: H 86 ILE cc_start: 0.8944 (mt) cc_final: 0.8695 (tt) REVERT: H 114 LEU cc_start: 0.9245 (tp) cc_final: 0.8655 (tt) REVERT: H 118 VAL cc_start: 0.9350 (p) cc_final: 0.9060 (p) REVERT: H 269 MET cc_start: 0.7785 (mtt) cc_final: 0.7413 (mtp) REVERT: H 301 MET cc_start: 0.8383 (mmm) cc_final: 0.7785 (mmt) outliers start: 128 outliers final: 83 residues processed: 640 average time/residue: 0.5208 time to fit residues: 559.0570 Evaluate side-chains 551 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 466 time to evaluate : 4.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 203 MET Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 295 CYS Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 0.4980 chunk 344 optimal weight: 0.0270 chunk 237 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 218 optimal weight: 0.4980 chunk 307 optimal weight: 5.9990 chunk 460 optimal weight: 5.9990 chunk 487 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 436 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 GLN G 192 HIS D 11 GLN D 136 GLN D 349 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN A 256 GLN B 11 GLN B 14 ASN B 37 HIS ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 41436 Z= 0.155 Angle : 0.541 11.248 56304 Z= 0.275 Chirality : 0.042 0.191 6156 Planarity : 0.004 0.063 7338 Dihedral : 11.588 178.921 5729 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.51 % Allowed : 17.50 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.50 (0.12), residues: 5088 helix: 2.13 (0.11), residues: 2334 sheet: 1.37 (0.18), residues: 786 loop : -0.58 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 346 HIS 0.005 0.001 HIS C 88 PHE 0.020 0.001 PHE H 418 TYR 0.017 0.001 TYR K 210 ARG 0.006 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 582 time to evaluate : 4.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 33 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7610 (p0) REVERT: E 302 MET cc_start: 0.8049 (mmm) cc_final: 0.7704 (mtt) REVERT: E 413 MET cc_start: 0.7781 (ttm) cc_final: 0.7377 (ttm) REVERT: F 269 MET cc_start: 0.7542 (mtt) cc_final: 0.7298 (mtp) REVERT: F 323 MET cc_start: 0.7647 (mtp) cc_final: 0.7396 (mtm) REVERT: J 50 ASN cc_start: 0.8278 (t0) cc_final: 0.7930 (m-40) REVERT: J 203 MET cc_start: 0.8176 (mmm) cc_final: 0.7843 (tpp) REVERT: J 424 ASP cc_start: 0.7864 (t70) cc_final: 0.7543 (t0) REVERT: G 145 THR cc_start: 0.8473 (m) cc_final: 0.8209 (p) REVERT: G 207 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: G 238 VAL cc_start: 0.8339 (t) cc_final: 0.8097 (t) REVERT: G 269 MET cc_start: 0.7650 (mtt) cc_final: 0.7321 (mtp) REVERT: G 398 MET cc_start: 0.8359 (mtp) cc_final: 0.8110 (mtp) REVERT: G 408 TYR cc_start: 0.8433 (m-80) cc_final: 0.8114 (m-80) REVERT: G 415 GLU cc_start: 0.7924 (tt0) cc_final: 0.7245 (tm-30) REVERT: C 425 MET cc_start: 0.7895 (tpp) cc_final: 0.7613 (mmp) REVERT: D 356 CYS cc_start: 0.8054 (m) cc_final: 0.7464 (t) REVERT: D 413 MET cc_start: 0.7773 (ttp) cc_final: 0.7247 (ttp) REVERT: D 435 TYR cc_start: 0.8323 (m-10) cc_final: 0.8016 (m-10) REVERT: L 158 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8855 (t) REVERT: L 424 ASP cc_start: 0.7718 (t70) cc_final: 0.7339 (t0) REVERT: I 214 PHE cc_start: 0.8729 (t80) cc_final: 0.8431 (t80) REVERT: I 281 GLN cc_start: 0.7726 (pm20) cc_final: 0.7496 (pm20) REVERT: I 332 MET cc_start: 0.8984 (mmp) cc_final: 0.8681 (mmm) REVERT: I 413 MET cc_start: 0.7995 (ttp) cc_final: 0.7644 (ttm) REVERT: I 415 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6481 (tm-30) REVERT: A 413 MET cc_start: 0.7932 (ttm) cc_final: 0.7485 (ttm) REVERT: B 44 LEU cc_start: 0.8366 (tt) cc_final: 0.8067 (tp) REVERT: B 332 MET cc_start: 0.8357 (mmp) cc_final: 0.7991 (mmt) REVERT: K 391 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8719 (tt) REVERT: H 269 MET cc_start: 0.7618 (mtt) cc_final: 0.7360 (mtp) REVERT: H 301 MET cc_start: 0.8247 (mmm) cc_final: 0.7939 (mmt) outliers start: 109 outliers final: 59 residues processed: 666 average time/residue: 0.4951 time to fit residues: 552.0890 Evaluate side-chains 551 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 488 time to evaluate : 4.