Starting phenix.real_space_refine on Fri Feb 23 11:12:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5j_0669/02_2024/6j5j_0669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5j_0669/02_2024/6j5j_0669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5j_0669/02_2024/6j5j_0669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5j_0669/02_2024/6j5j_0669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5j_0669/02_2024/6j5j_0669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5j_0669/02_2024/6j5j_0669_updated.pdb" } resolution = 3.45 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= 0.000 sd= 0.005 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 13 5.49 5 Mg 5 5.21 5 S 145 5.16 5 C 24166 2.51 5 N 6600 2.21 5 O 7239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "E GLU 368": "OE1" <-> "OE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 456": "OE1" <-> "OE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "F GLU 401": "OE1" <-> "OE2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J GLU 40": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "S ARG 113": "NH1" <-> "NH2" Residue "S GLU 115": "OE1" <-> "OE2" Residue "S ARG 165": "NH1" <-> "NH2" Residue "b GLU 87": "OE1" <-> "OE2" Residue "b GLU 137": "OE1" <-> "OE2" Residue "b GLU 171": "OE1" <-> "OE2" Residue "b ARG 175": "NH1" <-> "NH2" Residue "b GLU 178": "OE1" <-> "OE2" Residue "b GLU 190": "OE1" <-> "OE2" Residue "b GLU 192": "OE1" <-> "OE2" Residue "f GLU 77": "OE1" <-> "OE2" Residue "f ARG 82": "NH1" <-> "NH2" Residue "f ARG 84": "NH1" <-> "NH2" Residue "a ARG 159": "NH1" <-> "NH2" Residue "a GLU 203": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "Q ARG 38": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38168 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3837 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 485} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3814 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain breaks: 1 Chain: "C" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3722 Classifications: {'peptide': 488} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain: "D" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3555 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3522 Classifications: {'peptide': 465} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 440} Chain: "F" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3527 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 441} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 406 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'HIS:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2112 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 970 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "S" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1429 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 177} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1478 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "c" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 428 Classifications: {'peptide': 70} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 64} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "d" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 741 Classifications: {'peptide': 147} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 125} Link IDs: {'PTRANS': 8, 'TRANS': 138} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 472 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 238 Chain: "e" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 315 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'UNK:plan-1': 63} Unresolved non-hydrogen planarities: 63 Chain: "f" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 530 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "g" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 420 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'UNK:plan-1': 84} Unresolved non-hydrogen planarities: 84 Chain: "i" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 301 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "8" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 374 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 52} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "a" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1702 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "u" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'UNK:plan-1': 42} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.37, per 1000 atoms: 0.53 Number of scatterers: 38168 At special positions: 0 Unit cell: (149.04, 231.84, 191.82, 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 145 16.00 P 13 15.00 Mg 5 11.99 O 7239 8.00 N 6600 7.00 C 24166 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.99 Conformation dependent library (CDL) restraints added in 7.9 seconds 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 219 helices and 29 sheets defined 47.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.60 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 removed outlier: 3.609A pdb=" N LEU A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.666A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.035A pdb=" N LYS A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 256 through 259 No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 271 through 284 removed outlier: 4.546A pdb=" N ALA A 275 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL A 276 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN A 280 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 283 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 284 " --> pdb=" O MET A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.979A pdb=" N ARG A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.962A pdb=" N ILE A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 375 through 378 removed outlier: 4.075A pdb=" N ALA A 378 " --> pdb=" O GLY A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 381 through 399 removed outlier: 3.627A pdb=" N GLN A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 412 through 426 removed outlier: 3.776A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.670A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 removed outlier: 3.648A pdb=" N SER A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.508A pdb=" N LEU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 16 removed outlier: 4.347A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.902A pdb=" N ASP B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.533A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 271 through 285 removed outlier: 3.597A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 285 " --> pdb=" O MET B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 298 through 306 removed outlier: 4.049A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 338 through 341 No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.808A pdb=" N VAL B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 423 removed outlier: 4.182A pdb=" N VAL B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 438 through 449 removed outlier: 4.092A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.749A pdb=" N ASN B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 removed outlier: 3.506A pdb=" N GLY B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 504 removed outlier: 3.685A pdb=" N ALA B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.535A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 190 removed outlier: 4.022A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 184 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 210 through 222 removed outlier: 4.608A pdb=" N GLN C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 240 through 243 No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.694A pdb=" N ASN C 260 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.747A pdb=" N TYR C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.317A pdb=" N HIS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 338 through 341 No H-bonds generated for 'chain 'C' and resid 338 through 341' Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.854A pdb=" N TYR C 358 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 359' Processing helix chain 'C' and resid 388 through 398 removed outlier: 3.829A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU C 393 " --> pdb=" O THR C 389 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 418 No H-bonds generated for 'chain 'C' and resid 415 through 418' Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'C' and resid 438 through 449 removed outlier: 3.649A pdb=" N ALA C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY C 448 " --> pdb=" O VAL C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 475 removed outlier: 3.909A pdb=" N ILE C 461 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 465 " --> pdb=" O THR C 462 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN C 466 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 467 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU C 469 " --> pdb=" O ASN C 466 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL C 472 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 473 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER C 474 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN C 475 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 508 removed outlier: 3.650A pdb=" N ALA C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.513A pdb=" N LEU D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.592A pdb=" N LEU D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 173 " --> pdb=" O MET D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 195 removed outlier: 3.555A pdb=" N GLY D 195 " --> pdb=" O THR D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 192 through 195' Processing helix chain 'D' and resid 235 through 247 removed outlier: 3.705A pdb=" N THR D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 267 removed outlier: 3.848A pdb=" N ALA D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 267 " --> pdb=" O PHE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 274 No H-bonds generated for 'chain 'D' and resid 271 through 274' Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.550A pdb=" N MET D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'D' and resid 339 through 344 removed outlier: 4.553A pdb=" N LEU D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 390 removed outlier: 3.559A pdb=" N ASP D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 379 " --> pdb=" O GLY D 375 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 416 removed outlier: 3.751A pdb=" N VAL D 406 " --> pdb=" O ASP D 402 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 407 " --> pdb=" O LYS D 403 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 427 No H-bonds generated for 'chain 'D' and resid 424 through 427' Processing helix chain 'D' and resid 436 through 448 removed outlier: 3.700A pdb=" N ILE D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 446 " --> pdb=" O GLY D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 