Starting phenix.real_space_refine on Fri Feb 23 10:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5i_0677/02_2024/6j5i_0677_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5i_0677/02_2024/6j5i_0677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5i_0677/02_2024/6j5i_0677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5i_0677/02_2024/6j5i_0677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5i_0677/02_2024/6j5i_0677_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5i_0677/02_2024/6j5i_0677_updated.pdb" } resolution = 3.34 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 143 5.16 5 C 24146 2.51 5 N 6603 2.21 5 O 7234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A GLU 440": "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 492": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E GLU 368": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J GLU 40": "OE1" <-> "OE2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G GLU 264": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "S GLU 15": "OE1" <-> "OE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "S ARG 113": "NH1" <-> "NH2" Residue "S GLU 115": "OE1" <-> "OE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ARG 165": "NH1" <-> "NH2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "S ARG 187": "NH1" <-> "NH2" Residue "b GLU 111": "OE1" <-> "OE2" Residue "b TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 175": "NH1" <-> "NH2" Residue "b GLU 190": "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" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38144 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3873 Classifications: {'peptide': 509} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 490} Chain: "B" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3669 Classifications: {'peptide': 481} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 462} Chain breaks: 1 Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3821 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} 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: "D" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3564 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3532 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3536 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 411 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 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: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 973 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} 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: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1435 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain: "b" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1476 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 115 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: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 495 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 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: {'TRANS': 83} 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: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 303 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 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: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1687 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 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: 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: "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: 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: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 19.79, per 1000 atoms: 0.52 Number of scatterers: 38144 At special positions: 0 Unit cell: (182.16, 224.94, 168.36, 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 143 16.00 P 13 15.00 Mg 5 11.99 O 7234 8.00 N 6603 7.00 C 24146 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: 14.43 Conformation dependent library (CDL) restraints added in 7.4 seconds 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 202 helices and 26 sheets defined 45.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 11 through 17 removed outlier: 3.934A pdb=" N ARG A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.802A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.081A pdb=" N GLN A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (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 248 through 253 removed outlier: 3.730A pdb=" N MET A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.818A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A 281 " --> pdb=" O ALA A 277 " (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 296 through 304 removed outlier: 4.413A pdb=" N PHE A 299 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG A 304 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.840A pdb=" N ILE A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.684A pdb=" N GLY A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.584A pdb=" N SER A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.501A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 448 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 removed outlier: 4.600A pdb=" N ASN A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 494 No H-bonds generated for 'chain 'A' and resid 491 through 494' Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.663A pdb=" N THR A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 176 through 190 removed outlier: 4.607A pdb=" N ASP B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.513A pdb=" N LYS B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.920A pdb=" N MET B 281 " --> pdb=" O ALA B 277 " (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 300 through 308 removed outlier: 3.532A pdb=" N ARG B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.792A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 384 No H-bonds generated for 'chain 'B' and resid 381 through 384' Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 414 through 424 removed outlier: 3.687A pdb=" N SER B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 removed outlier: 3.535A pdb=" N VAL B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.562A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 475 " --> pdb=" O HIS B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 removed outlier: 3.803A pdb=" N LYS B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 507 removed outlier: 3.804A pdb=" N GLU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 506 " --> pdb=" O THR B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.787A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 removed outlier: 5.268A pdb=" N GLN C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 228 removed outlier: 3.547A pdb=" N TYR C 228 " --> pdb=" O ALA C 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 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 257 removed outlier: 3.814A pdb=" N SER C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 removed outlier: 3.634A pdb=" N GLN C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 276 through 281' 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 303 Processing helix chain 'C' and resid 337 through 345 removed outlier: 3.605A pdb=" N VAL C 342 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 381 through 398 removed outlier: 3.761A pdb=" N GLN C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 428 removed outlier: 3.636A pdb=" N VAL C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 427 " --> pdb=" O ARG C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 449 removed outlier: 3.785A pdb=" N VAL C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 448 " --> pdb=" O VAL C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 475 removed outlier: 3.726A pdb=" N ILE C 461 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THR C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 465 " --> pdb=" O THR C 462 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN C 466 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 467 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE C 473 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 474 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN C 475 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 removed outlier: 3.512A pdb=" N GLY C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 506 removed outlier: 3.520A pdb=" N LYS C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 145 No H-bonds generated for 'chain 'D' and resid 142 through 145' Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.599A pdb=" N LEU D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 173 " --> pdb=" O MET D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 200 removed outlier: 3.963A pdb=" N LEU D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 244 removed outlier: 3.567A pdb=" N GLY D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 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: 4.119A pdb=" N GLY D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 322 through 