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain I residue 417 GLU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 362 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 415 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 437 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 GLN J 28 HIS D 258 ASN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS A 101 ASN A 256 GLN B 14 ASN B 193 GLN B 206 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41436 Z= 0.250 Angle : 0.561 9.996 56304 Z= 0.287 Chirality : 0.043 0.247 6156 Planarity : 0.004 0.068 7338 Dihedral : 11.457 178.038 5725 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.11 % Allowed : 18.42 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.12), residues: 5088 helix: 2.08 (0.11), residues: 2340 sheet: 1.52 (0.18), residues: 738 loop : -0.58 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 346 HIS 0.006 0.001 HIS C 88 PHE 0.023 0.001 PHE A 49 TYR 0.021 0.001 TYR A 108 ARG 0.006 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 513 time to evaluate : 5.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 33 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7655 (p0) REVERT: E 302 MET cc_start: 0.8077 (mmm) cc_final: 0.7756 (mtt) REVERT: E 413 MET cc_start: 0.7748 (ttm) cc_final: 0.7410 (ttm) REVERT: E 415 GLU cc_start: 0.8136 (pm20) cc_final: 0.7495 (tt0) REVERT: F 269 MET cc_start: 0.7650 (mtt) cc_final: 0.7389 (mtp) REVERT: F 323 MET cc_start: 0.7469 (mtp) cc_final: 0.7199 (mtm) REVERT: J 50 ASN cc_start: 0.8379 (t0) cc_final: 0.8062 (m-40) REVERT: J 203 MET cc_start: 0.8326 (mmm) cc_final: 0.8084 (mmp) REVERT: G 207 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: G 269 MET cc_start: 0.7774 (mtt) cc_final: 0.7414 (mtp) REVERT: G 415 GLU cc_start: 0.7996 (tt0) cc_final: 0.7276 (tm-30) REVERT: C 413 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7552 (ttm) REVERT: C 425 MET cc_start: 0.7831 (tpp) cc_final: 0.7508 (mmp) REVERT: D 356 CYS cc_start: 0.8159 (m) cc_final: 0.7681 (t) REVERT: D 413 MET cc_start: 0.7876 (ttp) cc_final: 0.7358 (ttp) REVERT: D 435 TYR cc_start: 0.8269 (m-10) cc_final: 0.7959 (m-10) REVERT: L 424 ASP cc_start: 0.7758 (t70) cc_final: 0.7458 (t0) REVERT: I 214 PHE cc_start: 0.8769 (t80) cc_final: 0.8440 (t80) REVERT: I 217 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8626 (tt) REVERT: I 332 MET cc_start: 0.8838 (mmp) cc_final: 0.8471 (mmm) REVERT: I 413 MET cc_start: 0.8056 (ttp) cc_final: 0.7685 (ttm) REVERT: I 415 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6674 (tm-30) REVERT: A 413 MET cc_start: 0.7982 (ttm) cc_final: 0.7546 (ttm) REVERT: B 44 LEU cc_start: 0.8406 (tt) cc_final: 0.8134 (tp) REVERT: B 228 ASN cc_start: 0.8028 (m-40) cc_final: 0.7532 (m110) REVERT: B 332 MET cc_start: 0.8396 (mmp) cc_final: 0.8010 (mmt) REVERT: K 391 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8765 (tt) REVERT: H 269 MET cc_start: 0.7772 (mtt) cc_final: 0.7457 (mtp) outliers start: 135 outliers final: 101 residues processed: 613 average time/residue: 0.5139 time to fit residues: 524.6886 Evaluate side-chains 576 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 470 time to evaluate : 5.