459 removed outlier: 3.503A pdb=" N PHE D 459 " --> pdb=" O GLU D 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 459' Processing helix chain 'D' and resid 465 through 474 removed outlier: 3.622A pdb=" N VAL D 469 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D 470 " --> pdb=" O GLU D 467 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS D 471 " --> pdb=" O ALA D 468 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP D 473 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS D 474 " --> pdb=" O LYS D 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 142 through 145 No H-bonds generated for 'chain 'E' and resid 142 through 145' Processing helix chain 'E' and resid 164 through 178 removed outlier: 3.889A pdb=" N ASN E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 205 removed outlier: 3.836A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 205 " --> pdb=" O GLU E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 247 removed outlier: 3.861A pdb=" N LEU E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 267 removed outlier: 3.679A pdb=" N ALA E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 273 No H-bonds generated for 'chain 'E' and resid 270 through 273' Processing helix chain 'E' and resid 287 through 290 No H-bonds generated for 'chain 'E' and resid 287 through 290' Processing helix chain 'E' and resid 292 through 295 No H-bonds generated for 'chain 'E' and resid 292 through 295' Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.766A pdb=" N THR E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 329' Processing helix chain 'E' and resid 339 through 342 No H-bonds generated for 'chain 'E' and resid 339 through 342' Processing helix chain 'E' and resid 366 through 392 removed outlier: 3.834A pdb=" N VAL E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 375 " --> pdb=" O ASP E 371 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP E 388 " --> pdb=" O LYS E 384 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE E 389 " --> pdb=" O SER E 385 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 415 removed outlier: 4.091A pdb=" N LEU E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR E 405 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 410 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'E' and resid 436 through 446 removed outlier: 3.534A pdb=" N LYS E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 466 through 472 removed outlier: 3.831A pdb=" N ALA E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 471 " --> pdb=" O GLU E 467 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 472 " --> pdb=" O ALA E 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 466 through 472' Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 144 removed outlier: 3.560A pdb=" N LEU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 140 through 144' Processing helix chain 'F' and resid 168 through 174 removed outlier: 3.522A pdb=" N ASN F 173 " --> pdb=" O MET F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 201 removed outlier: 3.508A pdb=" N TYR F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 No H-bonds generated for 'chain 'F' and resid 228 through 231' Processing helix chain 'F' and resid 237 through 247 removed outlier: 3.908A pdb=" N ALA F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 271 removed outlier: 3.752A pdb=" N GLY F 267 " --> pdb=" O PHE F 263 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 297 removed outlier: 3.803A pdb=" N GLY F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 328 through 330 No H-bonds generated for 'chain 'F' and resid 328 through 330' Processing helix chain 'F' and resid 339 through 342 No H-bonds generated for 'chain 'F' and resid 339 through 342' Processing helix chain 'F' and resid 369 through 382 removed outlier: 3.746A pdb=" N GLN F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN F 381 " --> pdb=" O GLN F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 393 removed outlier: 3.611A pdb=" N ALA F 391 " --> pdb=" O GLN F 387 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE F 392 " --> pdb=" O ASP F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 397 No H-bonds generated for 'chain 'F' and resid 395 through 397' Processing helix chain 'F' and resid 402 through 415 removed outlier: 3.959A pdb=" N VAL F 406 " --> pdb=" O ASP F 402 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER F 407 " --> pdb=" O LYS F 403 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS F 411 " --> pdb=" O SER F 407 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 427 removed outlier: 4.385A pdb=" N VAL F 425 " --> pdb=" O VAL F 422 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR F 427 " --> pdb=" O GLU F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 441 No H-bonds generated for 'chain 'F' and resid 438 through 441' Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'F' and resid 465 through 469 removed outlier: 3.723A pdb=" N VAL F 469 " --> pdb=" O GLU F 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 18 No H-bonds generated for 'chain 'J' and resid 15 through 18' Processing helix chain 'J' and resid 22 through 25 No H-bonds generated for 'chain 'J' and resid 22 through 25' Processing helix chain 'J' and resid 27 through 33 removed outlier: 3.572A pdb=" N ARG J 32 " --> pdb=" O ALA J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 43 removed outlier: 3.568A pdb=" N GLN J 41 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'G' and resid 3 through 53 removed outlier: 3.641A pdb=" N ARG G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.919A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR G 44 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER G 48 " --> pdb=" O TYR G 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 99 removed outlier: 3.632A pdb=" N VAL G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 removed outlier: 3.623A pdb=" N ILE G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 removed outlier: 3.601A pdb=" N ALA G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 191 No H-bonds generated for 'chain 'G' and resid 188 through 191' Processing helix chain 'G' and resid 200 through 231 removed outlier: 3.513A pdb=" N GLU G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU G 209 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 270 removed outlier: 4.031A pdb=" N ALA G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 243 " --> pdb=" O ALA G 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 246 " --> pdb=" O MET G 242 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 247 " --> pdb=" O ILE G 243 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU G 264 " --> pdb=" O LYS G 260 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 120 removed outlier: 3.934A pdb=" N ALA H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 115 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 144 removed outlier: 3.638A pdb=" N GLU H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 23 removed outlier: 3.968A pdb=" N ILE I 18 " --> pdb=" O ARG I 14 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL I 23 " --> pdb=" O CYS I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 38 removed outlier: 4.125A pdb=" N ALA I 33 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN I 34 " --> pdb=" O PHE I 31 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS I 37 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR I 38 " --> pdb=" O ALA I 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 21 removed outlier: 3.514A pdb=" N ALA S 21 " --> pdb=" O ARG S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 26 No H-bonds generated for 'chain 'S' and resid 23 through 26' Processing helix chain 'S' and resid 28 through 30 No H-bonds generated for 'chain 'S' and resid 28 through 30' Processing helix chain 'S' and resid 34 through 42 removed outlier: 3.920A pdb=" N ARG S 41 " --> pdb=" O LYS S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 70 removed outlier: 3.757A pdb=" N LEU S 69 " --> pdb=" O LYS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 75 No H-bonds generated for 'chain 'S' and resid 72 through 75' Processing helix chain 'S' and resid 81 through 91 removed outlier: 3.817A pdb=" N ILE S 86 " --> pdb=" O SER S 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU S 89 " --> pdb=" O ILE S 86 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA S 90 " --> pdb=" O ASN S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 110 removed outlier: 3.685A pdb=" N THR S 98 " --> pdb=" O LEU S 95 " (cutoff:3.500A) Proline residue: S 99 - end of helix removed outlier: 3.600A pdb=" N ILE S 102 " --> pdb=" O PRO S 99 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER S 103 " --> pdb=" O GLY S 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA S 104 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER S 106 " --> pdb=" O SER S 103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR S 107 " --> pdb=" O ALA S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 137 removed outlier: 3.534A pdb=" N LEU S 134 " --> pdb=" O THR S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 142 No H-bonds generated for 'chain 'S' and resid 139 through 142' Processing helix chain 'S' and resid 175 through 184 removed outlier: 3.954A pdb=" N GLN S 180 " --> pdb=" O THR S 177 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU S 182 " --> pdb=" O ILE S 179 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER S 183 " --> pdb=" O GLN S 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 29 removed outlier: 3.906A pdb=" N HIS b 8 " --> pdb=" O PRO b 4 " (cutoff:3.500A) Proline residue: b 18 - end of helix Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 38 through 41 No H-bonds generated for 'chain 'b' and resid 38 through 41' Processing helix chain 'b' and resid 44 through 47 No H-bonds generated for 'chain 'b' and resid 44 through 47' Processing helix chain 'b' and resid 59 through 137 removed outlier: 3.671A pdb=" N THR b 63 " --> pdb=" O SER b 59 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU b 67 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS b 72 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS b 73 " --> pdb=" O TYR b 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY b 75 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY b 79 " --> pdb=" O GLY b 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA b 91 " --> pdb=" O GLU b 87 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN b 92 " --> pdb=" O GLN b 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS b 102 " --> pdb=" O GLN b 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA b 107 " --> pdb=" O GLN b 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU b 110 " --> pdb=" O ASP b 106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN b 114 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU b 117 " --> pdb=" O SER b 113 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL b 118 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN b 119 " --> pdb=" O GLN b 115 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP b 126 " --> pdb=" O HIS b 122 