325 No H-bonds generated for 'chain 'D' and resid 322 through 325' Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 369 through 393 removed outlier: 3.779A pdb=" N GLY D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 402 through 415 Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 436 through 448 removed outlier: 3.602A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 446 " --> pdb=" O GLY D 442 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 474 through 477 No H-bonds generated for 'chain 'D' and resid 474 through 477' Processing helix chain 'E' and resid 140 through 145 removed outlier: 3.742A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.728A pdb=" N ALA E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYS E 177 " --> pdb=" O ASN E 173 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 205 removed outlier: 3.813A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU E 204 " --> pdb=" O HIS E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 244 removed outlier: 4.305A pdb=" N ALA E 232 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG E 233 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 235 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU E 236 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR E 237 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY E 238 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 240 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL E 241 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 243 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 244 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 274 removed outlier: 3.735A pdb=" N THR E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.640A pdb=" N MET E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) 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 322 through 328 Processing helix chain 'E' and resid 339 through 343 removed outlier: 3.864A pdb=" N GLU E 343 " --> pdb=" O ARG E 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 339 through 343' Processing helix chain 'E' and resid 362 through 365 No H-bonds generated for 'chain 'E' and resid 362 through 365' Processing helix chain 'E' and resid 370 through 373 No H-bonds generated for 'chain 'E' and resid 370 through 373' Processing helix chain 'E' and resid 379 through 385 removed outlier: 4.140A pdb=" N TYR E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 392 No H-bonds generated for 'chain 'E' and resid 389 through 392' Processing helix chain 'E' and resid 412 through 415 No H-bonds generated for 'chain 'E' and resid 412 through 415' Processing helix chain 'E' and resid 424 through 427 No H-bonds generated for 'chain 'E' and resid 424 through 427' Processing helix chain 'E' and resid 436 through 447 removed outlier: 3.634A pdb=" N ILE E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY E 442 " --> pdb=" O GLU E 438 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE E 446 " --> pdb=" O GLY E 442 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU E 447 " --> pdb=" O PHE E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 474 removed outlier: 3.503A pdb=" N VAL E 469 " --> pdb=" O ILE E 465 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) 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 140 through 145 removed outlier: 3.691A pdb=" N LEU F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.553A pdb=" N LEU F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 247 removed outlier: 3.595A pdb=" N LEU F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU F 243 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 265 removed outlier: 4.165A pdb=" N GLN F 265 " --> pdb=" O ARG F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 294 removed outlier: 3.944A pdb=" N MET F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) 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 392 removed outlier: 3.844A pdb=" N ILE F 379 " --> pdb=" O GLY F 375 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN F 387 " --> pdb=" O TYR F 383 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP F 388 " --> pdb=" O LYS F 384 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE F 389 " --> pdb=" O SER F 385 " (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 410 through 416 removed outlier: 3.841A pdb=" N ARG F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 410 through 416' Processing helix chain 'F' and resid 424 through 427 No H-bonds generated for 'chain 'F' and resid 424 through 427' Processing helix chain 'F' and resid 437 through 447 removed outlier: 3.689A pdb=" N LYS F 441 " --> pdb=" O LYS F 437 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE F 446 " --> pdb=" O GLY F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 474 removed outlier: 3.803A pdb=" N VAL F 469 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 471 " --> pdb=" O ALA F 468 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 472 " --> pdb=" O VAL F 469 " (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 24 through 27 No H-bonds generated for 'chain 'J' and resid 24 through 27' Processing helix chain 'J' and resid 37 through 54 removed outlier: 3.736A pdb=" N LEU J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS J 47 " --> pdb=" O ALA J 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 34 removed outlier: 3.648A pdb=" N LYS G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA G 29 " --> pdb=" O MET G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 42 Proline residue: G 40 - end of helix No H-bonds generated for 'chain 'G' and resid 36 through 42' Processing helix chain 'G' and resid 44 through 54 removed outlier: 4.034A pdb=" N SER G 48 " --> pdb=" O TYR G 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 removed outlier: 3.738A pdb=" N LYS G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN G 88 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 117 removed outlier: 3.664A pdb=" N ILE G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 147 removed outlier: 3.684A pdb=" N LEU G 146 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 185 No H-bonds generated for 'chain 'G' and resid 182 through 185' Processing helix chain 'G' and resid 188 through 191 Processing helix chain 'G' and resid 198 through 214 removed outlier: 3.513A pdb=" N ASN G 203 " --> pdb=" O ASP G 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR G 207 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 269 removed outlier: 3.513A pdb=" N ALA G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR G 230 " --> pdb=" O SER G 226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA G 235 " --> pdb=" O ALA G 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN G 238 " --> pdb=" O ASN G 234 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU G 241 " --> pdb=" O LYS G 237 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU G 248 " --> pdb=" O ASP G 244 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL G 257 " --> pdb=" O THR G 253 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS G 260 " --> pdb=" O ALA G 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 117 removed outlier: 4.414A pdb=" N ALA H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 144 removed outlier: 3.645A pdb=" N GLN H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL H 142 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 23 removed outlier: 3.654A pdb=" N ILE I 17 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL I 22 " --> pdb=" O CYS I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 37 removed outlier: 3.784A pdb=" N THR I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 30 removed outlier: 4.126A pdb=" N TYR S 18 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR S 23 " --> pdb=" O ALA S 19 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLN S 29 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN S 30 " --> pdb=" O ALA S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 45 removed outlier: 3.827A pdb=" N GLU S 36 " --> pdb=" O LEU S 32 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG S 41 " --> pdb=" O LYS S 37 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE S 45 " --> pdb=" O ARG S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 75 removed outlier: 4.116A pdb=" N LEU S 69 " --> pdb=" O LYS S 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA S 74 " --> pdb=" O SER S 70 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS S 75 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 92 Processing helix chain 'S' and resid 96 through 112 Proline residue: S 99 - end of helix removed outlier: 3.753A pdb=" N ILE S 102 " --> pdb=" O PRO S 99 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE S 105 " --> pdb=" O ILE S 102 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER S 106 " --> pdb=" O SER S 103 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR S 107 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER S 110 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL S 111 " --> pdb=" O MET S 108 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS S 112 " --> pdb=" O MET S 109 