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain I residue 417 GLU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 203 MET Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 295 CYS Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 2.9990 chunk 438 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 487 optimal weight: 3.9990 chunk 404 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN F 339 ASN F 349 ASN F 385 GLN F 433 GLN D 206 ASN D 337 ASN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS K 406 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 41436 Z= 0.309 Angle : 0.586 12.505 56304 Z= 0.300 Chirality : 0.044 0.171 6156 Planarity : 0.004 0.064 7338 Dihedral : 11.413 178.576 5725 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.64 % Allowed : 18.14 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.12), residues: 5088 helix: 1.96 (0.11), residues: 2340 sheet: 1.44 (0.19), residues: 738 loop : -0.64 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 346 HIS 0.006 0.001 HIS C 88 PHE 0.021 0.002 PHE A 49 TYR 0.017 0.001 TYR K 210 ARG 0.009 0.000 ARG J 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 490 time to evaluate : 4.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 141 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: E 302 MET cc_start: 0.8154 (mmm) cc_final: 0.7949 (mtt) REVERT: E 413 MET cc_start: 0.7807 (ttm) cc_final: 0.7479 (ttm) REVERT: E 415 GLU cc_start: 0.8104 (pm20) cc_final: 0.7508 (tt0) REVERT: F 269 MET cc_start: 0.7674 (mtt) cc_final: 0.7404 (mtp) REVERT: J 50 ASN cc_start: 0.8417 (t0) cc_final: 0.8106 (m-40) REVERT: J 203 MET cc_start: 0.8416 (mmm) cc_final: 0.8179 (mmp) REVERT: G 2 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7992 (mtm180) REVERT: G 207 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: G 269 MET cc_start: 0.7979 (mtt) cc_final: 0.7689 (mtp) REVERT: G 398 MET cc_start: 0.8416 (mtp) cc_final: 0.8213 (mtm) REVERT: G 415 GLU cc_start: 0.8107 (tt0) cc_final: 0.7350 (tm-30) REVERT: C 145 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8616 (t) REVERT: C 413 MET cc_start: 0.7774 (ttm) cc_final: 0.7550 (ttm) REVERT: C 425 MET cc_start: 0.7873 (tpp) cc_final: 0.7542 (mmp) REVERT: D 413 MET cc_start: 0.7881 (ttp) cc_final: 0.7351 (ttp) REVERT: D 435 TYR cc_start: 0.8354 (m-10) cc_final: 0.8049 (m-10) REVERT: L 424 ASP cc_start: 0.7811 (t70) cc_final: 0.7511 (t0) REVERT: I 44 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8665 (tt) REVERT: I 214 PHE cc_start: 0.8789 (t80) cc_final: 0.8461 (t80) REVERT: I 217 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8848 (tt) REVERT: I 332 MET cc_start: 0.8796 (mmp) cc_final: 0.8556 (mmm) REVERT: I 413 MET cc_start: 0.8007 (ttp) cc_final: 0.7629 (ttm) REVERT: I 415 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6694 (tm-30) REVERT: A 413 MET cc_start: 0.7974 (ttm) cc_final: 0.7459 (ttm) REVERT: B 44 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8274 (tp) REVERT: B 145 THR cc_start: 0.8590 (m) cc_final: 0.8311 (m) REVERT: B 332 MET cc_start: 0.8490 (mmp) cc_final: 0.8115 (mmt) REVERT: B 435 TYR cc_start: 0.8128 (m-10) cc_final: 0.7824 (m-10) REVERT: K 391 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8819 (tt) REVERT: H 269 MET cc_start: 0.7764 (mtt) cc_final: 0.7471 (mtp) REVERT: H 301 MET cc_start: 0.8288 (mmp) cc_final: 0.7954 (mmp) outliers start: 158 outliers final: 120 residues processed: 611 average time/residue: 0.5224 time to fit residues: 538.4747 Evaluate side-chains 587 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 459 time to evaluate : 4.