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG b 129 " --> pdb=" O PHE b 125 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE b 132 " --> pdb=" O GLN b 128 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA b 135 " --> pdb=" O ASN b 131 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU b 136 " --> pdb=" O ILE b 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU b 137 " --> pdb=" O ALA b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 162 removed outlier: 3.602A pdb=" N VAL b 147 " --> pdb=" O ARG b 143 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE b 151 " --> pdb=" O VAL b 147 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG b 154 " --> pdb=" O GLU b 150 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE b 159 " --> pdb=" O LEU b 155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER b 160 " --> pdb=" O ASP b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 180 removed outlier: 3.652A pdb=" N LYS b 168 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU b 169 " --> pdb=" O MET b 165 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE b 174 " --> pdb=" O GLN b 170 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL b 177 " --> pdb=" O MET b 173 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU b 178 " --> pdb=" O ILE b 174 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS b 179 " --> pdb=" O ARG b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 210 removed outlier: 3.991A pdb=" N CYS b 197 " --> pdb=" O THR b 193 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP b 200 " --> pdb=" O LYS b 196 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU b 201 " --> pdb=" O CYS b 197 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS b 202 " --> pdb=" O ILE b 198 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA b 208 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 22 removed outlier: 3.670A pdb=" N ASP c 13 " --> pdb=" O LYS c 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU c 17 " --> pdb=" O ASP c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 50 removed outlier: 3.527A pdb=" N LEU c 39 " --> pdb=" O TYR c 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP c 40 " --> pdb=" O GLN c 36 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET c 49 " --> pdb=" O LYS c 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 43 removed outlier: 3.972A pdb=" N ASN d 34 " --> pdb=" O LEU d 30 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR d 39 " --> pdb=" O GLU d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 59 removed outlier: 4.001A pdb=" N ALA d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 72 removed outlier: 3.944A pdb=" N PHE d 69 " --> pdb=" O LEU d 65 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 125 removed outlier: 3.719A pdb=" N VAL d 89 " --> pdb=" O TYR d 85 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP d 90 " --> pdb=" O THR d 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU d 93 " --> pdb=" O VAL d 89 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN d 94 " --> pdb=" O ASP d 90 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS d 98 " --> pdb=" O GLN d 94 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA d 101 " --> pdb=" O VAL d 97 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU d 102 " --> pdb=" O LYS d 98 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE d 103 " --> pdb=" O ARG d 99 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU d 104 " --> pdb=" O CYS d 100 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS d 108 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA d 109 " --> pdb=" O SER d 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU d 119 " --> pdb=" O GLU d 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS d 122 " --> pdb=" O LEU d 118 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE d 125 " --> pdb=" O MET d 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 6 through 33 removed outlier: 3.896A pdb=" N UNK e 12 " --> pdb=" O UNK e 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N UNK e 13 " --> pdb=" O UNK e 9 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK e 27 " --> pdb=" O UNK e 23 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N UNK e 28 " --> pdb=" O UNK e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 36 through 38 No H-bonds generated for 'chain 'e' and resid 36 through 38' Processing helix chain 'e' and resid 40 through 58 removed outlier: 3.965A pdb=" N UNK e 46 " --> pdb=" O UNK e 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK e 49 " --> pdb=" O UNK e 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 12 removed outlier: 3.501A pdb=" N LYS f 7 " --> pdb=" O VAL f 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG f 9 " --> pdb=" O PRO f 5 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU f 11 " --> pdb=" O LYS f 7 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 34 Proline residue: f 30 - end of helix removed outlier: 3.545A pdb=" N ILE f 33 " --> pdb=" O THR f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 43 removed outlier: 4.118A pdb=" N ARG f 43 " --> pdb=" O GLY f 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 40 through 43' Processing helix chain 'f' and resid 56 through 59 No H-bonds generated for 'chain 'f' and resid 56 through 59' Processing helix chain 'f' and resid 62 through 76 removed outlier: 3.527A pdb=" N VAL f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL f 68 " --> pdb=" O ALA f 64 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS f 72 " --> pdb=" O VAL f 68 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG f 73 " --> pdb=" O PHE f 69 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER f 74 " --> pdb=" O ASN f 70 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS f 76 " --> pdb=" O CYS f 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 31 removed outlier: 3.669A pdb=" N UNK g 7 " --> pdb=" O UNK g 3 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N UNK g 8 " --> pdb=" O UNK g 4 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK g 18 " --> pdb=" O UNK g 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK g 21 " --> pdb=" O UNK g 17 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK g 24 " --> pdb=" O UNK g 20 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N UNK g 25 " --> pdb=" O UNK g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 61 through 64 No H-bonds generated for 'chain 'g' and resid 61 through 64' Processing helix chain 'g' and resid 66 through 83 removed outlier: 3.565A pdb=" N UNK g 74 " --> pdb=" O UNK g 70 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N UNK g 77 " --> pdb=" O UNK g 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK g 78 " --> pdb=" O UNK g 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNK g 79 " --> pdb=" O UNK g 75 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N UNK g 83 " --> pdb=" O UNK g 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 15 through 25 removed outlier: 3.976A pdb=" N ASN i 19 " --> pdb=" O LYS i 15 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER i 20 " --> pdb=" O LYS i 16 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR i 24 " --> pdb=" O SER i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 36 Processing helix chain 'i' and resid 40 through 47 removed outlier: 3.535A pdb=" N LEU i 46 " --> pdb=" O LEU i 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 18 Processing helix chain '8' and resid 13 through 15 No H-bonds generated for 'chain '8' and resid 13 through 15' Processing helix chain '8' and resid 20 through 27 removed outlier: 4.517A pdb=" N GLN 8 25 " --> pdb=" O PHE 8 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain '8' and resid 35 through 59 removed outlier: 3.962A pdb=" N ILE 8 40 " --> pdb=" O PRO 8 37 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU 8 41 " --> pdb=" O GLU 8 38 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS 8 43 " --> pdb=" O ILE 8 40 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR 8 44 " --> pdb=" O GLU 8 41 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS 8 46 " --> pdb=" O LYS 8 43 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS 8 47 " --> pdb=" O THR 8 44 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER 8 48 " --> pdb=" O GLN 8 45 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR 8 49 " --> pdb=" O LYS 8 46 " (cutoff:3.500A) Proline residue: 8 50 - end of helix removed outlier: 3.830A pdb=" N LYS 8 57 " --> pdb=" O LYS 8 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 28 removed outlier: 4.071A pdb=" N MET a 25 " --> pdb=" O THR a 21 " (cutoff:3.500A) Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 44 through 53 removed outlier: 3.795A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN a 51 " --> pdb=" O GLN a 47 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 67 through 72 removed outlier: 3.767A pdb=" N LEU a 70 " --> pdb=" O THR a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 81 removed outlier: 3.847A pdb=" N ILE a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 87 No H-bonds generated for 'chain 'a' and resid 85 through 87' Processing helix chain 'a' and resid 94 through 96 No H-bonds generated for 'chain 'a' and resid 94 through 96' Processing helix chain 'a' and resid 98 through 101 No H-bonds generated for 'chain 'a' and resid 98 through 101' Processing helix chain 'a' and resid 106 through 116 removed outlier: 4.140A pdb=" N ALA a 111 " --> pdb=" O PRO a 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL a 113 " --> pdb=" O TRP a 109 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE a 114 " --> pdb=" O SER a 110 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY a 116 " --> pdb=" O THR a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 151 through 179 removed outlier: 4.049A pdb=" N ARG a 159 " --> pdb=" O ALA a 155 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN a 163 " --> pdb=" O ARG a 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR a 165 " --> pdb=" O THR a 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA a 166 " --> pdb=" O ALA a 162 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU a 170 " --> pdb=" O ALA a 166 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR a 178 " --> pdb=" O ILE a 174 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU a 179 " --> pdb=" O GLY a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 187 through 203 removed outlier: 4.034A pdb=" N THR a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU a 203 " --> pdb=" O LEU a 199 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 221 removed outlier: 3.821A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR a 212 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR a 215 " --> pdb=" O ALA a 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU a 216 " --> pdb=" O TYR a 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER a 219 " --> pdb=" O THR a 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 removed outlier: 3.699A pdb=" N ILE K 9 " --> pdb=" O ALA K 5 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY K 12 " --> pdb=" O PHE K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 