Starting phenix.real_space_refine on Sun Mar 24 11:54:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/03_2024/3ja7_6324.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/03_2024/3ja7_6324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/03_2024/3ja7_6324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/03_2024/3ja7_6324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/03_2024/3ja7_6324.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/03_2024/3ja7_6324.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.001 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: 4 Type Number sf(0) Gaussians S 228 5.16 5 C 25968 2.51 5 N 7296 2.21 5 O 7788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 155": "NH1" <-> "NH2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E GLU 497": "OE1" <-> "OE2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "G ARG 155": "NH1" <-> "NH2" Residue "G GLU 497": "OE1" <-> "OE2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H GLU 497": "OE1" <-> "OE2" Residue "I ARG 155": "NH1" <-> "NH2" Residue "I PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 497": "OE1" <-> "OE2" Residue "J ARG 155": "NH1" <-> "NH2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "K ARG 155": "NH1" <-> "NH2" Residue "K GLU 497": "OE1" <-> "OE2" Residue "L ARG 155": "NH1" <-> "NH2" Residue "L PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 497": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41280 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "F" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "G" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "H" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "I" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "J" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "K" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "L" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 20.90, per 1000 atoms: 0.51 Number of scatterers: 41280 At special positions: 0 Unit cell: (185, 185, 137, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 228 16.00 O 7788 8.00 N 7296 7.00 C 25968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.69 Conformation dependent library (CDL) restraints added in 7.0 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9864 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 60 sheets defined 47.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 70 through 81 removed outlier: 3.602A pdb=" N ARG A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.627A pdb=" N ILE A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.691A pdb=" N HIS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 304 " --> pdb=" O HIS A 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 307 " --> pdb=" O HIS A 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 424 Proline residue: A 421 - end of helix removed outlier: 3.815A pdb=" N THR A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 441 " --> pdb=" O TRP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 304 " --> pdb=" O HIS B 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET B 305 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 307 " --> pdb=" O HIS B 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 424 Proline residue: B 421 - end of helix removed outlier: 3.815A pdb=" N THR B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 441 " --> pdb=" O TRP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 482 through 490 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 277 removed outlier: 3.631A pdb=" N LYS C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 266 " --> pdb=" O ASN C 262 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 304 " --> pdb=" O HIS C 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET C 305 " --> pdb=" O MET C 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 307 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.945A pdb=" N GLN C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 411 removed outlier: 3.530A pdb=" N LEU C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 424 Proline residue: C 421 - end of helix removed outlier: 3.815A pdb=" N THR C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP C 439 " --> pdb=" O ASP C 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 440 " --> pdb=" O GLU C 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 441 " --> pdb=" O TRP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 473 Processing helix chain 'C' and resid 482 through 490 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 509 " --> pdb=" O ILE C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.627A pdb=" N ILE D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP D 132 " --> pdb=" O ASP D 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 266 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 298 through 309 removed outlier: 3.691A pdb=" N HIS D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL D 304 " --> pdb=" O HIS D 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET D 305 " --> pdb=" O MET D 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 306 " --> pdb=" O GLN D 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN D 367 " --> pdb=" O ARG D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 424 Proline residue: D 421 - end of helix removed outlier: 3.815A pdb=" N THR D 424 " --> pdb=" O ASP D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP D 439 " --> pdb=" O ASP D 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 441 " --> pdb=" O TRP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 482 through 490 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU D 506 " --> pdb=" O ALA D 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU D 507 " --> pdb=" O LYS D 503 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER D 509 " --> pdb=" O ILE D 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 100 " --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN E 124 " --> pdb=" O PRO E 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP E 132 " --> pdb=" O ASP E 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 137 " --> pdb=" O VAL E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 266 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU E 267 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 272 " --> pdb=" O GLU E 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'E' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL E 304 " --> pdb=" O HIS E 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET E 305 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E 306 " --> pdb=" O GLN E 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR E 307 " --> pdb=" O HIS E 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN E 367 " --> pdb=" O ARG E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 405 " --> pdb=" O LEU E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 424 Proline residue: E 421 - end of helix removed outlier: 3.815A pdb=" N THR E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP E 439 " --> pdb=" O ASP E 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 441 " --> pdb=" O TRP E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 473 Processing helix chain 'E' and resid 482 through 490 Processing helix chain 'E' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU E 506 " --> pdb=" O ALA E 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU E 507 " --> pdb=" O LYS E 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU E 508 " --> pdb=" O GLN E 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER E 509 " --> pdb=" O ILE E 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG F 80 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 100 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP F 128 " --> pdb=" O ASN F 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP F 132 " --> pdb=" O ASP F 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU F 137 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER F 144 " --> pdb=" O GLN F 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 277 removed outlier: 3.631A pdb=" N LYS F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 266 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU F 267 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL F 272 " --> pdb=" O GLU F 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 Processing helix chain 'F' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS F 303 " --> pdb=" O GLU F 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL F 304 " --> pdb=" O HIS F 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET F 305 " --> pdb=" O MET F 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 306 " --> pdb=" O GLN F 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 307 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET F 308 " --> pdb=" O VAL F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.945A pdb=" N GLN F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 411 removed outlier: 3.530A pdb=" N LEU F 401 " --> pdb=" O THR F 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 405 " --> pdb=" O LEU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 424 Proline residue: F 421 - end of helix removed outlier: 3.815A pdb=" N THR F 424 " --> pdb=" O ASP F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 429 Processing helix chain 'F' and resid 433 through 441 removed outlier: 5.021A pdb=" N ASP F 439 " --> pdb=" O ASP F 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU F 440 " --> pdb=" O GLU F 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE F 441 " --> pdb=" O TRP F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 473 Processing helix chain 'F' and resid 482 through 490 Processing helix chain 'F' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU F 507 " --> pdb=" O LYS F 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER F 509 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG G 80 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 100 removed outlier: 3.627A pdb=" N ILE G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN G 124 " --> pdb=" O PRO G 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP G 132 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU G 137 " --> pdb=" O VAL G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 256 No H-bonds generated for 'chain 'G' and resid 254 through 256' Processing helix chain 'G' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS G 265 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU G 266 " --> pdb=" O ASN G 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU G 267 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 268 " --> pdb=" O LEU G 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 272 " --> pdb=" O GLU G 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR G 277 " --> pdb=" O ILE G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 Processing helix chain 'G' and resid 298 through 309 removed outlier: 3.691A pdb=" N HIS G 303 " --> pdb=" O GLU G 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL G 304 " --> pdb=" O HIS G 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET G 305 " --> pdb=" O MET G 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN G 306 " --> pdb=" O GLN G 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR G 307 " --> pdb=" O HIS G 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU G 401 " --> pdb=" O THR G 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS G 405 " --> pdb=" O LEU G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 424 Proline residue: G 421 - end of helix removed outlier: 3.815A pdb=" N THR G 424 " --> pdb=" O ASP G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 429 Processing helix chain 'G' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP G 439 " --> pdb=" O