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 413 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain I residue 417 GLU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 203 MET Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 295 CYS Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 chunk 356 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 410 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 485 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN F 206 ASN G 206 ASN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41436 Z= 0.189 Angle : 0.543 11.585 56304 Z= 0.275 Chirality : 0.042 0.187 6156 Planarity : 0.004 0.063 7338 Dihedral : 11.154 179.978 5725 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.11 % Allowed : 18.70 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.44 (0.12), residues: 5088 helix: 2.07 (0.11), residues: 2340 sheet: 1.43 (0.19), residues: 738 loop : -0.60 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 346 HIS 0.005 0.001 HIS C 88 PHE 0.019 0.001 PHE J 49 TYR 0.015 0.001 TYR K 210 ARG 0.005 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 511 time to evaluate : 4.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 302 MET cc_start: 0.8077 (mmm) cc_final: 0.7870 (mtt) REVERT: E 413 MET cc_start: 0.7834 (ttm) cc_final: 0.7505 (ttm) REVERT: E 415 GLU cc_start: 0.8091 (pm20) cc_final: 0.7448 (tt0) REVERT: F 269 MET cc_start: 0.7545 (mtt) cc_final: 0.7292 (mtp) REVERT: F 323 MET cc_start: 0.7492 (mtp) cc_final: 0.7230 (mtm) REVERT: J 50 ASN cc_start: 0.8487 (t0) cc_final: 0.8231 (m-40) REVERT: J 203 MET cc_start: 0.8327 (mmm) cc_final: 0.8115 (mmp) REVERT: G 2 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7997 (mtm180) REVERT: G 207 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: G 269 MET cc_start: 0.7977 (mtt) cc_final: 0.7581 (mtp) REVERT: G 415 GLU cc_start: 0.8036 (tt0) cc_final: 0.7292 (tm-30) REVERT: C 145 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8560 (t) REVERT: C 413 MET cc_start: 0.7756 (ttm) cc_final: 0.7519 (ttm) REVERT: C 425 MET cc_start: 0.7987 (tpp) cc_final: 0.7607 (mmp) REVERT: D 413 MET cc_start: 0.7808 (ttp) cc_final: 0.7280 (ttp) REVERT: L 424 ASP cc_start: 0.7767 (t70) cc_final: 0.7477 (t0) REVERT: I 214 PHE cc_start: 0.8717 (t80) cc_final: 0.8400 (t80) REVERT: I 332 MET cc_start: 0.8807 (mmp) cc_final: 0.8556 (mmm) REVERT: I 413 MET cc_start: 0.7936 (ttp) cc_final: 0.7567 (ttm) REVERT: A 415 GLU cc_start: 0.7956 (pm20) cc_final: 0.7470 (tt0) REVERT: B 44 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8250 (tp) REVERT: B 71 GLU cc_start: 0.6818 (tt0) cc_final: 0.6189 (tt0) REVERT: B 214 PHE cc_start: 0.8018 (t80) cc_final: 0.7737 (t80) REVERT: B 228 ASN cc_start: 0.7721 (m-40) cc_final: 0.7496 (m-40) REVERT: B 332 MET cc_start: 0.8474 (mmp) cc_final: 0.8101 (mmt) REVERT: B 435 TYR cc_start: 0.8204 (m-10) cc_final: 0.7940 (m-10) REVERT: K 391 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8764 (tt) REVERT: H 269 MET cc_start: 0.7715 (mtt) cc_final: 0.7412 (mtp) outliers start: 135 outliers final: 108 residues processed: 610 average time/residue: 0.5177 time to fit residues: 526.3862 Evaluate side-chains 578 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 465 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 413 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 249 ASN 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 381 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 295 CYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 381 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN F 339 ASN J 107 HIS D 193 GLN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41436 Z= 0.221 Angle : 0.557 12.290 56304 Z= 0.281 Chirality : 0.043 0.276 6156 Planarity : 0.004 0.062 7338 Dihedral : 11.015 178.186 5723 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.18 % Allowed : 18.95 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.40 (0.12), residues: 5088 helix: 2.05 (0.11), residues: 2340 sheet: 1.38 (0.19), residues: 738 loop : -0.60 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 346 HIS 0.005 0.001 HIS C 88 PHE 0.017 0.001 PHE A 49 TYR 0.014 0.001 TYR K 210 ARG 