36 removed outlier: 4.128A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY K 26 " --> pdb=" O GLY K 22 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 72 removed outlier: 3.611A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 14 removed outlier: 3.631A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA L 11 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L 13 " --> pdb=" O ILE L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 23 No H-bonds generated for 'chain 'L' and resid 20 through 23' Processing helix chain 'L' and resid 25 through 28 No H-bonds generated for 'chain 'L' and resid 25 through 28' Processing helix chain 'L' and resid 31 through 34 No H-bonds generated for 'chain 'L' and resid 31 through 34' Processing helix chain 'L' and resid 45 through 72 removed outlier: 3.630A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA L 68 " --> pdb=" O CYS L 64 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 30 removed outlier: 3.536A pdb=" N LYS M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY M 12 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA M 14 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY M 26 " --> pdb=" O GLY M 22 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 38 removed outlier: 3.555A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 58 removed outlier: 5.071A pdb=" N ALA M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY M 53 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU M 56 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 70 removed outlier: 3.913A pdb=" N VAL M 67 " --> pdb=" O PHE M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 12 removed outlier: 3.513A pdb=" N PHE N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY N 10 " --> pdb=" O ALA N 6 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA N 11 " --> pdb=" O LYS N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 18 removed outlier: 3.631A pdb=" N GLY N 17 " --> pdb=" O ALA N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 36 removed outlier: 3.569A pdb=" N ILE N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET N 32 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 72 removed outlier: 3.553A pdb=" N ALA N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE N 51 " --> pdb=" O PHE N 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL N 67 " --> pdb=" O PHE N 63 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA N 68 " --> pdb=" O CYS N 64 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU N 70 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE N 71 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 14 removed outlier: 3.697A pdb=" N PHE O 8 " --> pdb=" O THR O 4 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA O 13 " --> pdb=" O ILE O 9 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA O 14 " --> pdb=" O GLY O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 38 removed outlier: 3.934A pdb=" N THR O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET O 32 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE O 34 " --> pdb=" O GLY O 30 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY O 35 " --> pdb=" O SER O 31 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG O 38 " --> pdb=" O ILE O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.541A pdb=" N ALA O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 72 Processing helix chain 'P' and resid 4 through 13 removed outlier: 3.784A pdb=" N PHE P 8 " --> pdb=" O THR P 4 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE P 9 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY P 12 " --> pdb=" O PHE P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 25 removed outlier: 3.742A pdb=" N GLY P 22 " --> pdb=" O ALA P 19 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA P 23 " --> pdb=" O GLY P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 30 No H-bonds generated for 'chain 'P' and resid 27 through 30' Processing helix chain 'P' and resid 33 through 36 No H-bonds generated for 'chain 'P' and resid 33 through 36' Processing helix chain 'P' and resid 45 through 72 removed outlier: 3.575A pdb=" N ALA P 50 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU P 70 " --> pdb=" O MET P 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE P 71 " --> pdb=" O VAL P 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 23 removed outlier: 3.808A pdb=" N GLY Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA Q 11 " --> pdb=" O LYS Q 7 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 38 removed outlier: 3.952A pdb=" N MET Q 32 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG Q 38 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 72 removed outlier: 3.517A pdb=" N TYR Q 49 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA Q 68 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Q 70 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 38 removed outlier: 3.560A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA R 14 " --> pdb=" O GLY R 10 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 71 removed outlier: 3.816A pdb=" N ALA R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 55 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'u' and resid 4 through 8 Processing helix chain 'u' and resid 16 through 34 removed outlier: 3.601A pdb=" N UNK u 19 " --> pdb=" O UNK u 16 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK u 20 " --> pdb=" O UNK u 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK u 23 " --> pdb=" O UNK u 20 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N UNK u 25 " --> pdb=" O UNK u 22 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N UNK u 28 " --> pdb=" O UNK u 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK u 32 " --> pdb=" O UNK u 29 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N UNK u 33 " --> pdb=" O UNK u 30 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.719A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA A 93 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLU A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 91 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.756A pdb=" N VAL A 99 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.852A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 265 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL A 204 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 267 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE A 206 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP A 269 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 Processing sheet with id= F, first strand: chain 'B' and resid 33 through 36 removed outlier: 3.733A pdb=" N SER B 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY B 35 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 38 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.557A pdb=" N ARG B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 167 through 169 Processing sheet with id= I, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.626A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.896A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE C 76 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY C 61 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.903A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 348 through 351 removed outlier: 3.591A pdb=" N LEU C 166 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 169 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 230 through 234 removed outlier: 7.068A pdb=" N HIS C 263 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE C 202 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU C 265 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL C 204 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR C 322 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 324 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 14 through 19 removed outlier: 6.702A pdb=" N ASP D 24 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL D 18 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE D 63 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL D 51 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 85 through 88 removed outlier: 3.660A pdb=" N GLN D 114 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 308 through 311 removed outlier: 6.601A pdb=" N ALA D 333 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 217 through 222 removed outlier: 6.793A pdb=" N SER D 183 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL D 220 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE D 185 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY D 222 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY D 187 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 254 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA D 186 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE D 256 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL D 188 " --> pdb=" O PHE D 256 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 13 through 19 removed outlier: 6.726A pdb=" N ASP E 24 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL E 18 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL E 22 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE E 63 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL E 51 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU E 39 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS E 76 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.502A pdb=" N ALA E 116 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 88 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN E 114 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 333 through 336 removed outlier: 3.603A pdb=" N ALA E 333 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ILE E 154 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER E 308 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU E 156 " --> pdb=" O SER E 308 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN E 310 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 184 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 38 through 40 removed outlier: 6.720A pdb=" N ASP F 24 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL F 18 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 23 " --> pdb=" O THR F 62 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 25 " --> pdb=" O VAL F 60 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 85 through 88 removed outlier: 3.591A pdb=" N ALA F 116 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL F 88 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN F 114 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 217 through 222 removed outlier: 6.846A pdb=" N SER F 183 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N VAL F 220 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE F 185 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLY F 222 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY F 187 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER F 305 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU F 255 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR F 307 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE F 257 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL F 309 " --> pdb=" O ILE F 257 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 104 through 107 removed outlier: 7.310A pdb=" N SER G 159 " --> pdb=" O ILE G 69 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 36 through 40 removed outlier: 3.556A pdb=" N VAL H 36 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL H 38 " --> pdb=" O PHE H 45 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE H 45 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY H 43 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 55 through 57 Processing sheet with id= AA, first strand: chain 'H' and resid 61 through 66 removed outlier: 3.781A pdb=" N GLY H 61 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 118 through 121 removed outlier: 3.710A pdb=" N GLU S 151 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL S 120 " --> pdb=" O GLU S 151 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'S' and resid 162 through 164 1073 hydrogen bonds defined for protein. 