ASP G 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 440 " --> pdb=" O GLU G 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 441 " --> pdb=" O TRP G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU G 456 " --> pdb=" O SER G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 473 Processing helix chain 'G' and resid 482 through 490 Processing helix chain 'G' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU G 506 " --> pdb=" O ALA G 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU G 507 " --> pdb=" O LYS G 503 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU G 508 " --> pdb=" O GLN G 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER G 509 " --> pdb=" O ILE G 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG H 80 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP H 98 " --> pdb=" O GLU H 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 100 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN H 124 " --> pdb=" O PRO H 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU H 127 " --> pdb=" O LYS H 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP H 128 " --> pdb=" O ASN H 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP H 132 " --> pdb=" O ASP H 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER H 144 " --> pdb=" O GLN H 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP H 145 " --> pdb=" O ARG H 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS H 146 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG H 148 " --> pdb=" O SER H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS H 265 " --> pdb=" O ALA H 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU H 266 " --> pdb=" O ASN H 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL H 272 " --> pdb=" O GLU H 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR H 277 " --> pdb=" O ILE H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 Processing helix chain 'H' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS H 303 " --> pdb=" O GLU H 299 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL H 304 " --> pdb=" O HIS H 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET H 305 " --> pdb=" O MET H 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN H 306 " --> pdb=" O GLN H 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR H 307 " --> pdb=" O HIS H 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET H 308 " --> pdb=" O VAL H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN H 367 " --> pdb=" O ARG H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU H 401 " --> pdb=" O THR H 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS H 405 " --> pdb=" O LEU H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 424 Proline residue: H 421 - end of helix removed outlier: 3.815A pdb=" N THR H 424 " --> pdb=" O ASP H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 424 through 429 Processing helix chain 'H' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP H 439 " --> pdb=" O ASP H 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU H 440 " --> pdb=" O GLU H 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 441 " --> pdb=" O TRP H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU H 456 " --> pdb=" O SER H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 473 Processing helix chain 'H' and resid 482 through 490 Processing helix chain 'H' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU H 506 " --> pdb=" O ALA H 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU H 507 " --> pdb=" O LYS H 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU H 508 " --> pdb=" O GLN H 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 509 " --> pdb=" O ILE H 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG I 80 " --> pdb=" O ILE I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP I 98 " --> pdb=" O GLU I 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 100 " --> pdb=" O VAL I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN I 124 " --> pdb=" O PRO I 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU I 127 " --> pdb=" O LYS I 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP I 128 " --> pdb=" O ASN I 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP I 132 " --> pdb=" O ASP I 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN I 135 " --> pdb=" O SER I 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER I 144 " --> pdb=" O GLN I 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 256 No H-bonds generated for 'chain 'I' and resid 254 through 256' Processing helix chain 'I' and resid 257 through 277 removed outlier: 3.631A pdb=" N LYS I 265 " --> pdb=" O ALA I 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU I 266 " --> pdb=" O ASN I 262 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU I 267 " --> pdb=" O GLN I 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU I 268 " --> pdb=" O LEU I 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA I 270 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 272 " --> pdb=" O GLU I 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR I 277 " --> pdb=" O ILE I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 298 Processing helix chain 'I' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS I 303 " --> pdb=" O GLU I 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL I 304 " --> pdb=" O HIS I 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET I 305 " --> pdb=" O MET I 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN I 306 " --> pdb=" O GLN I 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR I 307 " --> pdb=" O HIS I 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET I 308 " --> pdb=" O VAL I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 373 removed outlier: 3.945A pdb=" N GLN I 367 " --> pdb=" O ARG I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 411 removed outlier: 3.530A pdb=" N LEU I 401 " --> pdb=" O