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 134 No H-bonds generated for 'chain 'S' and resid 131 through 134' Processing helix chain 'S' and resid 179 through 182 Processing helix chain 'b' and resid 4 through 32 Proline residue: b 18 - end of helix Proline residue: b 27 - end of helix removed outlier: 3.505A pdb=" N VAL b 31 " --> pdb=" O PRO b 27 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) 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 83 removed outlier: 3.671A pdb=" N THR b 63 " --> pdb=" O SER b 59 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU b 67 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS b 72 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS b 73 " --> pdb=" O TYR b 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY b 75 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY b 79 " --> pdb=" O GLY b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 104 removed outlier: 4.497A pdb=" N GLU b 95 " --> pdb=" O ALA b 91 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER b 100 " --> pdb=" O VAL b 96 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE b 101 " --> pdb=" O LYS b 97 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN b 103 " --> pdb=" O ALA b 99 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 121 removed outlier: 3.732A pdb=" N GLU b 111 " --> pdb=" O ALA b 107 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN b 114 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL b 118 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN b 119 " --> pdb=" O GLN b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 135 removed outlier: 3.681A pdb=" N ALA b 133 " --> pdb=" O ARG b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 138 through 184 removed outlier: 3.860A pdb=" N GLU b 142 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL b 147 " --> pdb=" O ARG b 143 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS b 152 " --> pdb=" O TYR b 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET b 164 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG b 166 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU b 171 " --> pdb=" O GLN b 167 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS b 172 " --> pdb=" O LYS b 168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL b 177 " --> pdb=" O MET b 173 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL b 181 " --> pdb=" O VAL b 177 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL b 182 " --> pdb=" O GLU b 178 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER b 184 " --> pdb=" O HIS b 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 191 through 210 removed outlier: 3.536A pdb=" N CYS b 197 " --> pdb=" O THR b 193 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE b 198 " --> pdb=" O ILE b 194 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA b 208 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 19 removed outlier: 3.742A pdb=" N ASP c 13 " --> pdb=" O LYS c 9 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE c 15 " --> pdb=" O PHE c 11 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU c 17 " --> pdb=" O ASP c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 48 removed outlier: 3.559A pdb=" N ASP c 40 " --> pdb=" O GLN c 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS c 45 " --> pdb=" O ARG c 41 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS c 47 " --> pdb=" O LEU c 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 28 Processing helix chain 'd' and resid 30 through 45 removed outlier: 4.093A pdb=" N THR d 36 " --> pdb=" O SER d 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER d 38 " --> pdb=" O ASN d 34 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR d 39 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG d 40 " --> pdb=" O THR d 36 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Proline residue: d 45 - end of helix Processing helix chain 'd' and resid 53 through 59 removed outlier: 3.807A pdb=" N LYS d 57 " --> pdb=" O TRP d 53 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR d 59 " --> pdb=" O TYR d 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 53 through 59' Processing helix chain 'd' and resid 67 through 72 Processing helix chain 'd' and resid 87 through 90 No H-bonds generated for 'chain 'd' and resid 87 through 90' Processing helix chain 'd' and resid 94 through 119 removed outlier: 3.552A pdb=" N ALA d 101 " --> pdb=" O VAL d 97 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU d 102 " --> pdb=" O LYS d 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER d 105 " --> pdb=" O ALA d 101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS d 108 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR d 114 " --> pdb=" O ARG d 110 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU d 118 " --> pdb=" O TYR d 114 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU d 119 " --> pdb=" O GLU d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 124 No H-bonds generated for 'chain 'd' and resid 121 through 124' Processing helix chain 'e' and resid 6 through 62 removed outlier: 3.502A pdb=" N UNK e 42 " --> pdb=" O UNK e 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 16 removed outlier: 3.502A pdb=" N LYS f 7 " --> pdb=" O VAL f 3 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG f 9 " --> pdb=" O PRO f 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU f 11 " --> pdb=" O LYS f 7 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 34 No H-bonds generated for 'chain 'f' and resid 31 through 34' 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: 3.526A 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: 4.384A 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: 3.668A 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: 3.688A 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: 3.564A 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: 3.512A pdb=" N UNK g 78 " --> pdb=" O UNK g 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK g 79 " --> pdb=" O UNK g 75 " (cutoff:3.500A) removed outlier: 4.181A 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: 4.862A pdb=" N LEU i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR i 24 " --> pdb=" O SER i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 47 Processing helix chain 'k' and resid 13 through 28 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: 3.636A pdb=" N LEU 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain '8' and resid 34 through 40 Processing helix chain '8' and resid 45 through 59 Proline residue: 8 50 - end of helix removed outlier: 3.621A pdb=" N MET 8 53 " --> pdb=" O THR 8 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 28 removed outlier: 4.069A 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 54 removed outlier: 3.796A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 3.656A 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: 4.138A 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: 3.658A pdb=" N VAL a 113 " --> pdb=" O TRP a 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE a 114 " --> pdb=" O SER a 110 " (cutoff:3.500A) removed outlier: 3.938A 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: 4.050A pdb=" N ARG a 159 " --> pdb=" O ALA a 155 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN a 163 " --> pdb=" O ARG a 159 " (cutoff:3.500A) removed outlier: 3.503A 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: 3.579A 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: 3.717A pdb=" N THR a 178 " --> pdb=" O ILE a 174 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU a 179 " --> pdb=" O GLY a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 187 through 203 removed outlier: 4.032A 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: 3.820A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.174A 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: 3.700A 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: 4.129A 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: 3.867A 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: 3.792A 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: 4.189A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.563A 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: 3.645A 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: 3.572A 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: 3.631A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.818A 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: 3.912A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.028A 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: 3.671A pdb=" N LEU L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 30 removed outlier: 3.537A pdb=" N LYS M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY M 12 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 3.921A 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: 5.028A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.386A 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: 3.902A 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: 3.921A pdb=" N VAL