3030 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: 13.29 Time building geometry restraints manager: 16.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12547 1.34 - 1.46: 7163 1.46 - 1.58: 18696 1.58 - 1.70: 21 1.70 - 1.82: 270 Bond restraints: 38697 Sorted by residual: bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.99e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.68e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.41e+01 ... (remaining 38692 not shown) Histogram of bond angle deviations from ideal: 98.55 - 106.40: 880 106.40 - 114.24: 22714 114.24 - 122.09: 22118 122.09 - 129.94: 6616 129.94 - 137.79: 112 Bond angle restraints: 52440 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.74 20.13 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.98 18.89 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.61 18.26 1.00e+00 1.00e+00 3.33e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 119.05 17.78 1.00e+00 1.00e+00 3.16e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.85 15.98 1.00e+00 1.00e+00 2.55e+02 ... (remaining 52435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 22818 33.47 - 66.94: 535 66.94 - 100.41: 52 100.41 - 133.88: 1 133.88 - 167.36: 2 Dihedral angle restraints: 23408 sinusoidal: 8551 harmonic: 14857 Sorted by residual: dihedral pdb=" CA GLU H 68 " pdb=" C GLU H 68 " pdb=" N ASP H 69 " pdb=" CA ASP H 69 " ideal model delta harmonic sigma weight residual 180.00 131.14 48.86 0 5.00e+00 4.00e-02 9.55e+01 dihedral pdb=" CA THR 8 6 " pdb=" C THR 8 6 " pdb=" N SER 8 7 " pdb=" CA SER 8 7 " ideal model delta harmonic sigma weight residual -180.00 -131.90 -48.10 0 5.00e+00 4.00e-02 9.25e+01 dihedral pdb=" CA ALA D 280 " pdb=" C ALA D 280 " pdb=" N VAL D 281 " pdb=" CA VAL D 281 " ideal model delta harmonic sigma weight residual -180.00 -131.97 -48.03 0 5.00e+00 4.00e-02 9.23e+01 ... (remaining 23405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5277 0.069 - 0.138: 839 0.138 - 0.206: 117 0.206 - 0.275: 14 0.275 - 0.344: 3 Chirality restraints: 6250 Sorted by residual: chirality pdb=" CA ALA H 49 " pdb=" N ALA H 49 " pdb=" C ALA H 49 " pdb=" CB ALA H 49 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ASN b 86 " pdb=" N ASN b 86 " pdb=" C ASN b 86 " pdb=" CB ASN b 86 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB ILE A 489 " pdb=" CA ILE A 489 " pdb=" CG1 ILE A 489 " pdb=" CG2 ILE A 489 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 6247 not shown) Planarity restraints: 6755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 39 " 0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO O 40 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO O 40 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO O 40 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 246 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A 247 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 240 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO C 241 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 241 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 241 " -0.045 5.00e-02 4.00e+02 ... (remaining 6752 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 258 2.53 - 3.13: 26062 3.13 - 3.72: 56501 3.72 - 4.31: 78920 4.31 - 4.90: 129486 Nonbonded interactions: 291227 Sorted by model distance: nonbonded pdb=" NE ARG Q 38 " pdb=" NH1 ARG R 38 " model vdw 1.943 3.200 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 2.051 2.170 nonbonded pdb=" O1B ADP D 501 " pdb="MG MG D 502 " model vdw 2.087 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 2.089 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.101 2.170 ... (remaining 291222 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' and (resid 23 through 401 or resid 410 through 510 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 23 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 510 or resid 601 through 602)) selection = (chain 'C' and (resid 23 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 401 or resid 410 through 510 or re \ sid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 12 through 476) selection = chain 'E' selection = (chain 'F' and resid 12 through 476) } ncs_group { reference = (chain 'K' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'M' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = chain 'N' selection = (chain 'O' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'Q' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'R' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.040 Extract box with map and model: 5.330 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 101.540 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.006 0.090 38697 Z= 0.393 Angle : 1.012 20.127 52440 Z= 0.614 Chirality : 0.053 0.344 6250 Planarity : 0.007 0.094 6755 Dihedral : 15.158 167.355 13870 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.37 % Favored : 93.32 % Rotamer: Outliers : 0.46 % Allowed : 10.29 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.69 (0.08), residues: 4942 helix: -4.57 (0.05), residues: 2227 sheet: -2.55 (0.20), residues: 528 loop : -3.04 (0.10), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 68 HIS 0.011 0.001 HIS F 369 PHE 0.029 0.002 PHE A 406 TYR 0.030 0.002 TYR i 21 ARG 0.013 0.001 ARG a 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 621 time to evaluate : 4.424 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: A 54 GLU cc_start: 0.7551 (pt0) cc_final: 0.7281 (pt0) REVERT: B 390 MET cc_start: 0.8653 (ttp) cc_final: 0.8264 (ttp) REVERT: B 393 GLU cc_start: 0.8120 (mp0) cc_final: 0.7910 (mp0) REVERT: C 140 ILE cc_start: 0.9090 (tp) cc_final: 0.8861 (tp) REVERT: C 226 MET cc_start: 0.7849 (mmm) cc_final: 0.7399 (mmm) REVERT: D 65 MET cc_start: 0.8567 (mmt) cc_final: 0.8298 (mmm) REVERT: E 169 MET cc_start: 0.8062 (mtm) cc_final: 0.7759 (mtp) REVERT: E 446 ILE cc_start: 0.8658 (mm) cc_final: 0.8451 (mt) REVERT: E 471 LYS cc_start: 0.8133 (tttt) cc_final: 0.7632 (ttmt) REVERT: F 170 GLU cc_start: 0.8183 (tp30) cc_final: 0.7826 (tp30) REVERT: G 204 TYR cc_start: 0.7772 (t80) cc_final: 0.7474 (t80) REVERT: G 229 MET cc_start: 0.8418 (ttp) cc_final: 0.8102 (ttp) REVERT: G 242 MET cc_start: 0.8454 (ttm) cc_final: 0.8225 (ttp) REVERT: H 111 ASN cc_start: 0.7377 (t0) cc_final: 0.6991 (t0) REVERT: H 135 ILE cc_start: 0.8080 (pt) cc_final: 0.7486 (mp) REVERT: H 139 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7773 (mt-10) REVERT: H 143 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7517 (mmtm) REVERT: I 21 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7348 (tptm) REVERT: S 6 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7526 (mmm-85) REVERT: S 109 MET cc_start: 0.8563 (tpt) cc_final: 0.8205 (tpp) REVERT: b 129 ARG cc_start: 0.6771 (ttp80) cc_final: 0.6429 (tmm160) REVERT: b 143 ARG cc_start: 0.7252 (mtt-85) cc_final: 0.6990 (mtp180) REVERT: b 148 TYR cc_start: 0.7121 (t80) cc_final: 0.6792 (t80) REVERT: b 154 ARG cc_start: 0.6301 (mmt90) cc_final: 0.5786 (mmm160) REVERT: c 21 LYS cc_start: 0.6558 (tptt) cc_final: 0.6252 (mmmt) REVERT: c 29 VAL cc_start: 0.6057 (p) cc_final: 0.5760 (t) REVERT: i 27 MET cc_start: 0.6411 (mmp) cc_final: 0.6088 (tpp) REVERT: 8 5 ASP cc_start: 0.6296 (t70) cc_final: 0.6025 (m-30) REVERT: a 24 ILE cc_start: 0.6718 (mt) cc_final: 0.6242 (mt) REVERT: a 41 ARG cc_start: 0.5461 (ptt-90) cc_final: 0.5237 (ptt180) REVERT: a 185 ASN cc_start: 0.2752 (OUTLIER) cc_final: 0.1944 (p0) REVERT: M 60 MET cc_start: 0.6097 (tpp) cc_final: 0.5616 (mmt) REVERT: M 72 LEU cc_start: 0.6189 (tp) cc_final: 0.5772 (mt) REVERT: P 36 TYR cc_start: 0.4907 (t80) cc_final: 0.3502 (t80) REVERT: Q 60 MET cc_start: 0.5537 (mmp) cc_final: 0.5186 (mmt) REVERT: R 49 TYR cc_start: 0.5087 (m-10) cc_final: 0.4549 (m-10) REVERT: R 60 MET cc_start: 0.6294 (tpp) cc_final: 0.5843 (tpp) outliers start: 17 outliers final: 2 residues processed: 635 average time/residue: 0.5385 time to fit residues: 539.5354 Evaluate side-chains 432 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 429 time to evaluate : 5.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain a residue 185 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 429 optimal weight: 9.9990 chunk 385 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 398 optimal weight: 40.0000 chunk 154 optimal weight: 6.9990 chunk 242 optimal weight: 0.8980 chunk 296 optimal weight: 0.0060 chunk 462 optimal weight: 9.