THR I 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS I 405 " --> pdb=" O LEU I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 424 Proline residue: I 421 - end of helix removed outlier: 3.815A pdb=" N THR I 424 " --> pdb=" O ASP I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 429 Processing helix chain 'I' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP I 439 " --> pdb=" O ASP I 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU I 440 " --> pdb=" O GLU I 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE I 441 " --> pdb=" O TRP I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU I 456 " --> pdb=" O SER I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 473 Processing helix chain 'I' and resid 482 through 490 Processing helix chain 'I' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU I 506 " --> pdb=" O ALA I 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU I 507 " --> pdb=" O LYS I 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU I 508 " --> pdb=" O GLN I 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER I 509 " --> pdb=" O ILE I 505 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG J 80 " --> pdb=" O ILE J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 100 removed outlier: 3.627A pdb=" N ILE J 95 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP J 98 " --> pdb=" O GLU J 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE J 100 " --> pdb=" O VAL J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN J 124 " --> pdb=" O PRO J 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU J 127 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP J 128 " --> pdb=" O ASN J 124 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP J 132 " --> pdb=" O ASP J 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU J 137 " --> pdb=" O VAL J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER J 144 " --> pdb=" O GLN J 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP J 145 " --> pdb=" O ARG J 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG J 148 " --> pdb=" O SER J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 256 No H-bonds generated for 'chain 'J' and resid 254 through 256' Processing helix chain 'J' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS J 265 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU J 266 " --> pdb=" O ASN J 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU J 267 " --> pdb=" O GLN J 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU J 268 " --> pdb=" O LEU J 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA J 270 " --> pdb=" O LEU J 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL J 272 " --> pdb=" O GLU J 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR J 277 " --> pdb=" O ILE J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 298 Processing helix chain 'J' and resid 298 through 309 removed outlier: 3.691A pdb=" N HIS J 303 " --> pdb=" O GLU J 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL J 304 " --> pdb=" O HIS J 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET J 305 " --> pdb=" O MET J 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN J 306 " --> pdb=" O GLN J 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR J 307 " --> pdb=" O HIS J 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET J 308 " --> pdb=" O VAL J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN J 367 " --> pdb=" O ARG J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU J 401 " --> pdb=" O THR J 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS J 405 " --> pdb=" O LEU J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 424 Proline residue: J 421 - end of helix removed outlier: 3.815A pdb=" N THR J 424 " --> pdb=" O ASP J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 424 through 429 Processing helix chain 'J' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP J 439 " --> pdb=" O ASP J 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU J 440 " --> pdb=" O GLU J 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE J 441 " --> pdb=" O TRP J 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU J 456 " --> pdb=" O SER J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 473 Processing helix chain 'J' and resid 482 through 490 Processing helix chain 'J' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU J 506 " --> pdb=" O ALA J 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU J 507 " --> pdb=" O LYS J 503 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER J 509 " --> pdb=" O ILE J 505 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG K 80 " --> pdb=" O ILE K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE K 100 " --> pdb=" O VAL K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN K 124 " --> pdb=" O PRO K 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP K 128 " --> pdb=" O ASN K 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP K 132 " --> pdb=" O ASP K 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN K 135 " --> pdb=" O SER K 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU K 137 " --> pdb=" O VAL K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER K 144 " --> pdb=" O GLN K 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP K 145 " --> pdb=" O ARG K 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG K 148 " --> pdb=" O SER K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 256 No H-bonds generated for 'chain 'K' and resid 254 through 256' Processing helix chain 'K' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS K 265 " --> pdb=" O ALA K 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU K 266 " --> pdb=" O ASN K 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU K 267 " --> pdb=" O GLN K 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 268 " --> pdb=" O LEU K 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA K 270 