0.005 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 479 time to evaluate : 4.838 Fit side-chains revert: symmetry clash REVERT: E 141 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: E 413 MET cc_start: 0.7842 (ttm) cc_final: 0.7515 (ttm) REVERT: E 415 GLU cc_start: 0.8082 (pm20) cc_final: 0.7459 (tt0) REVERT: E 435 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7912 (t) REVERT: F 269 MET cc_start: 0.7653 (mtt) cc_final: 0.7369 (mtp) REVERT: F 323 MET cc_start: 0.7541 (mtp) cc_final: 0.7216 (mtm) REVERT: F 339 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7579 (t0) REVERT: J 203 MET cc_start: 0.8333 (mmm) cc_final: 0.8113 (mmp) REVERT: G 2 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.8019 (mtm180) REVERT: G 207 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: G 269 MET cc_start: 0.7903 (mtt) cc_final: 0.7610 (mtp) REVERT: G 415 GLU cc_start: 0.8089 (tt0) cc_final: 0.7314 (tm-30) REVERT: C 145 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8555 (t) REVERT: C 413 MET cc_start: 0.7784 (ttm) cc_final: 0.7538 (ttm) REVERT: C 425 MET cc_start: 0.7839 (tpp) cc_final: 0.7462 (mmp) REVERT: D 413 MET cc_start: 0.7799 (ttp) cc_final: 0.7335 (ttp) REVERT: D 435 TYR cc_start: 0.7810 (m-10) cc_final: 0.7433 (m-10) REVERT: L 424 ASP cc_start: 0.7791 (t70) cc_final: 0.7506 (t0) REVERT: I 214 PHE cc_start: 0.8717 (t80) cc_final: 0.8368 (t80) REVERT: I 332 MET cc_start: 0.8772 (mmp) cc_final: 0.8477 (mmm) REVERT: I 413 MET cc_start: 0.7922 (ttp) cc_final: 0.7564 (ttm) REVERT: A 413 MET cc_start: 0.7984 (ttm) cc_final: 0.7521 (ttm) REVERT: B 44 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 214 PHE cc_start: 0.8010 (t80) cc_final: 0.7750 (t80) REVERT: B 228 ASN cc_start: 0.7710 (m-40) cc_final: 0.7458 (m-40) REVERT: B 295 MET cc_start: 0.8382 (mmm) cc_final: 0.8103 (mtt) REVERT: B 332 MET cc_start: 0.8513 (mmp) cc_final: 0.8065 (mmt) REVERT: B 435 TYR cc_start: 0.8224 (m-10) cc_final: 0.7964 (m-10) REVERT: K 391 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8784 (tt) REVERT: H 259 MET cc_start: 0.8487 (mmm) cc_final: 0.8002 (mpp) REVERT: H 269 MET cc_start: 0.7745 (mtt) cc_final: 0.7444 (mtp) outliers start: 138 outliers final: 116 residues processed: 581 average time/residue: 0.4848 time to fit residues: 471.8245 Evaluate side-chains 588 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 464 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 413 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 249 ASN 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 381 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 295 CYS Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 3.9990 chunk 465 optimal weight: 0.6980 chunk 424 optimal weight: 3.9990 chunk 452 optimal weight: 5.9990 chunk 272 optimal weight: 0.4980 chunk 197 optimal weight: 0.9980 chunk 355 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 409 optimal weight: 3.9990 chunk 428 optimal weight: 3.9990 chunk 451 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN D 37 HIS ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS ** I 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41436 Z= 0.238 Angle : 0.562 12.819 56304 Z= 0.285 Chirality : 0.043 0.226 6156 Planarity : 0.004 0.062 7338 Dihedral : 10.914 176.258 5723 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.18 % Allowed : 19.34 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.38 (0.12), residues: 5088 helix: 2.05 (0.11), residues: 2328 sheet: 1.32 (0.19), residues: 738 loop : -0.61 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 346 HIS 0.005 0.001 HIS C 88 PHE 0.017 0.001 PHE A 49 TYR 0.014 0.001 TYR B 312 ARG 0.005 0.000 ARG I 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 472 time to evaluate : 5.106 Fit side-chains revert: symmetry clash REVERT: E 141 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8061 (m-10) REVERT: E 413 MET cc_start: 0.7775 (ttm) cc_final: 0.7450 (ttm) REVERT: E 415 GLU cc_start: 0.8082 (pm20) cc_final: 0.7466 (tt0) REVERT: E 435 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8008 (t) REVERT: F 269 MET cc_start: 0.7660 (mtt) cc_final: 0.7316 (mtp) REVERT: F 323 MET cc_start: 0.7509 (mtp) cc_final: 0.7194 (mtm) REVERT: J 50 ASN cc_start: 0.8154 (t0) cc_final: 0.7743 (m-40) REVERT: J 203 MET cc_start: 0.8290 (mmm) cc_final: 0.8081 (mmp) REVERT: J 279 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7568 (mp0) REVERT: G 2 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7970 (mtm180) REVERT: G 207 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: G 269 MET cc_start: 0.7848 (mtt) cc_final: 0.7557 (mtp) REVERT: G 415 GLU cc_start: 0.8088 (tt0) cc_final: 0.7337 (tm-30) REVERT: C 145 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8585 (t) REVERT: C 413 MET cc_start: 0.7769 (ttm) cc_final: 0.7532 (ttm) REVERT: C 425 MET cc_start: 0.7868 (tpp) cc_final: 0.7476 (mmp) REVERT: D 413 MET cc_start: 0.7798 (ttp) cc_final: 0.7336 (ttp) REVERT: D 435 TYR cc_start: 0.7821 (m-10) cc_final: 0.7356 (m-10) REVERT: L 424 ASP cc_start: 0.7801 (t70) cc_final: 0.7522 (t0) REVERT: I 214 PHE cc_start: 0.8687 (t80) cc_final: 0.8344 (t80) REVERT: I 332 MET cc_start: 0.8784 (mmp) cc_final: 0.8489 (mmm) REVERT: I 413 MET cc_start: 0.7856 (ttp) cc_final: 0.7498 (ttm) REVERT: A 413 MET cc_start: 0.7888 (ttm) cc_final: 0.7436 (ttm) REVERT: A 415 GLU cc_start: 0.8027 (pm20) cc_final: 0.7580 (tt0) REVERT: B 44 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (tp) REVERT: B 214 PHE cc_start: 0.8000 (t80) cc_final: 0.7749 (t80) REVERT: B 228 ASN cc_start: 0.7777 (m-40) cc_final: 0.7518 (m-40) REVERT: B 259 MET cc_start: 0.8523 (mmm) cc_final: 0.8299 (mmt) REVERT: B 332 MET cc_start: 0.8507 (mmp) cc_final: 0.8048 (mmt) REVERT: B 435 TYR cc_start: 0.8242 (m-10) cc_final: 0.7990 (m-10) REVERT: K 391 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8807 (tt) REVERT: H 259 MET cc_start: 0.8494 (mmm) cc_final: 0.8028 (mpp) REVERT: H 269 MET cc_start: 0.7756 (mtt) cc_final: 0.7452 (mtp) outliers start: 138 outliers final: 126 residues processed: 577 average time/residue: 0.4988 time to fit residues: 481.2134 Evaluate side-chains 592 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 459 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 413 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 249 ASN 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 381 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 295 CYS Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 374 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 0.0170 chunk 478 optimal weight: 0.0060 chunk 292 optimal weight: 0.0060 chunk 227 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 502 optimal weight: 10.0000 chunk 462 optimal weight: 7.9990 chunk 399 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 overall best weight: 0.6054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN F 339 ASN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 41436 Z= 0.157 Angle : 0.540 13.231 56304 Z= 0.271 Chirality : 0.041 0.189 6156 Planarity : 0.004 0.062 7338 Dihedral : 10.595 172.975 5723 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 19.94 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.12), residues: 5088 helix: 2.06 (0.11), residues: 2370 sheet: 1.35 (0.19), residues: 738 loop : -0.50 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 346 HIS 0.005 0.001 HIS C 88 PHE 0.016 0.001 PHE J 49 TYR 0.015 0.001 TYR K 210 ARG 0.005 0.000 ARG I 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 519 time to evaluate : 4.