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 415 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 190 ASN C 330 GLN C 341 ASN C 441 GLN C 466 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 GLN C 503 ASN D 54 HIS D 196 ASN D 479 HIS E 26 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 53 GLN E 387 GLN E 429 HIS F 174 ASN F 179 HIS F 363 ASN F 421 GLN J 27 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN H 51 HIS H 56 GLN H 138 ASN I 17 GLN b 162 GLN b 163 ASN a 47 GLN ** a 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 GLN a 66 GLN a 83 ASN a 90 HIS K 45 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38697 Z= 0.254 Angle : 0.642 11.169 52440 Z= 0.335 Chirality : 0.043 0.166 6250 Planarity : 0.005 0.061 6755 Dihedral : 7.568 172.701 5667 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 2.40 % Allowed : 15.76 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.45 (0.10), residues: 4942 helix: -3.23 (0.08), residues: 2297 sheet: -1.92 (0.22), residues: 535 loop : -2.73 (0.11), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 8 9 HIS 0.009 0.001 HIS B 471 PHE 0.022 0.002 PHE R 47 TYR 0.017 0.002 TYR f 71 ARG 0.010 0.000 ARG b 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 463 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 MET cc_start: 0.9024 (mmm) cc_final: 0.8609 (mmp) REVERT: B 390 MET cc_start: 0.8431 (ttp) cc_final: 0.8201 (ttp) REVERT: C 281 MET cc_start: 0.8691 (tmm) cc_final: 0.8367 (ttt) REVERT: C 475 GLN cc_start: 0.8184 (mt0) cc_final: 0.7942 (mp10) REVERT: D 65 MET cc_start: 0.8390 (mmt) cc_final: 0.8031 (mmm) REVERT: D 169 MET cc_start: 0.7963 (mmt) cc_final: 0.7671 (mmt) REVERT: D 234 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8495 (m) REVERT: E 169 MET cc_start: 0.7925 (mtm) cc_final: 0.7642 (mtp) REVERT: E 387 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: F 360 MET cc_start: 0.8321 (tpt) cc_final: 0.7849 (tpt) REVERT: G 87 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8096 (mtmt) REVERT: G 229 MET cc_start: 0.8236 (ttp) cc_final: 0.7917 (ttp) REVERT: G 242 MET cc_start: 0.8501 (ttm) cc_final: 0.8281 (ttp) REVERT: H 128 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7265 (ttm-80) REVERT: H 135 ILE cc_start: 0.8194 (pt) cc_final: 0.7715 (mp) REVERT: H 139 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7796 (mt-10) REVERT: I 21 LYS cc_start: 0.7792 (ttmm) cc_final: 0.7525 (tptm) REVERT: S 109 MET cc_start: 0.8115 (tpt) cc_final: 0.7809 (tpp) REVERT: b 148 TYR cc_start: 0.7350 (t80) cc_final: 0.6976 (t80) REVERT: b 154 ARG cc_start: 0.6195 (mmt90) cc_final: 0.5976 (mmm160) REVERT: b 176 TRP cc_start: 0.6952 (t60) cc_final: 0.6731 (t-100) REVERT: c 21 LYS cc_start: 0.6337 (tptt) cc_final: 0.5618 (tppt) REVERT: f 66 TYR cc_start: 0.6586 (t80) cc_final: 0.6235 (t80) REVERT: f 78 LEU cc_start: 0.5194 (OUTLIER) cc_final: 0.4945 (pp) REVERT: i 27 MET cc_start: 0.6665 (mmp) cc_final: 0.6266 (tpp) REVERT: 8 9 TRP cc_start: 0.4268 (OUTLIER) cc_final: 0.3884 (t60) REVERT: a 6 PHE cc_start: 0.2415 (m-10) cc_final: 0.1724 (m-10) REVERT: a 52 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7625 (tt) REVERT: a 185 ASN cc_start: 0.3524 (OUTLIER) cc_final: 0.2462 (p0) REVERT: M 60 MET cc_start: 0.6038 (tpp) cc_final: 0.5701 (mmt) REVERT: M 72 LEU cc_start: 0.6372 (tp) cc_final: 0.6016 (mt) REVERT: N 2 ILE cc_start: 0.1336 (OUTLIER) cc_final: 0.1057 (tp) REVERT: O 66 MET cc_start: 0.1238 (ttt) cc_final: 0.0971 (mmm) REVERT: P 32 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.5039 (ttm) REVERT: R 56 LEU cc_start: 0.8155 (tp) cc_final: 0.7883 (tp) outliers start: 89 outliers final: 45 residues processed: 520 average time/residue: 0.5193 time to fit residues: 442.1017 Evaluate side-chains 483 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 430 time to evaluate : 4.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain b residue 69 TYR Chi-restraints excluded: chain c residue 17 GLU Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain 8 residue 13 ILE Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 90 HIS Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 256 optimal weight: 0.2980 chunk 143 optimal weight: 7.9990 chunk 384 optimal weight: 50.0000 chunk 314 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 463 optimal weight: 30.0000 chunk 500 optimal weight: 10.0000 chunk 412 optimal weight: 40.0000 chunk 459 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 371 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 GLN b 114 GLN b 158 HIS b 163 ASN a 61 HIS ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 38697 Z= 0.306 Angle : 0.627 11.577 52440 Z= 0.322 Chirality : 0.044 0.266 6250 Planarity : 0.004 0.056 6755 Dihedral : 7.255 149.342 5667 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.45 % Favored : 93.28 % Rotamer: Outliers : 3.18 % Allowed : 17.83 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.76 (0.10), residues: 4942 helix: -2.49 (0.09), residues: 2311 sheet: -1.77 (0.22), residues: 529 loop : -2.55 (0.12), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 8 9 HIS 0.017 0.001 HIS a 90 PHE 0.025 0.002 PHE L 47 TYR 0.028 0.002 TYR c 18 ARG 0.009 0.000 ARG b 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 447 time to evaluate : 4.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8168 (tp30) cc_final: 0.7915 (tp30) REVERT: A 157 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.8990 (t) REVERT: B 312 MET cc_start: 0.9044 (mmm) cc_final: 0.8655 (mmp) REVERT: B 390 MET cc_start: 0.8692 (ttp) cc_final: 0.8315 (ttp) REVERT: C 349 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7758 (mp-120) REVERT: D 65 MET cc_start: 0.8381 (mmt) cc_final: 0.8104 (mmm) REVERT: D 234 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8556 (m) REVERT: D 360 MET cc_start: 0.8567 (tpp) cc_final: 0.8293 (tpt) REVERT: E 169 MET cc_start: 0.8097 (mtm) cc_final: 0.7830 (mtp) REVERT: E 436 LEU cc_start: 0.8716 (tp) cc_final: 0.8253 (tp) REVERT: G 242 MET cc_start: 0.8538 (ttm) cc_final: 0.8323 (ttp) REVERT: H 47 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6745 (mm) REVERT: H 128 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7219 (ttm-80) REVERT: H 135 ILE cc_start: 0.8039 (pt) cc_final: 0.7548 (mp) REVERT: I 21 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7486 (tptm) REVERT: S 109 MET cc_start: 0.8291 (tpt) cc_final: 0.8035 (tpp) REVERT: b 148 TYR cc_start: 0.7338 (t80) cc_final: 0.6921 (t80) REVERT: b 154 ARG cc_start: 0.6271 (mmt90) cc_final: 0.5902 (mmm160) REVERT: c 14 LYS cc_start: 0.6635 (mttt) cc_final: 0.6284 (mttt) REVERT: f 78 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.5019 (pp) REVERT: i 27 MET cc_start: 0.6817 (mmp) cc_final: 0.6257 (tpp) REVERT: 8 5 ASP cc_start: 0.5878 (t70) cc_final: 0.4708 (t0) REVERT: 8 9 TRP cc_start: 0.4836 (OUTLIER) cc_final: 0.4202 (t60) REVERT: a 6 PHE cc_start: 0.2645 (m-10) cc_final: 0.2216 (m-10) REVERT: a 15 MET cc_start: 0.6569 (tpp) cc_final: 0.5320 (mmt) REVERT: M 60 MET cc_start: 0.6345 (tpp) cc_final: 0.5838 (mmt) REVERT: M 72 LEU cc_start: 0.6198 (tp) cc_final: 0.5827 (mt) REVERT: N 2 ILE cc_start: 0.1410 (OUTLIER) cc_final: 0.1038 (tp) REVERT: N 44 GLN cc_start: 0.6070 (OUTLIER) cc_final: 0.5857 (tm-30) REVERT: O 66 MET cc_start: 0.1707 (ttt) cc_final: 0.1164 (mmm) REVERT: P 32 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.4878 (ttm) REVERT: Q 60 MET cc_start: 0.7159 (tpt) cc_final: 0.6719 (tpp) outliers start: 118 outliers final: 63 residues processed: 531 average time/residue: 0.4934 time to fit residues: 430.5986 Evaluate side-chains 492 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 420 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 69 TYR Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 59 LEU Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain 8 residue 13 ILE Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 457 optimal weight: 8.9990 chunk 348 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 310 optimal weight: 0.6980 chunk 464 optimal weight: 30.0000 chunk 492 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 440 optimal weight: 4.9990 chunk 132 optimal weight: 0.0670 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN F 369 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 ASN L 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 38697 Z= 0.236 Angle : 0.582 11.131 52440 Z= 0.298 Chirality : 0.043 0.323 6250 Planarity : 0.004 0.054 6755 Dihedral : 6.775 118.873 5665 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.85 % Favored : 93.93 % Rotamer: Outliers : 3.47 % Allowed : 19.26 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.19 (0.11), residues: 4942 helix: -1.93 (0.10), residues: 2314 sheet: -1.56 (0.23), residues: 512 loop : -2.34 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 8 9 HIS 0.007 0.001 HIS F 369 PHE 0.025 0.001 PHE Q 63 TYR 0.026 0.001 TYR c 18 ARG 0.005 0.000 ARG b 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 452 time to evaluate : 4.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8116 (tp30) cc_final: 0.7892 (tp30) REVERT: A 157 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8933 (t) REVERT: B 312 MET cc_start: 0.9034 (mmm) cc_final: 0.8661 (mmp) REVERT: B 390 MET cc_start: 0.8690 (ttp) cc_final: 0.8451 (ttp) REVERT: C 349 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7227 (mt0) REVERT: D 65 MET cc_start: 0.8305 (mmt) cc_final: 0.8064 (mmm) REVERT: D 234 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8538 (m) REVERT: D 360 MET cc_start: 0.8559 (tpp) cc_final: 0.8344 (tpt) REVERT: D 479 HIS cc_start: 0.7276 (m-70) cc_final: 0.6969 (m90) REVERT: E 169 MET cc_start: 0.7977 (mtm) cc_final: 0.7636 (mtp) REVERT: F 168 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8853 (tt) REVERT: F 360 MET cc_start: 0.8312 (tpt) cc_final: 0.7777 (tpt) REVERT: H 128 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.7145 (ttm-80) REVERT: I 21 LYS cc_start: 0.7724 (ttmm) cc_final: 0.7405 (tptm) REVERT: I 27 LEU cc_start: 0.7932 (mt) cc_final: 0.7711 (mm) REVERT: S 109 MET cc_start: 0.8293 (tpt) cc_final: 0.8035 (tpp) REVERT: b 148 TYR cc_start: 0.7361 (t80) cc_final: 0.6899 (t80) REVERT: b 154 ARG cc_start: 0.6394 (mmt90) cc_final: 0.5898 (mmm160) REVERT: f 78 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.4457 (pp) REVERT: i 27 MET cc_start: 0.6597 (mmp) cc_final: 0.6184 (tpp) REVERT: 8 5 ASP cc_start: 0.5652 (t70) cc_final: 0.4966 (t0) REVERT: 8 9 TRP cc_start: 0.4483 (OUTLIER) cc_final: 0.4067 (t60) REVERT: a 6 PHE cc_start: 0.2469 (m-80) cc_final: 0.1540 (m-10) REVERT: a 52 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7585 (tt) REVERT: a 56 GLN cc_start: 0.6163 (mp-120) cc_final: 0.5913 (mp10) REVERT: a 58 MET cc_start: 0.4970 (tmm) cc_final: 0.4453 (tmm) REVERT: M 72 LEU cc_start: 0.6325 (tp) cc_final: 0.5846 (mt) REVERT: N 2 ILE cc_start: 0.1426 (OUTLIER) cc_final: 0.1062 (tp) REVERT: N 44 GLN cc_start: 0.6269 (OUTLIER) cc_final: 0.5916 (tm-30) REVERT: O 66 MET cc_start: 0.1808 (ttt) cc_final: 0.1328 (mmm) REVERT: Q 60 MET cc_start: 0.7187 (tpt) cc_final: 0.6816 (tpp) REVERT: Q 66 MET cc_start: 0.5618 (mmt) cc_final: 0.4868 (mtt) REVERT: R 72 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7174 (mm) outliers start: 129 outliers final: 84 residues processed: 548 average time/residue: 0.4856 time to fit residues: 439.1188 Evaluate side-chains 525 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 431 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 163 ASN Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain 8 residue 13 ILE Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 146 THR Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 409 optimal weight: 30.0000 chunk 279 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 366 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 chunk 340 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 251 optimal weight: 0.7980 chunk 441 optimal weight: 0.0870 chunk 124 optimal weight: 0.1980 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN C 466 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 HIS ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38697 Z= 0.207 Angle : 0.566 11.061 52440 Z= 0.287 Chirality : 0.042 0.186 6250 Planarity : 0.004 0.053 6755 Dihedral : 6.494 112.252 5665 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.63 % Favored : 94.17 % Rotamer: Outliers : 3.80 % Allowed : 19.90 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.80 (0.11), residues: 4942 helix: -1.56 (0.10), residues: 2323 sheet: -1.43 (0.23), residues: 515 loop : -2.20 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 8 9 HIS 0.003 0.001 HIS F 369 PHE 0.019 0.001 PHE S 141 TYR 0.021 0.001 TYR c 18 ARG 0.006 0.000 ARG J 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 445 time to evaluate : 4.