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL K 272 " --> pdb=" O GLU K 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR K 277 " --> pdb=" O ILE K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 298 Processing helix chain 'K' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS K 303 " --> pdb=" O GLU K 299 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL K 304 " --> pdb=" O HIS K 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET K 305 " --> pdb=" O MET K 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN K 306 " --> pdb=" O GLN K 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR K 307 " --> pdb=" O HIS K 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET K 308 " --> pdb=" O VAL K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN K 367 " --> pdb=" O ARG K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU K 401 " --> pdb=" O THR K 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 405 " --> pdb=" O LEU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 424 Proline residue: K 421 - end of helix removed outlier: 3.815A pdb=" N THR K 424 " --> pdb=" O ASP K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 424 through 429 Processing helix chain 'K' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP K 439 " --> pdb=" O ASP K 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU K 440 " --> pdb=" O GLU K 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE K 441 " --> pdb=" O TRP K 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU K 456 " --> pdb=" O SER K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 473 Processing helix chain 'K' and resid 482 through 490 Processing helix chain 'K' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU K 507 " --> pdb=" O LYS K 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU K 508 " --> pdb=" O GLN K 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER K 509 " --> pdb=" O ILE K 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG L 80 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE L 95 " --> pdb=" O ALA L 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 100 " --> pdb=" O VAL L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN L 124 " --> pdb=" O PRO L 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU L 127 " --> pdb=" O LYS L 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP L 128 " --> pdb=" O ASN L 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER L 144 " --> pdb=" O GLN L 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP L 145 " --> pdb=" O ARG L 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG L 148 " --> pdb=" O SER L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 256 No H-bonds generated for 'chain 'L' and resid 254 through 256' Processing helix chain 'L' and resid 257 through 277 removed outlier: 3.631A pdb=" N LYS L 265 " --> pdb=" O ALA L 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU L 266 " --> pdb=" O ASN L 262 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU L 267 " --> pdb=" O GLN L 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL L 272 " --> pdb=" O GLU L 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR L 277 " --> pdb=" O ILE L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 298 Processing helix chain 'L' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS L 303 " --> pdb=" O GLU L 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL L 304 " --> pdb=" O HIS L 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET L 305 " --> pdb=" O MET L 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN L 306 " --> pdb=" O GLN L 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR L 307 " --> pdb=" O HIS L 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET L 308 " --> pdb=" O VAL L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 373 removed outlier: 3.945A pdb=" N GLN L 367 " --> pdb=" O ARG L 363 " (cutoff:3.500A) Processing helix chain 'L' and resid 397 through 411 removed outlier: 3.530A pdb=" N LEU L 401 " --> pdb=" O THR L 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS L 405 " --> pdb=" O LEU L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 424 Proline residue: L 421 - end of helix removed outlier: 3.815A pdb=" N THR L 424 " --> pdb=" O ASP L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 429 Processing helix chain 'L' and resid 433 through 441 removed outlier: 5.021A pdb=" N ASP L 439 " --> pdb=" O ASP L 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU L 440 " --> pdb=" O GLU L 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 441 " --> pdb=" O TRP L 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU L 456 " --> pdb=" O SER L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 473 Processing helix chain 'L' and resid 482 through 490 Processing helix chain 'L' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU L 506 " --> pdb=" O ALA L 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU L 507 " --> pdb=" O LYS L 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU L 508 " --> pdb=" O GLN L 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER L 509 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 110 through 111 Processing sheet with id= B, first strand: chain 'A' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE A 157 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 182 through 183 Processing sheet with id= D, first strand: chain 'A' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG A 283 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR A 314 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 328 through 329 removed outlier: 3.730A pdb=" N TYR L 314 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.776A pdb=" N GLU A 332 " --> pdb=" O ARG L 283 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TRP L 285 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR A 334 " --> pdb=" O TRP L 285 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 