M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 38 removed outlier: 3.554A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 58 removed outlier: 5.070A 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: 3.513A pdb=" N GLY M 53 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 70 removed outlier: 3.912A 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: 3.630A 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: 3.764A pdb=" N VAL N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.648A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 4.867A 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: 3.544A 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: 3.695A 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: 3.935A pdb=" N THR O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.751A 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: 4.297A 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: 4.038A 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: 3.883A 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: 4.383A pdb=" N ILE P 9 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.652A 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: 3.805A 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: 3.587A 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: 5.034A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.579A 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: 4.522A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 36 removed outlier: 3.952A pdb=" N MET Q 32 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 72 removed outlier: 3.518A pdb=" N TYR Q 49 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.646A pdb=" N ALA Q 68 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.656A pdb=" N GLY R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA R 14 " --> pdb=" O GLY R 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.821A 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: 4.294A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) removed outlier: 3.639A 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: 4.181A 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: 3.602A pdb=" N UNK u 19 " --> pdb=" O UNK u 16 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N UNK u 20 " --> pdb=" O UNK u 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N UNK u 23 " --> pdb=" O UNK u 20 " (cutoff:3.500A) removed outlier: 3.892A 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 30 through 35 removed outlier: 6.691A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A 76 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY A 61 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.589A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.846A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 265 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL A 204 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 267 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 206 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP A 269 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 324 " --> pdb=" O TYR A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.630A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA B 93 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.987A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 349 through 351 removed outlier: 7.269A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B 169 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.284A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 51 through 54 removed outlier: 4.147A pdb=" N GLU C 51 " --> pdb=" O SER C 63 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.273A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.982A pdb=" N ARG C 106 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN C 208 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 348 through 351 Processing sheet with id= M, first strand: chain 'D' and resid 14 through 18 removed outlier: 6.759A pdb=" N ASP D 24 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL D 23 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE D 63 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL D 51 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.730A pdb=" N GLU D 39 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 85 through 88 removed outlier: 3.528A pdb=" N ILE D 86 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN D 114 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 333 through 335 removed outlier: 7.764A pdb=" N ILE D 154 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER D 308 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU D 156 " --> pdb=" O SER D 308 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN D 310 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR D 182 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE D 256 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 184 " --> pdb=" O PHE D 256 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 14 through 19 removed outlier: 3.508A pdb=" N ARG E 14 " --> pdb=" O GLN E 26 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP E 24 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL E 18 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 22 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 25 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG E 61 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE E 63 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL E 51 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU E 39 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 85 through 87 removed outlier: 3.510A pdb=" N ALA E 116 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 254 through 258 removed outlier: 3.521A pdb=" N ASP E 258 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 62 through 64 removed outlier: 6.691A pdb=" N ASP F 24 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL F 18 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 85 through 88 removed outlier: 3.555A pdb=" N VAL F 88 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN F 114 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 155 through 158 removed outlier: 8.293A pdb=" N LEU F 156 " --> pdb=" O SER F 308 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN F 310 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY F 158 " --> pdb=" O GLN F 310 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE F 312 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 255 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 184 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 104 through 108 removed outlier: 3.519A pdb=" N VAL G 71 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 80 through 84 removed outlier: 3.652A pdb=" N SER H 81 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'S' and resid 118 through 120 Processing sheet with id= Z, first strand: chain 'S' and resid 162 through 164 removed outlier: 3.647A pdb=" N MET S 173 " --> pdb=" O MET S 162 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL S 164 " --> pdb=" O VAL S 171 " (cutoff:3.500A) 1055 hydrogen bonds defined for protein. 3009 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: 11.57 Time building geometry restraints manager: 15.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9945 1.33 - 1.45: 7076 1.45 - 1.58: 21364 1.58 - 1.70: 22 1.70 - 1.82: 266 Bond restraints: 38673 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.60e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.63e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.53e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.53e+01 ... (remaining 38668 not shown) Histogram of bond angle deviations from ideal: 95.49 - 103.82: 501 103.82 - 112.16: 19083 112.16 - 120.49: 18464 120.49 - 128.83: 14219 128.83 - 137.17: 138 Bond angle restraints: 52405 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 119.76 20.11 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.00 18.87 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.19 18.68 1.00e+00 1.00e+00 3.49e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.89 15.94 1.00e+00 1.00e+00 2.54e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 124.52 12.31 1.00e+00 1.00e+00 1.52e+02 ... (remaining 52400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 22806 34.61 - 69.22: 541 69.22 - 103.84: 36 103.84 - 138.45: 2 138.45 - 173.06: 2 Dihedral angle restraints: 23387 sinusoidal: 8538 harmonic: 14849 Sorted by residual: dihedral pdb=" CA ALA E 280 " pdb=" C ALA E 280 " pdb=" N VAL E 281 " pdb=" CA VAL E 281 " ideal model delta harmonic sigma weight residual -180.00 -128.27 -51.73 0 5.00e+00 4.00e-02 1.07e+02 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 -131.74 -48.26 0 5.00e+00 4.00e-02 9.32e+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 -132.40 -47.60 0 5.00e+00 4.00e-02 9.06e+01 ... (remaining 23384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 5209 0.077 - 0.154: 926 0.154 - 0.231: 92 0.231 - 0.309: 11 0.309 - 0.386: 4 Chirality restraints: 6242 Sorted by residual: chirality pdb=" CA LEU b 85 " pdb=" N