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8946 (t) REVERT: B 62 MET cc_start: 0.8365 (ttp) cc_final: 0.8106 (ttm) REVERT: B 312 MET cc_start: 0.9012 (mmm) cc_final: 0.8625 (mmp) REVERT: B 390 MET cc_start: 0.8694 (ttp) cc_final: 0.8337 (ttp) REVERT: D 65 MET cc_start: 0.8018 (mmt) cc_final: 0.7743 (mmm) REVERT: D 234 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8495 (m) REVERT: D 254 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8706 (mp) REVERT: D 356 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8430 (t) REVERT: D 360 MET cc_start: 0.8511 (tpp) cc_final: 0.8296 (tpt) REVERT: E 169 MET cc_start: 0.7969 (mtm) cc_final: 0.7655 (mtp) REVERT: F 360 MET cc_start: 0.8257 (tpt) cc_final: 0.7767 (tpt) REVERT: G 52 TYR cc_start: 0.7215 (m-80) cc_final: 0.6710 (m-80) REVERT: H 47 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6958 (mm) REVERT: H 128 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7153 (ttm-80) REVERT: I 21 LYS cc_start: 0.7697 (ttmm) cc_final: 0.7396 (tptm) REVERT: I 27 LEU cc_start: 0.7920 (mt) cc_final: 0.7701 (mm) REVERT: S 109 MET cc_start: 0.8286 (tpt) cc_final: 0.8030 (tpp) REVERT: b 148 TYR cc_start: 0.7063 (t80) cc_final: 0.6634 (t80) REVERT: b 154 ARG cc_start: 0.6448 (mmt90) cc_final: 0.5944 (mmm160) REVERT: f 78 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4744 (pp) REVERT: i 27 MET cc_start: 0.6588 (mmp) cc_final: 0.6180 (tpp) REVERT: 8 5 ASP cc_start: 0.5613 (t70) cc_final: 0.5007 (t0) REVERT: 8 9 TRP cc_start: 0.4027 (OUTLIER) cc_final: 0.3714 (t60) REVERT: a 15 MET cc_start: 0.6227 (tpp) cc_final: 0.5337 (mmt) REVERT: a 52 LEU cc_start: 0.7869 (mp) cc_final: 0.7448 (tt) REVERT: a 56 GLN cc_start: 0.6099 (mp-120) cc_final: 0.5765 (mp-120) REVERT: K 49 TYR cc_start: 0.5110 (m-10) cc_final: 0.4798 (m-10) REVERT: M 66 MET cc_start: 0.6961 (ppp) cc_final: 0.6312 (ppp) REVERT: M 72 LEU cc_start: 0.6319 (tp) cc_final: 0.5799 (mt) REVERT: N 2 ILE cc_start: 0.1435 (OUTLIER) cc_final: 0.1083 (tp) REVERT: Q 60 MET cc_start: 0.7106 (tpt) cc_final: 0.6745 (tpp) outliers start: 141 outliers final: 102 residues processed: 550 average time/residue: 0.4739 time to fit residues: 433.5093 Evaluate side-chains 532 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 422 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 69 TYR Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain i residue 39 LEU Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain 8 residue 13 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 90 HIS Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 165 optimal weight: 6.9990 chunk 443 optimal weight: 5.9990 chunk 97 optimal weight: 0.0980 chunk 288 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 492 optimal weight: 5.9990 chunk 408 optimal weight: 30.0000 chunk 228 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 GLN D 479 HIS ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 128 GLN b 153 ASN b 163 ASN L 45 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 38697 Z= 0.423 Angle : 0.681 12.051 52440 Z= 0.347 Chirality : 0.046 0.214 6250 Planarity : 0.005 0.052 6755 Dihedral : 6.831 104.308 5665 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.91 % Favored : 91.87 % Rotamer: Outliers : 4.74 % Allowed : 20.25 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.89 (0.11), residues: 4942 helix: -1.54 (0.10), residues: 2321 sheet: -1.59 (0.23), residues: 511 loop : -2.33 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 8 9 HIS 0.043 0.001 HIS a 90 PHE 0.022 0.002 PHE C 504 TYR 0.033 0.002 TYR c 18 ARG 0.006 0.001 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 430 time to evaluate : 4.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9075 (t) REVERT: B 206 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8830 (mt) REVERT: B 312 MET cc_start: 0.9063 (mmm) cc_final: 0.8693 (mmp) REVERT: B 390 MET cc_start: 0.8655 (ttp) cc_final: 0.8289 (ttp) REVERT: C 349 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7484 (mp-120) REVERT: D 234 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8572 (m) REVERT: D 254 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8675 (mp) REVERT: E 169 MET cc_start: 0.7943 (mtm) cc_final: 0.7668 (mtp) REVERT: F 168 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8913 (tt) REVERT: F 360 MET cc_start: 0.8188 (tpt) cc_final: 0.7557 (tpt) REVERT: G 95 ASN cc_start: 0.7328 (t0) cc_final: 0.6806 (t0) REVERT: G 161 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6982 (mt) REVERT: H 47 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6900 (mm) REVERT: H 128 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.6901 (ttm-80) REVERT: I 21 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7484 (tptm) REVERT: I 27 LEU cc_start: 0.7958 (mt) cc_final: 0.7726 (mm) REVERT: S 109 MET cc_start: 0.8315 (tpt) cc_final: 0.8059 (tpp) REVERT: b 148 TYR cc_start: 0.7506 (t80) cc_final: 0.7047 (t80) REVERT: b 154 ARG cc_start: 0.6634 (mmt90) cc_final: 0.5988 (mmm160) REVERT: f 78 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5563 (pp) REVERT: i 27 MET cc_start: 0.6610 (mmp) cc_final: 0.6201 (tpp) REVERT: 8 9 TRP cc_start: 0.4741 (OUTLIER) cc_final: 0.3454 (t60) REVERT: a 15 MET cc_start: 0.6628 (tpp) cc_final: 0.5742 (mmt) REVERT: a 52 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7274 (tt) REVERT: a 56 GLN cc_start: 0.6256 (mp-120) cc_final: 0.5809 (mp-120) REVERT: M 66 MET cc_start: 0.6784 (ppp) cc_final: 0.6144 (ppp) REVERT: M 69 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6223 (m-80) REVERT: N 2 ILE cc_start: 0.1430 (OUTLIER) cc_final: 0.1035 (tp) REVERT: N 72 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5266 (mt) outliers start: 176 outliers final: 128 residues processed: 572 average time/residue: 0.4807 time to fit residues: 459.1044 Evaluate side-chains 555 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 413 time to evaluate : 4.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 69 TYR Chi-restraints excluded: chain b residue 163 ASN Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain i residue 39 LEU Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 99 SER Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 474 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 359 optimal weight: 7.9990 chunk 278 optimal weight: 0.5980 chunk 414 optimal weight: 30.0000 chunk 275 optimal weight: 6.9990 chunk 490 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 299 optimal weight: 0.6980 chunk 226 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 HIS ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS E 387 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 146 GLN b 163 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38697 Z= 0.265 Angle : 0.602 13.155 52440 Z= 0.306 Chirality : 0.043 0.182 6250 Planarity : 0.004 0.053 6755 Dihedral : 6.595 99.797 5665 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.95 % Favored : 93.87 % Rotamer: Outliers : 4.34 % Allowed : 21.36 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.63 (0.11), residues: 4942 helix: -1.31 (0.10), residues: 2314 sheet: -1.52 (0.23), residues: 516 loop : -2.20 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 8 9 HIS 0.007 0.001 HIS a 90 PHE 0.032 0.001 PHE M 73 TYR 0.045 0.002 TYR c 18 ARG 0.006 0.000 ARG J 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 430 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9102 (t) REVERT: B 312 MET cc_start: 0.9037 (mmm) cc_final: 0.8646 (mmp) REVERT: B 390 MET cc_start: 0.8677 (ttp) cc_final: 0.8384 (ttp) REVERT: D 234 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8493 (m) REVERT: D 254 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8741 (mp) REVERT: D 360 MET cc_start: 0.8506 (tpp) cc_final: 0.8224 (tpt) REVERT: D 433 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8395 (tt) REVERT: D 479 HIS cc_start: 0.7367 (m-70) cc_final: 0.6912 (m90) REVERT: E 169 MET cc_start: 0.7894 (mtm) cc_final: 0.7602 (mtp) REVERT: F 168 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8869 (tt) REVERT: F 360 MET cc_start: 0.8255 (tpt) cc_final: 0.7544 (tpt) REVERT: J 35 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7621 (tpt170) REVERT: G 95 ASN cc_start: 0.7314 (t0) cc_final: 0.6801 (t0) REVERT: H 128 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7074 (ttm-80) REVERT: H 135 ILE cc_start: 0.8795 (mp) cc_final: 0.8587 (mp) REVERT: I 21 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7477 (tptm) REVERT: I 27 LEU cc_start: 0.7944 (mt) cc_final: 0.7720 (mm) REVERT: S 109 MET cc_start: 0.8313 (tpt) cc_final: 0.8048 (tpp) REVERT: b 148 TYR cc_start: 0.7396 (t80) cc_final: 0.6900 (t80) REVERT: b 154 ARG cc_start: 0.6636 (mmt90) cc_final: 0.5971 (mmm160) REVERT: c 22 ARG cc_start: 0.7038 (mtp85) cc_final: 0.6782 (mtt180) REVERT: i 27 MET cc_start: 0.6593 (mmp) cc_final: 0.6174 (tpp) REVERT: 8 9 TRP cc_start: 0.4575 (OUTLIER) cc_final: 0.3730 (t-100) REVERT: a 15 MET cc_start: 0.6654 (tpp) cc_final: 0.5559 (mmt) REVERT: a 52 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7215 (tt) REVERT: a 56 GLN cc_start: 0.6110 (mp-120) cc_final: 0.5663 (mp-120) REVERT: M 66 MET cc_start: 0.6726 (ppp) cc_final: 0.6093 (ppp) REVERT: M 69 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: M 72 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6217 (pp) REVERT: N 2 ILE cc_start: 0.1424 (OUTLIER) cc_final: 0.1051 (tp) REVERT: O 66 MET cc_start: 0.2512 (OUTLIER) cc_final: 0.2200 (mmm) REVERT: Q 60 MET cc_start: 0.6922 (tpt) cc_final: 0.6581 (tpp) outliers start: 161 outliers final: 127 residues processed: 552 average time/residue: 0.4741 time to fit residues: 433.6228 Evaluate side-chains 559 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 421 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 69 TYR Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain i residue 39 LEU Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 99 SER Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 66 MET Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 303 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 311 optimal weight: 4.9990 chunk 334 optimal weight: 8.9990 chunk 242 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 385 optimal weight: 0.6980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 200 HIS F 174 ASN F 445 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38697 Z= 0.169 Angle : 0.560 13.517 52440 Z= 0.281 Chirality : 0.042 0.294 6250 Planarity : 0.004 0.052 6755 Dihedral : 6.156 96.667 5665 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.26 % Favored : 94.56 % Rotamer: Outliers : 3.50 % Allowed : 22.54 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.23 (0.12), residues: 4942 helix: -0.97 (0.11), residues: 2310 sheet: -1.32 (0.23), residues: 522 loop : -2.01 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 8 9 HIS 0.004 0.001 HIS F 369 PHE 0.021 0.001 PHE R 8 TYR 0.041 0.001 TYR c 18 ARG 0.006 0.000 ARG J 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 449 time to evaluate : 4.