110 through 111 Processing sheet with id= I, first strand: chain 'B' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE B 157 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 182 through 183 Processing sheet with id= K, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG B 283 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.731A pdb=" N TYR B 314 " --> pdb=" O MET C 328 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 110 through 111 Processing sheet with id= N, first strand: chain 'C' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE C 157 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 182 through 183 Processing sheet with id= P, first strand: chain 'C' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG C 283 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR C 314 " --> pdb=" O MET D 328 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 110 through 111 Processing sheet with id= S, first strand: chain 'D' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE D 157 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 182 through 183 Processing sheet with id= U, first strand: chain 'D' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG D 283 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR D 314 " --> pdb=" O MET E 328 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 110 through 111 Processing sheet with id= X, first strand: chain 'E' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE E 157 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 182 through 183 Processing sheet with id= Z, first strand: chain 'E' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG E 283 " --> pdb=" O GLU F 332 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 313 through 314 removed outlier: 3.731A pdb=" N TYR E 314 " --> pdb=" O MET F 328 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 110 through 111 Processing sheet with id= AC, first strand: chain 'F' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE F 157 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 182 through 183 Processing sheet with id= AE, first strand: chain 'F' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG F 283 " --> pdb=" O GLU G 332 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR F 314 " --> pdb=" O MET G 328 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 110 through 111 Processing sheet with id= AH, first strand: chain 'G' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE G 157 " --> pdb=" O LEU G 177 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 182 through 183 Processing sheet with id= AJ, first strand: chain 'G' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG G 283 " --> pdb=" O GLU H 332 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR G 314 " --> pdb=" O MET H 328 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 110 through 111 Processing sheet with id= AM, first strand: chain 'H' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE H 157 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 182 through 183 Processing sheet with id= AO, first strand: chain 'H' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG H 283 " --> pdb=" O GLU I 332 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 313 through 314 removed outlier: 3.731A pdb=" N TYR H 314 " --> pdb=" O MET I 328 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 110 through 111 Processing sheet with id= AR, first strand: chain 'I' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE I 157 " --> pdb=" O LEU I 177 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 182 through 183 Processing sheet with id= AT, first strand: chain 'I' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG I 283 " --> pdb=" O GLU J 332 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR I 314 " --> pdb=" O MET J 328 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 110 through 111 Processing sheet with id= AW, first strand: chain 'J' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE J 157 " --> pdb=" O LEU J 177 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 182 through 183 Processing sheet with id= AY, first strand: chain 'J' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG J 283 " --> pdb=" O GLU K 332 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'J' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR J 314 " --> pdb=" O MET K 328 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 110 through 111 Processing sheet with id= BB, first strand: chain 'K' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE K 157 " --> pdb=" O LEU K 177 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'K' and resid 182 through 183 Processing sheet with id= BD, first strand: chain 'K' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG K 283 " --> pdb=" O GLU L 332 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'K' and resid 313 through 314 removed outlier: 3.731A pdb=" N TYR K 314 " --> pdb=" O MET L 328 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 110 through 111 Processing sheet with id= BG, first strand: chain 'L' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE L 157 " --> pdb=" O LEU L 177 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'L' and resid 182 through 183 1414 hydrogen bonds defined for protein. 