LEU b 85 " pdb=" C LEU b 85 " pdb=" CB LEU b 85 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CB ILE C 489 " pdb=" CA ILE C 489 " pdb=" CG1 ILE C 489 " pdb=" CG2 ILE C 489 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB VAL B 157 " pdb=" CA VAL B 157 " pdb=" CG1 VAL B 157 " pdb=" CG2 VAL B 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 6239 not shown) Planarity restraints: 6752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 246 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 247 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 39 " 0.062 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO O 40 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO O 40 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO O 40 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 40 " 0.017 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C GLU J 40 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU J 40 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN J 41 " 0.021 2.00e-02 2.50e+03 ... (remaining 6749 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 7 2.07 - 2.77: 9205 2.77 - 3.48: 48250 3.48 - 4.19: 85856 4.19 - 4.90: 151175 Nonbonded interactions: 294493 Sorted by model distance: nonbonded pdb=" CB LEU H 48 " pdb=" OD1 ASN R 39 " model vdw 1.358 3.440 nonbonded pdb=" O VAL E 469 " pdb=" OD1 ASP E 473 " model vdw 1.789 3.040 nonbonded pdb=" O LYS f 53 " pdb=" O ARG a 41 " model vdw 1.880 3.040 nonbonded pdb=" OG1 THR G 2 " pdb=" OD2 ASP G 5 " model vdw 2.016 2.440 nonbonded pdb=" CD2 LEU H 48 " pdb=" CB SER R 41 " model vdw 2.033 3.860 ... (remaining 294488 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 22 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)) selection = (chain 'B' and (resid 22 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 22 through 401 or resid 410 through 510 or resid 601 throu \ gh 602)) } ncs_group { reference = (chain 'D' and resid 10 through 476) selection = chain 'E' selection = (chain 'F' and resid 10 through 476) } ncs_group { reference = (chain 'K' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'L' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'M' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'N' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 65 or (resid 66 and (name N or name C \ A or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'O' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'Q' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 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 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.140 Check model and map are aligned: 0.540 Set scattering table: 0.350 Process input model: 94.830 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 38673 Z= 0.574 Angle : 1.141 20.108 52405 Z= 0.676 Chirality : 0.059 0.386 6242 Planarity : 0.007 0.095 6752 Dihedral : 15.688 173.062 13855 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.67 % Favored : 92.08 % Rotamer: Outliers : 0.89 % Allowed : 13.16 % Favored : 85.95 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % 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: -5.57 (0.09), residues: 4939 helix: -4.28 (0.06), residues: 2255 sheet: -2.27 (0.23), residues: 482 loop : -3.25 (0.10), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP I 4 HIS 0.008 0.002 HIS F 200 PHE 0.029 0.003 PHE C 403 TYR 0.054 0.003 TYR A 337 ARG 0.015 0.001 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 513 time to evaluate : 4.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: A 446 TYR cc_start: 0.7165 (t80) cc_final: 0.6965 (t80) REVERT: B 390 MET cc_start: 0.7304 (ttp) cc_final: 0.6896 (ttp) REVERT: B 430 GLN cc_start: 0.7263 (tt0) cc_final: 0.6875 (tt0) REVERT: C 292 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7288 (mt-10) REVERT: C 373 ARG cc_start: 0.6975 (tmm160) cc_final: 0.6615 (mtt-85) REVERT: C 390 MET cc_start: 0.7831 (ttt) cc_final: 0.7353 (ttt) REVERT: D 168 ILE cc_start: 0.8682 (tt) cc_final: 0.8476 (tt) REVERT: D 202 MET cc_start: 0.7078 (mtm) cc_final: 0.6768 (mtm) REVERT: D 358 ARG cc_start: 0.6742 (mtt-85) cc_final: 0.6427 (mtt90) REVERT: D 395 MET cc_start: 0.7836 (tpt) cc_final: 0.7078 (tpp) REVERT: E 204 GLU cc_start: 0.7936 (pt0) cc_final: 0.7579 (pt0) REVERT: E 260 ILE cc_start: 0.8583 (tp) cc_final: 0.8253 (tp) REVERT: F 28 ASP cc_start: 0.7592 (t0) cc_final: 0.7148 (t0) REVERT: F 63 ILE cc_start: 0.8659 (mt) cc_final: 0.8270 (mt) REVERT: F 126 MET cc_start: 0.7427 (mmm) cc_final: 0.7168 (mmt) REVERT: F 395 MET cc_start: 0.8150 (tpp) cc_final: 0.7795 (tpp) REVERT: F 441 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8213 (ttpt) REVERT: F 474 LYS cc_start: 0.8147 (tptp) cc_final: 0.7915 (tptm) REVERT: H 55 LEU cc_start: 0.7432 (mt) cc_final: 0.7143 (pp) REVERT: S 162 MET cc_start: 0.7021 (ptm) cc_final: 0.5728 (pmm) REVERT: b 169 GLU cc_start: 0.7258 (tt0) cc_final: 0.7031 (tm-30) REVERT: b 171 GLU cc_start: 0.7988 (pp20) cc_final: 0.7292 (pp20) REVERT: c 23 GLN cc_start: 0.7170 (mm110) cc_final: 0.6916 (mm-40) REVERT: a 104 MET cc_start: 0.2375 (mtp) cc_final: 0.1108 (mmm) REVERT: a 114 PHE cc_start: 0.3336 (m-10) cc_final: 0.3027 (t80) REVERT: P 32 MET cc_start: 0.4917 (tmm) cc_final: 0.4197 (tpp) outliers start: 33 outliers final: 16 residues processed: 542 average time/residue: 0.5270 time to fit residues: 454.3773 Evaluate side-chains 387 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 370 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain a residue 142 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 6.9990 chunk 386 optimal weight: 0.0000 chunk 214 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 206 optimal weight: 0.0370 chunk 399 optimal weight: 50.0000 chunk 154 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 463 optimal weight: 6.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 415 GLN B 215 GLN B 366 ASN B 415 GLN C 190 ASN C 330 GLN C 341 ASN C 432 GLN C 441 GLN C 471 HIS C 503 ASN D 179 HIS D 225 ASN D 310 GLN E 132 GLN E 179 HIS ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 ASN F 225 ASN F 295 GLN G 82 HIS G 211 ASN G 234 ASN H 132 GLN H 138 ASN I 16 GLN b 188 GLN a 39 ASN a 47 GLN a 63 GLN a 83 ASN K 39 ASN L 44 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 38673 Z= 0.194 Angle : 0.628 10.157 52405 Z= 0.326 Chirality : 0.042 0.235 6242 Planarity : 0.005 0.068 6752 Dihedral : 8.472 178.234 5685 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.71 % Favored : 94.07 % Rotamer: Outliers : 2.67 % Allowed : 16.64 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % 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: -4.47 (0.10), residues: 4939 helix: -3.18 (0.08), residues: 2265 sheet: -1.96 (0.23), residues: 499 loop : -2.84 (0.11), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 8 9 HIS 0.003 0.001 HIS E 54 PHE 0.014 0.001 PHE R 47 TYR 0.018 0.001 TYR I 14 ARG 0.009 0.000 ARG S 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 409 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8053 (tp) REVERT: B 312 MET cc_start: 0.8071 (mmt) cc_final: 0.7839 (mmt) REVERT: B 390 MET cc_start: 0.7237 (ttp) cc_final: 0.6682 (ttp) REVERT: B 430 GLN cc_start: 0.7103 (tt0) cc_final: 0.6594 (tt0) REVERT: D 202 MET cc_start: 0.7473 (mtm) cc_final: 0.6990 (mtp) REVERT: D 395 MET cc_start: 0.7960 (tpt) cc_final: 0.7359 (tpp) REVERT: E 204 GLU cc_start: 0.7735 (pt0) cc_final: 0.7351 (pt0) REVERT: E 260 ILE cc_start: 0.8628 (tp) cc_final: 0.8384 (tp) REVERT: F 28 ASP cc_start: 0.7392 (t0) cc_final: 0.6965 (t0) REVERT: F 395 MET cc_start: 0.8019 (tpp) cc_final: 0.7426 (tpp) REVERT: F 441 LYS cc_start: 0.8081 (ttpp) cc_final: 0.7839 (ttpt) REVERT: I 13 ARG cc_start: 0.8649 (tpt170) cc_final: 0.8438 (tpt170) REVERT: I 44 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7192 (mp) REVERT: S 56 MET cc_start: 0.6886 (mtt) cc_final: 0.6646 (mtt) REVERT: S 94 ARG cc_start: 0.7807 (mpt180) cc_final: 0.7530 (mpt180) REVERT: S 162 MET cc_start: 0.6490 (ptm) cc_final: 0.5157 (pmm) REVERT: b 176 TRP cc_start: 0.6535 (t60) cc_final: 0.6024 (t60) REVERT: a 43 ILE cc_start: 0.3837 (OUTLIER) cc_final: 0.3162 (mt) REVERT: a 57 MET cc_start: 0.3045 (mtm) cc_final: 0.2813 (mtm) REVERT: a 104 MET cc_start: 0.2483 (mtp) cc_final: 0.1229 (mmm) REVERT: a 114 PHE cc_start: 0.3157 (m-10) cc_final: 0.2921 (t80) REVERT: L 60 MET cc_start: 0.3510 (mmm) cc_final: 0.2975 (tpp) REVERT: P 32 MET cc_start: 0.4661 (tmm) cc_final: 0.4142 (tpp) REVERT: R 66 MET cc_start: 0.3830 (ppp) cc_final: 0.2349 (ttt) outliers start: 99 outliers final: 53 residues processed: 487 average time/residue: 0.5258 time to fit residues: 418.1229 Evaluate side-chains 416 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 360 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 142 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 385 optimal weight: 0.1980 chunk 315 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 463 optimal weight: 7.9990 chunk 501 optimal weight: 8.9990 chunk 413 optimal weight: 30.0000 chunk 460 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 372 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN E 54 HIS ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38673 Z= 0.233 Angle : 0.606 9.780 52405 Z= 0.311 Chirality : 0.043 0.250 6242 Planarity : 0.004 0.052 6752 Dihedral : 8.028 179.073 5672 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.60 % Favored : 93.20 % Rotamer: Outliers : 3.64 % Allowed : 18.29 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % 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: -3.82 (0.10), residues: 4939 helix: -2.46 (0.09), residues: 2317 sheet: -1.77 (0.23), residues: 490 loop : -2.68 (0.12), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 8 9 HIS 0.004 0.001 HIS F 200 PHE 0.018 0.001 PHE G 155 TYR 0.020 0.001 TYR i 21 ARG 0.007 0.000 ARG E 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 370 time to evaluate : 4.