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9012 (t) REVERT: A 499 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: B 312 MET cc_start: 0.9024 (mmm) cc_final: 0.8601 (mmp) REVERT: B 390 MET cc_start: 0.8647 (ttp) cc_final: 0.8424 (ttp) REVERT: C 253 MET cc_start: 0.7444 (mtt) cc_final: 0.6901 (mtt) REVERT: C 328 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7848 (tm-30) REVERT: D 254 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8658 (mp) REVERT: D 356 THR cc_start: 0.8671 (p) cc_final: 0.8465 (t) REVERT: D 433 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8436 (tt) REVERT: E 169 MET cc_start: 0.7854 (mtm) cc_final: 0.7550 (mtp) REVERT: E 201 GLU cc_start: 0.7375 (tt0) cc_final: 0.7114 (tt0) REVERT: E 471 LYS cc_start: 0.8073 (tttm) cc_final: 0.7817 (ttmt) REVERT: F 168 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8812 (tt) REVERT: F 170 GLU cc_start: 0.7768 (tp30) cc_final: 0.7506 (tp30) REVERT: F 360 MET cc_start: 0.8273 (tpt) cc_final: 0.7632 (tpt) REVERT: J 35 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7705 (tpt170) REVERT: G 52 TYR cc_start: 0.7491 (m-80) cc_final: 0.6929 (m-80) REVERT: G 140 ASP cc_start: 0.7869 (m-30) cc_final: 0.7487 (m-30) REVERT: H 128 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7230 (ttm-80) REVERT: I 21 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7404 (tptm) REVERT: S 109 MET cc_start: 0.8251 (tpt) cc_final: 0.7997 (tpp) REVERT: b 148 TYR cc_start: 0.6771 (t80) cc_final: 0.6194 (t80) REVERT: b 154 ARG cc_start: 0.6792 (mmt90) cc_final: 0.6050 (mmm160) REVERT: i 27 MET cc_start: 0.6544 (mmp) cc_final: 0.6115 (tpp) REVERT: 8 9 TRP cc_start: 0.4294 (OUTLIER) cc_final: 0.3719 (t-100) REVERT: a 15 MET cc_start: 0.6272 (tpp) cc_final: 0.5465 (mmt) REVERT: a 52 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7157 (tt) REVERT: a 56 GLN cc_start: 0.5780 (mp-120) cc_final: 0.5464 (mp-120) REVERT: M 66 MET cc_start: 0.6768 (ppp) cc_final: 0.6279 (ppp) REVERT: M 69 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: M 72 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6329 (pp) REVERT: N 2 ILE cc_start: 0.1699 (OUTLIER) cc_final: 0.1411 (tp) REVERT: O 51 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5356 (tt) REVERT: O 66 MET cc_start: 0.2591 (OUTLIER) cc_final: 0.2267 (mmm) REVERT: Q 60 MET cc_start: 0.6820 (tpt) cc_final: 0.6484 (tpp) outliers start: 130 outliers final: 106 residues processed: 547 average time/residue: 0.4702 time to fit residues: 426.5407 Evaluate side-chains 546 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 428 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 163 ASN Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain i residue 39 LEU Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 99 SER Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain a residue 214 PHE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 66 MET Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 446 optimal weight: 9.9990 chunk 470 optimal weight: 7.9990 chunk 428 optimal weight: 0.5980 chunk 457 optimal weight: 9.9990 chunk 469 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 358 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 413 optimal weight: 20.0000 chunk 432 optimal weight: 0.0980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 243 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 GLN D 479 HIS F 445 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 38697 Z= 0.430 Angle : 0.693 13.212 52440 Z= 0.350 Chirality : 0.047 0.196 6250 Planarity : 0.005 0.049 6755 Dihedral : 6.613 110.132 5665 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.95 % Favored : 91.85 % Rotamer: Outliers : 4.26 % Allowed : 22.27 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.51 (0.12), residues: 4942 helix: -1.14 (0.11), residues: 2315 sheet: -1.52 (0.23), residues: 529 loop : -2.21 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 8 9 HIS 0.004 0.001 HIS H 51 PHE 0.032 0.002 PHE a 26 TYR 0.042 0.002 TYR c 18 ARG 0.005 0.001 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 426 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9111 (t) REVERT: A 499 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: B 312 MET cc_start: 0.9055 (mmm) cc_final: 0.8672 (mmp) REVERT: B 390 MET cc_start: 0.8616 (ttp) cc_final: 0.8300 (ttp) REVERT: D 234 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8567 (m) REVERT: D 254 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8759 (mp) REVERT: D 433 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8629 (tt) REVERT: E 131 GLU cc_start: 0.7690 (tp30) cc_final: 0.7266 (pm20) REVERT: E 169 MET cc_start: 0.7965 (mtm) cc_final: 0.7638 (mtp) REVERT: F 168 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8904 (tt) REVERT: F 170 GLU cc_start: 0.7781 (tp30) cc_final: 0.7484 (tp30) REVERT: F 360 MET cc_start: 0.8123 (tpt) cc_final: 0.7199 (tpt) REVERT: J 35 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7623 (tpt170) REVERT: G 95 ASN cc_start: 0.7336 (t0) cc_final: 0.6819 (t0) REVERT: G 140 ASP cc_start: 0.7913 (m-30) cc_final: 0.7492 (m-30) REVERT: H 128 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7039 (ttm-80) REVERT: I 21 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7482 (tptm) REVERT: S 109 MET cc_start: 0.8406 (tpt) cc_final: 0.8168 (tpp) REVERT: b 148 TYR cc_start: 0.7066 (t80) cc_final: 0.6541 (t80) REVERT: b 154 ARG cc_start: 0.6553 (mmt90) cc_final: 0.5899 (mmm160) REVERT: i 27 MET cc_start: 0.6579 (mmp) cc_final: 0.6156 (tpp) REVERT: 8 9 TRP cc_start: 0.4497 (OUTLIER) cc_final: 0.3916 (t-100) REVERT: a 15 MET cc_start: 0.6442 (tpp) cc_final: 0.5730 (mmt) REVERT: M 66 MET cc_start: 0.6886 (ppp) cc_final: 0.6276 (ppp) REVERT: M 69 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6441 (m-80) REVERT: M 72 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6134 (pp) REVERT: N 2 ILE cc_start: 0.1573 (OUTLIER) cc_final: 0.1241 (tp) REVERT: R 39 ASN cc_start: 0.6824 (p0) cc_final: 0.6159 (p0) outliers start: 158 outliers final: 133 residues processed: 547 average time/residue: 0.4744 time to fit residues: 431.6032 Evaluate side-chains 560 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 417 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 200 ASP Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain i residue 39 LEU Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 146 THR Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 455 optimal weight: 3.9990 chunk 300 optimal weight: 0.8980 chunk 483 optimal weight: 20.0000 chunk 295 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 507 optimal weight: 20.0000 chunk 466 optimal weight: 5.9990 chunk 403 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 ASN L 45 GLN P 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38697 Z= 0.227 Angle : 0.600 12.930 52440 Z= 0.300 Chirality : 0.043 0.208 6250 Planarity : 0.004 0.053 6755 Dihedral : 6.261 104.238 5665 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 3.66 % Allowed : 23.11 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.22 (0.12), residues: 4942 helix: -0.93 (0.11), residues: 2306 sheet: -1.32 (0.23), residues: 526 loop : -2.05 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 8 9 HIS 0.005 0.001 HIS F 369 PHE 0.031 0.001 PHE a 26 TYR 0.038 0.001 TYR c 18 ARG 0.005 0.000 ARG J 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 432 time to evaluate : 5.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.9031 (t) REVERT: A 499 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: B 312 MET cc_start: 0.9040 (mmm) cc_final: 0.8632 (mmp) REVERT: B 390 MET cc_start: 0.8582 (ttp) cc_final: 0.8352 (ttp) REVERT: B 415 GLN cc_start: 0.6701 (mp10) cc_final: 0.6243 (mp10) REVERT: C 328 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7890 (tm-30) REVERT: D 234 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8469 (m) REVERT: D 254 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8778 (mp) REVERT: D 433 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8456 (tt) REVERT: D 479 HIS cc_start: 0.7550 (m-70) cc_final: 0.7122 (m90) REVERT: E 131 GLU cc_start: 0.7745 (tp30) cc_final: 0.7342 (pm20) REVERT: E 169 MET cc_start: 0.7876 (mtm) cc_final: 0.7546 (mtp) REVERT: F 168 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8829 (tt) REVERT: F 170 GLU cc_start: 0.7768 (tp30) cc_final: 0.7442 (tp30) REVERT: J 35 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7655 (tpt170) REVERT: G 52 TYR cc_start: 0.7579 (m-80) cc_final: 0.7079 (m-80) REVERT: G 95 ASN cc_start: 0.7331 (t0) cc_final: 0.6814 (t0) REVERT: G 140 ASP cc_start: 0.7896 (m-30) cc_final: 0.7473 (m-30) REVERT: H 128 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.7123 (ttm-80) REVERT: I 21 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7488 (tptm) REVERT: S 109 MET cc_start: 0.8315 (tpt) cc_final: 0.8073 (tpp) REVERT: b 148 TYR cc_start: 0.6853 (t80) cc_final: 0.6242 (t80) REVERT: b 154 ARG cc_start: 0.6760 (mmt90) cc_final: 0.5971 (mmm160) REVERT: i 27 MET cc_start: 0.6557 (mmp) cc_final: 0.6125 (tpp) REVERT: 8 9 TRP cc_start: 0.4391 (OUTLIER) cc_final: 0.3884 (t-100) REVERT: a 15 MET cc_start: 0.6567 (tpp) cc_final: 0.5593 (mmt) REVERT: M 66 MET cc_start: 0.6786 (ppp) cc_final: 0.6280 (ppp) REVERT: M 69 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: N 2 ILE cc_start: 0.1816 (OUTLIER) cc_final: 0.1518 (tp) REVERT: O 51 ILE cc_start: 0.5546 (OUTLIER) cc_final: 0.5239 (tt) REVERT: Q 66 MET cc_start: 0.5398 (mmt) cc_final: 0.4695 (mtt) outliers start: 136 outliers final: 115 residues processed: 537 average time/residue: 0.5034 time to fit residues: 449.9938 Evaluate side-chains 548 residues out of total 4034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 423 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 163 ASN Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain i residue 39 LEU Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 247 optimal weight: 0.0370 chunk 320 optimal weight: 7.9990 chunk 430 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 372 optimal weight: 0.2980 chunk 59 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 404 optimal weight: 40.0000 chunk 169 optimal weight: 0.0020 chunk 415 optimal weight: 30.0000 chunk 51 optimal weight: 0.6980 overall best weight: 0.3066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.153850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119019 restraints weight = 60261.032| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.72 r_work: 0.3087 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 38697 Z= 0.236 Angle : 0.702 59.200 52440 Z= 0.377 Chirality : 0.042 0.476 6250 Planarity : 0.004 0.057 6755 Dihedral : 6.258 104.189 5665 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 3.69 % Allowed : 23.16 % Favored : 73.15 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.20 (0.12), residues: 4942 helix: -0.91 (0.11), residues: 2307 sheet: -1.31 (0.23), residues: 526 loop : -2.04 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 8 9 HIS 0.004 0.001 HIS C 471 PHE 0.028 0.001 PHE a 26 TYR 0.036 0.001 TYR c 18 ARG 0.004 0.000 ARG J 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9042.85 seconds wall clock time: 163 minutes 33.38 seconds (9813.38 seconds total)