4026 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: 15.04 Time building geometry restraints manager: 16.99 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: 13349 1.33 - 1.45: 6073 1.45 - 1.57: 22206 1.57 - 1.70: 0 1.70 - 1.82: 420 Bond restraints: 42048 Sorted by residual: bond pdb=" C ILE B 380 " pdb=" N PRO B 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C ILE H 380 " pdb=" N PRO H 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C ILE E 380 " pdb=" N PRO E 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C ILE K 380 " pdb=" N PRO K 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C ILE D 380 " pdb=" N PRO D 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 ... (remaining 42043 not shown) Histogram of bond angle deviations from ideal: 91.21 - 100.80: 84 100.80 - 110.39: 10878 110.39 - 119.98: 26426 119.98 - 129.57: 18988 129.57 - 139.16: 384 Bond angle restraints: 56760 Sorted by residual: angle pdb=" N ARG J 379 " pdb=" CA ARG J 379 " pdb=" C ARG J 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 angle pdb=" N ARG G 379 " pdb=" CA ARG G 379 " pdb=" C ARG G 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 angle pdb=" N ARG D 379 " pdb=" CA ARG D 379 " pdb=" C ARG D 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 angle pdb=" N ARG A 379 " pdb=" CA ARG A 379 " pdb=" C ARG A 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 angle pdb=" N ARG L 379 " pdb=" CA ARG L 379 " pdb=" C ARG L 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 ... (remaining 56755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.36: 21807 14.36 - 28.73: 2588 28.73 - 43.09: 817 43.09 - 57.45: 456 57.45 - 71.82: 72 Dihedral angle restraints: 25740 sinusoidal: 10596 harmonic: 15144 Sorted by residual: dihedral pdb=" CA GLY B 357 " pdb=" C GLY B 357 " pdb=" N ASN B 358 " pdb=" CA ASN B 358 " ideal model delta harmonic sigma weight residual 0.00 20.32 -20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY E 357 " pdb=" C GLY E 357 " pdb=" N ASN E 358 " pdb=" CA ASN E 358 " ideal model delta harmonic sigma weight residual 0.00 20.32 -20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY K 357 " pdb=" C GLY K 357 " pdb=" N ASN K 358 " pdb=" CA ASN K 358 " ideal model delta harmonic sigma weight residual 0.00 20.32 -20.32 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 25737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4804 0.073 - 0.145: 1244 0.145 - 0.218: 144 0.218 - 0.290: 24 0.290 - 0.363: 12 Chirality restraints: 6228 Sorted by residual: chirality pdb=" CA ARG L 379 " pdb=" N ARG L 379 " pdb=" C ARG L 379 " pdb=" CB ARG L 379 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ARG C 379 " pdb=" N ARG C 379 " pdb=" C ARG C 379 " pdb=" CB ARG C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ARG F 379 " pdb=" N ARG F 379 " pdb=" C ARG F 379 " pdb=" CB ARG F 379 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 6225 not shown) Planarity restraints: 7404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 279 " -0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO C 280 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 280 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 280 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 279 " 0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO I 280 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO I 280 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO I 280 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 279 " 0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO L 280 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO L 280 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 280 " 0.052 5.00e-02 4.00e+02 ... (remaining 7401 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 156 2.20 - 2.88: 16750 2.88 - 3.55: 56217 3.55 - 4.23: 93847 4.23 - 4.90: 151993 Nonbonded interactions: 318963 Sorted by model distance: nonbonded pdb=" NH2 ARG D 278 " pdb=" CB ASP E 281 " model vdw 1.528 3.520 nonbonded pdb=" NH2 ARG J 278 " pdb=" CB ASP K 281 " model vdw 1.528 3.520 nonbonded pdb=" NH2 ARG G 278 " pdb=" CB ASP H 281 " model vdw 1.528 3.520 nonbonded pdb=" NH2 ARG A 278 " pdb=" CB ASP B 281 " model vdw 1.528 3.520 nonbonded pdb=" NH2 ARG B 278 " pdb=" CB ASP C 281 " model vdw 1.528 3.520 ... (remaining 318958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 6.680 Check model and map are aligned: 0.590 Set scattering table: 0.340 Process input model: 103.410 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.280 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.010 0.086 42048 Z= 0.630 Angle : 1.539 19.291 56760 Z= 0.992 Chirality : 0.064 0.363 6228 Planarity : 0.006 0.100 7404 Dihedral : 15.936 71.818 15876 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 38.21 Ramachandran Plot: Outliers : 2.12 % Allowed : 11.05 % Favored : 86.83 % Rotamer: Outliers : 10.44 % Allowed : 10.74 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.09), residues: 5088 helix: -3.99 (0.07), residues: 1980 sheet: -3.23 (0.16), residues: 624 loop : -2.53 (0.10), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP I 150 HIS 0.007 0.001 HIS H 255 PHE 0.019 0.003 PHE B 157 TYR 0.014 0.003 TYR B 102 ARG 0.008 0.001 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 456 poor density : 1068 time to evaluate : 4.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8649 (mmm) cc_final: 0.8393 (tpp) REVERT: A 176 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7742 (ttt180) REVERT: A 221 MET cc_start: 0.5050 (tpt) cc_final: 0.4684 (mtp) REVERT: A 283 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8129 (ptp90) REVERT: A 296 LYS cc_start: 0.7711 (ttmm) cc_final: 0.6917 (tmtt) REVERT: A 320 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7491 (ptmt) REVERT: A 401 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8709 (tt) REVERT: A 420 ASP cc_start: 0.7738 (p0) cc_final: 0.7294 (t0) REVERT: A 468 ASN cc_start: 0.8584 (t0) cc_final: 0.8021 (t0) REVERT: A 507 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: B 92 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9254 (t) REVERT: B 221 MET cc_start: 0.5023 (tpt) cc_final: 0.4627 (mtp) REVERT: B 296 LYS cc_start: 0.7654 (ttmm) cc_final: 0.6930 (tmtt) REVERT: B 320 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7582 (ptmt) REVERT: B 361 ASP cc_start: 0.9022 (t0) cc_final: 0.8506 (t0) REVERT: B 371 MET cc_start: 0.8270 (mtp) cc_final: 0.7253 (mtp) REVERT: B 397 THR cc_start: 0.8924 (m) cc_final: 0.8672 (p) REVERT: B 457 