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B 216 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7993 (tp) REVERT: B 286 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7604 (mmm160) REVERT: B 312 MET cc_start: 0.8084 (mmt) cc_final: 0.7838 (mmt) REVERT: B 430 GLN cc_start: 0.7142 (tt0) cc_final: 0.6701 (tt0) REVERT: C 50 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6711 (mm-30) REVERT: C 186 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: C 373 ARG cc_start: 0.7089 (tmm160) cc_final: 0.6570 (mmt90) REVERT: D 202 MET cc_start: 0.7495 (mtm) cc_final: 0.6927 (mtp) REVERT: D 395 MET cc_start: 0.8000 (tpt) cc_final: 0.7440 (tpp) REVERT: F 28 ASP cc_start: 0.7312 (t0) cc_final: 0.6919 (t0) REVERT: F 395 MET cc_start: 0.7970 (tpp) cc_final: 0.7521 (tpp) REVERT: F 441 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7895 (ttpt) REVERT: G 20 THR cc_start: 0.9166 (m) cc_final: 0.8945 (m) REVERT: G 124 PHE cc_start: 0.7245 (m-80) cc_final: 0.6909 (m-80) REVERT: I 4 TRP cc_start: 0.6141 (p90) cc_final: 0.5793 (p90) REVERT: I 13 ARG cc_start: 0.8666 (tpt170) cc_final: 0.8435 (tpt170) REVERT: I 44 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7302 (mp) REVERT: S 29 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: S 44 GLN cc_start: 0.7508 (mm110) cc_final: 0.7206 (mm-40) REVERT: S 89 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8245 (mt) REVERT: S 94 ARG cc_start: 0.7712 (mpt180) cc_final: 0.7505 (mpt180) REVERT: S 162 MET cc_start: 0.6542 (ptm) cc_final: 0.5216 (pmm) REVERT: a 25 MET cc_start: 0.2465 (mtp) cc_final: 0.1729 (tpp) REVERT: a 104 MET cc_start: 0.3305 (mtp) cc_final: 0.2760 (tpp) REVERT: a 114 PHE cc_start: 0.3373 (m-10) cc_final: 0.2901 (t80) REVERT: L 60 MET cc_start: 0.3469 (mmm) cc_final: 0.3067 (tpp) REVERT: M 66 MET cc_start: 0.4173 (ppp) cc_final: 0.3727 (pmm) REVERT: O 32 MET cc_start: 0.4549 (mpp) cc_final: 0.3476 (tpt) REVERT: P 32 MET cc_start: 0.4552 (tmm) cc_final: 0.4025 (tpp) REVERT: Q 65 LEU cc_start: 0.0862 (OUTLIER) cc_final: 0.0599 (mp) REVERT: R 66 MET cc_start: 0.3600 (ppp) cc_final: 0.2474 (ttt) outliers start: 135 outliers final: 96 residues processed: 481 average time/residue: 0.5037 time to fit residues: 397.9957 Evaluate side-chains 452 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 349 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 142 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 2.9990 chunk 348 optimal weight: 0.4980 chunk 240 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 311 optimal weight: 8.9990 chunk 465 optimal weight: 30.0000 chunk 492 optimal weight: 0.0980 chunk 243 optimal weight: 2.9990 chunk 441 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN B 385 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38673 Z= 0.196 Angle : 0.568 10.560 52405 Z= 0.290 Chirality : 0.042 0.228 6242 Planarity : 0.004 0.052 6752 Dihedral : 7.575 178.639 5672 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.95 % Favored : 93.87 % Rotamer: Outliers : 3.86 % Allowed : 19.31 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % 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: -3.30 (0.11), residues: 4939 helix: -1.97 (0.10), residues: 2319 sheet: -1.57 (0.23), residues: 495 loop : -2.48 (0.12), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 8 9 HIS 0.003 0.001 HIS F 200 PHE 0.017 0.001 PHE a 117 TYR 0.020 0.001 TYR i 21 ARG 0.005 0.000 ARG E 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 364 time to evaluate : 4.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: A 226 MET cc_start: 0.8732 (tpt) cc_final: 0.8497 (tpt) REVERT: B 216 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7955 (tp) REVERT: B 312 MET cc_start: 0.8066 (mmt) cc_final: 0.7845 (mmt) REVERT: B 430 GLN cc_start: 0.7077 (tt0) cc_final: 0.6635 (tt0) REVERT: C 50 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6336 (mm-30) REVERT: C 186 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8056 (mm-40) REVERT: C 226 MET cc_start: 0.7028 (mmm) cc_final: 0.6774 (tpt) REVERT: C 373 ARG cc_start: 0.7118 (tmm160) cc_final: 0.6551 (mmt90) REVERT: D 202 MET cc_start: 0.7509 (mtm) cc_final: 0.7148 (mtm) REVERT: F 28 ASP cc_start: 0.7244 (t0) cc_final: 0.6858 (t0) REVERT: F 395 MET cc_start: 0.7999 (tpp) cc_final: 0.7543 (tpp) REVERT: J 16 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7422 (mtp180) REVERT: G 124 PHE cc_start: 0.7410 (m-80) cc_final: 0.6981 (m-80) REVERT: I 44 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7411 (mp) REVERT: S 29 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: S 44 GLN cc_start: 0.7345 (mm110) cc_final: 0.7040 (mm-40) REVERT: S 89 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8308 (mt) REVERT: S 162 MET cc_start: 0.6517 (ptm) cc_final: 0.5053 (pmm) REVERT: S 163 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.5971 (pt) REVERT: b 176 TRP cc_start: 0.6613 (t60) cc_final: 0.6288 (t60) REVERT: a 25 MET cc_start: 0.2451 (mtp) cc_final: 0.1181 (tpt) REVERT: a 104 MET cc_start: 0.3440 (mtp) cc_final: 0.1592 (mmm) REVERT: P 32 MET cc_start: 0.4691 (tmm) cc_final: 0.4258 (ttm) REVERT: R 66 MET cc_start: 0.3576 (ppp) cc_final: 0.2832 (ttp) outliers start: 143 outliers final: 103 residues processed: 478 average time/residue: 0.5023 time to fit residues: 391.9182 Evaluate side-chains 461 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 350 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 142 VAL Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain P residue 66 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 30.0000 chunk 279 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 367 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 420 optimal weight: 6.9990 chunk 340 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 0.0470 chunk 442 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 310 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38673 Z= 0.218 Angle : 0.581 18.708 52405 Z= 0.293 Chirality : 0.042 0.256 6242 Planarity : 0.004 0.049 6752 Dihedral : 7.346 178.755 5672 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.54 % Favored : 93.32 % Rotamer: Outliers : 4.32 % Allowed : 20.21 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.96 (0.11), residues: 4939 helix: -1.64 (0.10), residues: 2299 sheet: -1.47 (0.23), residues: 488 loop : -2.36 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 8 9 HIS 0.003 0.001 HIS D 429 PHE 0.024 0.001 PHE M 63 TYR 0.020 0.001 TYR i 21 ARG 0.008 0.000 ARG E 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 370 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6650 (mt) REVERT: A 14 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: A 226 MET cc_start: 0.8713 (tpt) cc_final: 0.8502 (tpt) REVERT: B 216 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7968 (tp) REVERT: B 312 MET cc_start: 0.8050 (mmt) cc_final: 0.7788 (mmt) REVERT: B 430 GLN cc_start: 0.7191 (tt0) cc_final: 0.6803 (tt0) REVERT: C 50 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6446 (mm-30) REVERT: C 186 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8063 (mm-40) REVERT: C 373 ARG cc_start: 0.7204 (tmm160) cc_final: 0.6746 (mmt90) REVERT: D 202 MET cc_start: 0.7480 (mtm) cc_final: 0.7159 (mtm) REVERT: D 433 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6422 (tt) REVERT: F 28 ASP cc_start: 0.7222 (t0) cc_final: 0.6849 (t0) REVERT: F 360 MET cc_start: 0.7844 (tpt) cc_final: 0.7575 (tpt) REVERT: F 395 MET cc_start: 0.7951 (tpp) cc_final: 0.7504 (tpp) REVERT: G 124 PHE cc_start: 0.7417 (m-80) cc_final: 0.6990 (m-80) REVERT: I 44 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7453 (mp) REVERT: S 44 GLN cc_start: 0.7220 (mm110) cc_final: 0.6907 (mm-40) REVERT: S 108 MET cc_start: 0.8137 (mtp) cc_final: 0.7854 (mtp) REVERT: S 162 MET cc_start: 0.6679 (ptm) cc_final: 0.5179 (pmm) REVERT: S 163 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.5973 (pt) REVERT: b 171 GLU cc_start: 0.7926 (pp20) cc_final: 0.7382 (pp20) REVERT: a 25 MET cc_start: 0.2598 (mtp) cc_final: 0.1396 (tpt) REVERT: a 73 MET cc_start: 0.0846 (mtm) cc_final: -0.0575 (tpt) REVERT: a 104 MET cc_start: 0.3595 (mtp) cc_final: 0.2976 (tpp) REVERT: a 187 MET cc_start: -0.0344 (tmm) cc_final: -0.0749 (tpt) REVERT: L 3 ASP cc_start: 0.4150 (OUTLIER) cc_final: 0.3803 (t0) REVERT: L 66 MET cc_start: 0.3883 (mmm) cc_final: 0.3430 (tpt) REVERT: M 66 MET