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 413 MET cc_start: 0.7703 (ttm) cc_final: 0.7366 (ttm) REVERT: E 415 GLU cc_start: 0.8063 (pm20) cc_final: 0.7451 (tt0) REVERT: E 435 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7881 (t) REVERT: F 269 MET cc_start: 0.7599 (mtt) cc_final: 0.7331 (mtp) REVERT: J 50 ASN cc_start: 0.8156 (t0) cc_final: 0.7766 (m-40) REVERT: J 203 MET cc_start: 0.8286 (mmm) cc_final: 0.8071 (mmm) REVERT: J 279 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7669 (mp0) REVERT: J 424 ASP cc_start: 0.7931 (t70) cc_final: 0.7649 (t0) REVERT: G 269 MET cc_start: 0.7862 (mtt) cc_final: 0.7532 (mtp) REVERT: G 415 GLU cc_start: 0.8045 (tt0) cc_final: 0.7276 (tm-30) REVERT: C 145 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8522 (t) REVERT: C 368 LEU cc_start: 0.8691 (mm) cc_final: 0.8485 (mp) REVERT: C 413 MET cc_start: 0.7716 (ttm) cc_final: 0.7470 (ttm) REVERT: C 425 MET cc_start: 0.7935 (tpp) cc_final: 0.7612 (mmp) REVERT: D 413 MET cc_start: 0.7704 (ttp) cc_final: 0.7263 (ttp) REVERT: D 435 TYR cc_start: 0.7711 (m-10) cc_final: 0.7352 (m-10) REVERT: L 424 ASP cc_start: 0.7743 (t70) cc_final: 0.7505 (t0) REVERT: I 314 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8632 (p) REVERT: I 332 MET cc_start: 0.8778 (mmp) cc_final: 0.8491 (mmm) REVERT: A 203 MET cc_start: 0.8675 (mmp) cc_final: 0.8427 (mmp) REVERT: A 413 MET cc_start: 0.7810 (ttm) cc_final: 0.7367 (ttm) REVERT: A 415 GLU cc_start: 0.7955 (pm20) cc_final: 0.7425 (tt0) REVERT: B 44 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8212 (tp) REVERT: B 214 PHE cc_start: 0.7915 (t80) cc_final: 0.7669 (t80) REVERT: B 259 MET cc_start: 0.8462 (mmm) cc_final: 0.8226 (mmt) REVERT: B 332 MET cc_start: 0.8411 (mmp) cc_final: 0.8015 (mmt) REVERT: K 302 MET cc_start: 0.7925 (mmm) cc_final: 0.7716 (mtt) REVERT: K 391 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8766 (tt) REVERT: H 259 MET cc_start: 0.8354 (mmm) cc_final: 0.7934 (mpp) REVERT: H 269 MET cc_start: 0.7711 (mtt) cc_final: 0.7406 (mtp) outliers start: 107 outliers final: 89 residues processed: 593 average time/residue: 0.4883 time to fit residues: 484.1553 Evaluate side-chains 568 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 474 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 413 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 249 ASN 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 381 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 314 THR Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 295 CYS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 10.0000 chunk 425 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 111 optimal weight: 8.9990 chunk 400 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 411 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS ** I 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084830 restraints weight = 67686.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088244 restraints weight = 32698.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090571 restraints weight = 19654.501| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 41436 Z= 0.244 Angle : 0.573 12.862 56304 Z= 0.288 Chirality : 0.043 0.179 6156 Planarity : 0.004 0.062 7338 Dihedral : 10.583 174.589 5723 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.79 % Allowed : 20.12 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.41 (0.12), residues: 5088 helix: 2.03 (0.11), residues: 2364 sheet: 1.18 (0.19), residues: 756 loop : -0.53 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 346 HIS 0.004 0.001 HIS C 88 PHE 0.028 0.001 PHE C 49 TYR 0.021 0.001 TYR A 108 ARG 0.004 0.000 ARG B 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9721.53 seconds wall clock time: 176 minutes 22.38 seconds (10582.38 seconds total)