cc_start: 0.4336 (OUTLIER) cc_final: 0.3255 (pmm) REVERT: O 32 MET cc_start: 0.5267 (mpp) cc_final: 0.3773 (tpp) REVERT: P 32 MET cc_start: 0.4737 (tmm) cc_final: 0.4273 (ttm) REVERT: P 38 ARG cc_start: 0.6601 (ttm-80) cc_final: 0.6396 (ttm-80) REVERT: R 66 MET cc_start: 0.3794 (ppp) cc_final: 0.2914 (ttt) REVERT: R 72 LEU cc_start: 0.3577 (OUTLIER) cc_final: 0.3121 (pt) outliers start: 160 outliers final: 127 residues processed: 504 average time/residue: 0.4921 time to fit residues: 410.5559 Evaluate side-chains 487 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 350 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 60 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 142 VAL Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 1.9990 chunk 443 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 289 optimal weight: 4.9990 chunk 121 optimal weight: 0.1980 chunk 493 optimal weight: 0.0470 chunk 409 optimal weight: 80.0000 chunk 228 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN E 251 GLN ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38673 Z= 0.172 Angle : 0.544 11.197 52405 Z= 0.276 Chirality : 0.041 0.257 6242 Planarity : 0.003 0.050 6752 Dihedral : 6.967 175.460 5672 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.10 % Favored : 94.76 % Rotamer: Outliers : 3.97 % Allowed : 21.77 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 4939 helix: -1.34 (0.11), residues: 2303 sheet: -1.33 (0.23), residues: 510 loop : -2.22 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 8 9 HIS 0.002 0.001 HIS F 200 PHE 0.023 0.001 PHE a 26 TYR 0.021 0.001 TYR I 14 ARG 0.006 0.000 ARG S 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 373 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6674 (mt) REVERT: A 14 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: A 121 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8072 (mm) REVERT: A 226 MET cc_start: 0.8697 (tpt) cc_final: 0.8354 (tpt) REVERT: B 216 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7923 (tp) REVERT: B 312 MET cc_start: 0.8041 (mmt) cc_final: 0.7820 (mmt) REVERT: B 430 GLN cc_start: 0.7111 (tt0) cc_final: 0.6688 (tt0) REVERT: C 50 GLU cc_start: 0.6464 (mm-30) cc_final: 0.6255 (mm-30) REVERT: C 186 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8032 (mm-40) REVERT: C 373 ARG cc_start: 0.7127 (tmm160) cc_final: 0.6571 (mmt90) REVERT: D 202 MET cc_start: 0.7533 (mtm) cc_final: 0.7097 (mtm) REVERT: D 433 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6221 (tt) REVERT: F 28 ASP cc_start: 0.7150 (t0) cc_final: 0.6785 (t0) REVERT: F 395 MET cc_start: 0.7978 (tpp) cc_final: 0.7518 (tpp) REVERT: G 39 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.6221 (mttt) REVERT: G 124 PHE cc_start: 0.7401 (m-80) cc_final: 0.6977 (m-80) REVERT: I 44 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7491 (mp) REVERT: S 44 GLN cc_start: 0.7282 (mm110) cc_final: 0.6962 (mm-40) REVERT: S 162 MET cc_start: 0.6724 (ptm) cc_final: 0.5263 (pmm) REVERT: a 25 MET cc_start: 0.2749 (mtp) cc_final: 0.1995 (tpp) REVERT: a 104 MET cc_start: 0.2759 (mtp) cc_final: 0.1952 (mmm) REVERT: a 187 MET cc_start: -0.0551 (tmm) cc_final: -0.1175 (tpt) REVERT: L 3 ASP cc_start: 0.4117 (OUTLIER) cc_final: 0.3815 (t0) REVERT: L 66 MET cc_start: 0.3303 (mmm) cc_final: 0.3009 (tpt) REVERT: M 69 PHE cc_start: 0.2136 (OUTLIER) cc_final: 0.0880 (m-10) REVERT: O 32 MET cc_start: 0.4973 (mpp) cc_final: 0.3538 (tpp) REVERT: P 32 MET cc_start: 0.4791 (tmm) cc_final: 0.4273 (ttm) REVERT: R 66 MET cc_start: 0.3195 (ppp) cc_final: 0.2783 (ttt) outliers start: 147 outliers final: 112 residues processed: 497 average time/residue: 0.4803 time to fit residues: 393.9413 Evaluate side-chains 475 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 353 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 142 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 16 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 360 optimal weight: 10.0000 chunk 279 optimal weight: 0.4980 chunk 415 optimal weight: 50.0000 chunk 275 optimal weight: 0.5980 chunk 491 optimal weight: 8.9990 chunk 307 optimal weight: 9.9990 chunk 299 optimal weight: 0.8980 chunk 226 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN E 265 GLN F 209 ASN b 145 HIS R 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 38673 Z= 0.143 Angle : 0.530 11.291 52405 Z= 0.267 Chirality : 0.041 0.250 6242 Planarity : 0.003 0.047 6752 Dihedral : 6.616 169.556 5671 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 3.80 % Allowed : 22.26 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.34 (0.11), residues: 4939 helix: -1.08 (0.11), residues: 2298 sheet: -1.20 (0.23), residues: 526 loop : -2.10 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP 8 9 HIS 0.003 0.000 HIS E 453 PHE 0.015 0.001 PHE R 73 TYR 0.026 0.001 TYR I 14 ARG 0.006 0.000 ARG E 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 372 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6576 (mt) REVERT: A 14 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: A 121 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8041 (mm) REVERT: A 226 MET cc_start: 0.8679 (tpt) cc_final: 0.8426 (tpt) REVERT: B 178 ILE cc_start: 0.8394 (mm) cc_final: 0.8157 (pt) REVERT: B 216 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7867 (tp) REVERT: B 430 GLN cc_start: 0.7064 (tt0) cc_final: 0.6594 (tt0) REVERT: C 226 MET cc_start: 0.6982 (mmm) cc_final: 0.6697 (tpt) REVERT: D 202 MET cc_start: 0.7584 (mtm) cc_final: 0.7174 (mtm) REVERT: D 433 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6028 (tt) REVERT: E 414 ARG cc_start: 0.7440 (mtt90) cc_final: 0.7051 (ttm110) REVERT: F 28 ASP cc_start: 0.7096 (t0) cc_final: 0.6718 (t0) REVERT: F 376 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7816 (p) REVERT: F 395 MET cc_start: 0.7952 (tpp) cc_final: 0.7493 (tpp) REVERT: G 39 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6243 (mttt) REVERT: G 229 MET cc_start: 0.7490 (ttm) cc_final: 0.7102 (ttp) REVERT: I 44 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7492 (mp) REVERT: S 44 GLN cc_start: 0.7241 (mm110) cc_final: 0.6923 (mm-40) REVERT: S 89 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8329 (mt) REVERT: S 162 MET cc_start: 0.6706 (ptm) cc_final: 0.5138 (pmm) REVERT: b 202 LYS cc_start: 0.6728 (tppt) cc_final: 0.6506 (ttmm) REVERT: a 25 MET cc_start: 0.2927 (mtp) cc_final: 0.2293 (tpp) REVERT: a 104 MET cc_start: 0.2594 (mtp) cc_final: 0.1950 (mmm) REVERT: a 187 MET cc_start: -0.0600 (tmm) cc_final: -0.1178 (tpt) REVERT: L 3 ASP cc_start: 0.4073 (OUTLIER) cc_final: 0.3811 (t0) REVERT: M 32 MET cc_start: 0.4469 (OUTLIER) cc_final: 0.4153 (mtp) REVERT: O 32 MET cc_start: 0.4952 (mpp) cc_final: 0.3585 (tpp) REVERT: P 32 MET cc_start: 0.4774 (tmm) cc_final: 0.4227 (ttm) REVERT: R 66 MET cc_start: 0.3143 (ppp) cc_final: 0.2777 (ttp) outliers start: 141 outliers final: 112 residues processed: 489 average time/residue: 0.4785 time to fit residues: 388.7328 Evaluate side-chains 477 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 354 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 PHE Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain M residue 32 MET Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 16 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 312 optimal weight: 0.5980 chunk 334 optimal weight: 4.9990 chunk 243 optimal weight: 0.0170 chunk 45 optimal weight: 0.0770 chunk 386 optimal weight: 0.9980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 132 GLN ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 38673 Z= 0.132 Angle : 0.522 11.763 52405 Z= 0.263 Chirality : 0.041 0.253 6242 Planarity : 0.004 0.117 6752 Dihedral : 6.213 160.206 5667 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Rotamer: Outliers : 3.48 % Allowed : 22.58 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.05 (0.12), residues: 4939 helix: -0.81 (0.11), residues: 2293 sheet: -1.08 (0.23), residues: 545 loop : -1.98 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP 8 9 HIS 0.002 0.000 HIS C 42 PHE 0.017 0.001 PHE E 263 TYR 0.023 0.001 TYR I 14 ARG 0.009 0.000 ARG b 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 369 time to evaluate : 4.141 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 14 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: A 121 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8012 (mm) REVERT: B 216 LEU cc_start: 0.8159 (tt) cc_final: 0.7886 (tp) REVERT: B 270 ASP cc_start: 0.8444 (p0) cc_final: 0.8238 (p0) REVERT: B 312 MET cc_start: 0.8159 (mmt) cc_final: 0.7912 (mmm) REVERT: B 430 GLN cc_start: 0.7021 (tt0) cc_final: 0.6467 (tt0) REVERT: C 226 MET cc_start: 0.6920 (mmm) cc_final: 0.6612 (tpt) REVERT: C 373 ARG cc_start: 0.7011 (tmm160) cc_final: 0.6512 (mmt90) REVERT: C 392 LEU cc_start: 0.8017 (mt) cc_final: 0.7781 (tp) REVERT: D 202 MET cc_start: 0.7547 (mtm) cc_final: 0.7148 (mtm) REVERT: D 214 THR cc_start: 0.8070 (p) cc_final: 0.7758 (m) REVERT: E 414 ARG cc_start: 0.7344 (mtt90) cc_final: 0.7068 (ttm110) REVERT: F 28 ASP cc_start: 0.7052 (t0) cc_final: 0.6678 (t0) REVERT: F 376 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7826 (p) REVERT: F 395 MET cc_start: 0.7942 (tpp) cc_final: 0.7484 (tpp) REVERT: G 39 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6090 (mttt) REVERT: I 44 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7429 (mp) REVERT: S 44 GLN cc_start: 0.7218 (mm110) cc_final: 0.6901 (mm-40) REVERT: S 162 MET cc_start: 0.6654 (ptm) cc_final: 0.5090 (pmm) REVERT: b 171 GLU cc_start: 0.7639 (pp20) cc_final: 0.7398 (pp20) REVERT: b 202 LYS cc_start: 0.6673 (tppt) cc_final: 0.6465 (ttmm) REVERT: a 104 MET cc_start: 0.2752 (mtp) cc_final: 0.2326 (mmm) REVERT: K 60 MET cc_start: 0.3779 (ttp) cc_final: 0.3421 (ttp) REVERT: L 3 ASP cc_start: 0.4033 (OUTLIER) cc_final: 0.3805 (t0) REVERT: M 32 MET cc_start: 0.3997 (OUTLIER) cc_final: 0.3676 (mtp) REVERT: M 69 PHE cc_start: 0.2081 (OUTLIER) cc_final: 0.0822 (m-10) REVERT: N 66 MET cc_start: 0.6127 (tmm) cc_final: 0.5123 (mmt) REVERT: P 32 MET cc_start: 0.4771 (tmm) cc_final: 0.4211 (ttm) REVERT: R 66 MET cc_start: 0.3467 (ppp) cc_final: 0.3006 (ttp) outliers start: 129 outliers final: 105 residues processed: 469 average time/residue: 0.4900 time to fit residues: 378.5259 Evaluate side-chains 467 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 354 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain 8 residue 8 THR Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 PHE Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain M residue 32 MET Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 20.0000 chunk 470 optimal weight: 8.9990 chunk 429 optimal weight: 0.7980 chunk 458 optimal weight: 30.0000 chunk 275 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 359 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 413 optimal weight: 40.0000 chunk 433 optimal weight: 6.9990 chunk 456 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 369 HIS F 132 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 38673 Z= 0.373 Angle : 0.655 11.736 52405 Z= 0.330 Chirality : 0.046 0.235 6242 Planarity : 0.004 0.049 6752 Dihedral : 7.160 179.754 5667 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.33 % Favored : 92.51 % Rotamer: Outliers : 4.15 % Allowed : 22.17 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.37 (0.11), residues: 4939 helix: -1.06 (0.11), residues: 2291 sheet: -1.20 (0.24), residues: 486 loop : -2.17 (0.12), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP 8 9 HIS 0.005 0.001 HIS F 200 PHE 0.018 0.002 PHE R 73 TYR 0.022 0.002 TYR i 21 ARG 0.006 0.001 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 352 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6802 (mt) REVERT: A 14 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: A 121 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8096 (mm) REVERT: B 216 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8166 (tp) REVERT: B 430 GLN cc_start: 0.7180 (tt0) cc_final: 0.6805 (tt0) REVERT: C 373 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6763 (mmt90) REVERT: D 202 MET cc_start: 0.7741 (mtm) cc_final: 0.7374 (mtm) REVERT: F 28 ASP cc_start: 0.7281 (t0) cc_final: 0.6887 (t0) REVERT: F 63 ILE cc_start: 0.8729 (mt) cc_final: 0.8495 (mt) REVERT: F 395 MET cc_start: 0.7916 (tpp) cc_final: 0.7431 (tpp) REVERT: J 16 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7527 (mtp180) REVERT: G 88 GLN cc_start: 0.6847 (tp-100) cc_final: 0.6558 (tp-100) REVERT: I 44 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7525 (mp) REVERT: S 89 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8300 (mt) REVERT: S 162 MET cc_start: 0.6953 (ptm) cc_final: 0.5508 (pmm) REVERT: S 163 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5729 (pt) REVERT: b 171 GLU cc_start: 0.7864 (pp20) cc_final: 0.7631 (pp20) REVERT: a 187 MET cc_start: 0.0353 (tmm) cc_final: -0.0858 (tpt) REVERT: L 3 ASP cc_start: 0.4269 (OUTLIER) cc_final: 0.3943 (t0) REVERT: M 32 MET cc_start: 0.3950 (OUTLIER) cc_final: 0.3622 (mtp) REVERT: M 69 PHE cc_start: 0.2174 (OUTLIER) cc_final: 0.0884 (m-10) REVERT: N 66 MET cc_start: 0.6130 (tmm) cc_final: 0.5134 (mmt) REVERT: O 32 MET cc_start: 0.5291 (mpp) cc_final: 0.3762 (tpp) REVERT: R 66 MET cc_start: 0.3407 (ppp) cc_final: 0.2747 (ttp) outliers start: 154 outliers final: 131 residues processed: 475 average time/residue: 0.4904 time to fit residues: 386.3644 Evaluate side-chains 485 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 342 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 173 MET Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 60 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 PHE Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain M residue 32 MET Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 1.9990 chunk 484 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 229 optimal weight: 0.0060 chunk 336 optimal weight: 5.9990 chunk 508 optimal weight: 40.0000 chunk 467 optimal weight: 8.9990 chunk 404 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN F 132 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38673 Z= 0.197 Angle : 0.569 13.749 52405 Z= 0.285 Chirality : 0.042 0.306 6242 Planarity : 0.003 0.050 6752 Dihedral : 6.701 174.683 5667 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.41 % Favored : 94.45 % Rotamer: Outliers : 3.72 % Allowed : 22.71 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.13 (0.12), residues: 4939 helix: -0.84 (0.11), residues: 2280 sheet: -1.17 (0.23), residues: 504 loop : -2.04 (0.12), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP 8 9 HIS 0.003 0.001 HIS D 369 PHE 0.016 0.001 PHE a 117 TYR 0.022 0.001 TYR I 14 ARG 0.005 0.000 ARG E 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 349 time to evaluate : 4.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6716 (mt) REVERT: A 14 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: A 121 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8096 (mm) REVERT: B 216 LEU cc_start: 0.8235 (tt) cc_final: 0.7938 (tp) REVERT: B 430 GLN cc_start: 0.7129 (tt0) cc_final: 0.6748 (tt0) REVERT: C 373 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6629 (mmt90) REVERT: D 202 MET cc_start: 0.7673 (mtm) cc_final: 0.7265 (mtm) REVERT: D 214 THR cc_start: 0.8045 (p) cc_final: 0.7716 (m) REVERT: F 28 ASP cc_start: 0.7178 (t0) cc_final: 0.6807 (t0) REVERT: F 376 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7825 (p) REVERT: F 395 MET cc_start: 0.7996 (tpp) cc_final: 0.7513 (tpp) REVERT: I 44 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7529 (mp) REVERT: S 89 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8331 (mt) REVERT: S 162 MET cc_start: 0.6949 (ptm) cc_final: 0.5403 (pmm) REVERT: S 163 ILE cc_start: 0.6213 (OUTLIER) cc_final: 0.5671 (pt) REVERT: b 171 GLU cc_start: 0.7851 (pp20) cc_final: 0.7623 (pp20) REVERT: a 100 MET cc_start: 0.4058 (ttt) cc_final: 0.3385 (ptm) REVERT: a 187 MET cc_start: 0.0485 (tmm) cc_final: -0.0709 (tpt) REVERT: L 3 ASP cc_start: 0.4201 (OUTLIER) cc_final: 0.3914 (t0) REVERT: M 32 MET cc_start: 0.3817 (OUTLIER) cc_final: 0.3614 (mmm) REVERT: M 66 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.2974 (pmm) REVERT: M 69 PHE cc_start: 0.2146 (OUTLIER) cc_final: 0.0861 (m-10) REVERT: N 66 MET cc_start: 0.5907 (tmm) cc_final: 0.5207 (mmt) REVERT: O 32 MET cc_start: 0.5304 (mpp) cc_final: 0.3838 (tpp) REVERT: R 66 MET cc_start: 0.3624 (ppp) cc_final: 0.2878 (ttp) outliers start: 138 outliers final: 120 residues processed: 461 average time/residue: 0.4787 time to fit residues: 365.3581 Evaluate side-chains 470 residues out of total 4027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 338 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 60 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 PHE Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain M residue 32 MET Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain P residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 8.9990 chunk 430 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 373 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 405 optimal weight: 50.0000 chunk 169 optimal weight: 0.6980 chunk 416 optimal weight: 40.0000 chunk 51 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** 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 = 0.4327 r_free = 0.4327 target = 0.191738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159636 restraints weight = 49391.662| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.55 r_work: 0.3693 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38673 Z= 0.264 Angle : 0.606 11.716 52405 Z= 0.303 Chirality : 0.043 0.289 6242 Planarity : 0.004 0.049 6752 Dihedral : 6.894 177.207 5667 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.92 % Favored : 92.93 % Rotamer: Outliers : 3.83 % Allowed : 22.71 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.17 (0.12), residues: 4939 helix: -0.86 (0.11), residues: 2267 sheet: -1.21 (0.24), residues: 491 loop : -2.07 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP 8 9 HIS 0.004 0.001 HIS D 429 PHE 0.022 0.001 PHE a 78 TYR 0.021 0.001 TYR i 21 ARG 0.005 0.000 ARG E 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8652.05 seconds wall clock time: 157 minutes 13.42 seconds (9433.42 seconds total)