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9208 (tt) REVERT: B 468 ASN cc_start: 0.8575 (t0) cc_final: 0.8013 (t0) REVERT: B 507 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: C 83 MET cc_start: 0.8605 (mmm) cc_final: 0.8280 (tpp) REVERT: C 86 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.6780 (t80) REVERT: C 176 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7541 (ttt180) REVERT: C 221 MET cc_start: 0.4642 (tpt) cc_final: 0.4328 (mtp) REVERT: C 275 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7416 (ttt180) REVERT: C 296 LYS cc_start: 0.7599 (ttmm) cc_final: 0.6924 (tmtt) REVERT: C 320 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7567 (ptmt) REVERT: C 361 ASP cc_start: 0.9006 (t0) cc_final: 0.8738 (t0) REVERT: C 369 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8834 (tp) REVERT: C 377 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8194 (mt) REVERT: C 397 THR cc_start: 0.9000 (m) cc_final: 0.8788 (p) REVERT: C 420 ASP cc_start: 0.7700 (p0) cc_final: 0.7313 (t0) REVERT: C 468 ASN cc_start: 0.8449 (t0) cc_final: 0.7878 (t0) REVERT: D 83 MET cc_start: 0.8645 (mmm) cc_final: 0.8388 (tpp) REVERT: D 176 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7739 (ttt180) REVERT: D 221 MET cc_start: 0.5053 (tpt) cc_final: 0.4690 (mtp) REVERT: D 283 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8122 (ptp90) REVERT: D 296 LYS cc_start: 0.7709 (ttmm) cc_final: 0.6919 (tmtt) REVERT: D 320 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7493 (ptmt) REVERT: D 401 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8706 (tt) REVERT: D 420 ASP cc_start: 0.7736 (p0) cc_final: 0.7292 (t0) REVERT: D 468 ASN cc_start: 0.8581 (t0) cc_final: 0.8003 (t0) REVERT: D 507 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: E 92 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9253 (t) REVERT: E 221 MET cc_start: 0.5026 (tpt) cc_final: 0.4628 (mtp) REVERT: E 296 LYS cc_start: 0.7655 (ttmm) cc_final: 0.6930 (tmtt) REVERT: E 320 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7580 (ptmt) REVERT: E 361 ASP cc_start: 0.9022 (t0) cc_final: 0.8505 (t0) REVERT: E 371 MET cc_start: 0.8270 (mtp) cc_final: 0.7249 (mtp) REVERT: E 397 THR cc_start: 0.8928 (m) cc_final: 0.8674 (p) REVERT: E 457 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9210 (tt) REVERT: E 468 ASN cc_start: 0.8574 (t0) cc_final: 0.8009 (t0) REVERT: E 507 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: F 83 MET cc_start: 0.8605 (mmm) cc_final: 0.8283 (tpp) REVERT: F 86 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6779 (t80) REVERT: F 176 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7541 (ttt180) REVERT: F 221 MET cc_start: 0.4636 (tpt) cc_final: 0.4324 (mtp) REVERT: F 275 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7410 (ttt180) REVERT: F 296 LYS cc_start: 0.7604 (ttmm) cc_final: 0.6929 (tmtt) REVERT: F 320 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7570 (ptmt) REVERT: F 361 ASP cc_start: 0.9009 (t0) cc_final: 0.8738 (t0) REVERT: F 369 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8836 (tp) REVERT: F 377 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8190 (mt) REVERT: F 397 THR cc_start: 0.9002 (m) cc_final: 0.8790 (p) REVERT: F 420 ASP cc_start: 0.7698 (p0) cc_final: 0.7315 (t0) REVERT: F 468 ASN cc_start: 0.8453 (t0) cc_final: 0.7881 (t0) REVERT: G 83 MET cc_start: 0.8643 (mmm) cc_final: 0.8388 (tpp) REVERT: G 176 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7737 (ttt180) REVERT: G 221 MET cc_start: 0.5054 (tpt) cc_final: 0.4692 (mtp) REVERT: G 283 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8121 (ptp90) REVERT: G 296 LYS cc_start: 0.7707 (ttmm) cc_final: 0.6917 (tmtt) REVERT: G 320 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7495 (ptmt) REVERT: G 401 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8709 (tt) REVERT: G 420 ASP cc_start: 0.7732 (p0) cc_final: 0.7293 (t0) REVERT: G 468 ASN cc_start: 0.8586 (t0) cc_final: 0.8006 (t0) REVERT: G 507 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: H 92 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9254 (t) REVERT: H 221 MET cc_start: 0.5026 (tpt) cc_final: 0.4627 (mtp) REVERT: H 296 LYS cc_start: 0.7661 (ttmm) cc_final: 0.6935 (tmtt) REVERT: H 320 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7580 (ptmt) REVERT: H 361 ASP cc_start: 0.9022 (t0) cc_final: 0.8503 (t0) REVERT: H 371 MET cc_start: 0.8270 (mtp) cc_final: 0.7224 (mtp) REVERT: H 397 THR cc_start: 0.8927 (m) cc_final: 0.8676 (p) REVERT: H 457 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9208 (tt) REVERT: H 468 ASN cc_start: 0.8572 (t0) cc_final: 0.8008 (t0) REVERT: H 507 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7756 (tp30) REVERT: I 83 MET cc_start: 0.8608 (mmm) cc_final: 0.8282 (tpp) REVERT: I 86 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6706 (t80) REVERT: I 176 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7545 (ttt180) REVERT: I 221 MET cc_start: 0.4638 (tpt) cc_final: 0.4324 (mtp) REVERT: I 275 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7411 (ttt180) REVERT: I 296 LYS cc_start: 0.7602 (ttmm) cc_final: 0.6930 (tmtt) REVERT: I 320 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7567 (ptmt) REVERT: I 361 ASP cc_start: 0.9008 (t0) cc_final: 0.8733 (t0) REVERT: I 369 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8834 (tp) REVERT: I 377 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8196 (mt) REVERT: I 397 THR cc_start: 0.9000 (m) cc_final: 0.8789 (p) REVERT: I 420 ASP cc_start: 0.7695 (p0) cc_final: 0.7310 (t0) REVERT: I 468 ASN cc_start: 0.8450 (t0) cc_final: 0.7879 (t0) REVERT: J 83 MET cc_start: 0.8648 (mmm) cc_final: 0.8395 (tpp) REVERT: J 176 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7735 (ttt180) REVERT: J 221 MET cc_start: 0.5052 (tpt) cc_final: 0.4690 (mtp) REVERT: J 283 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (ptp90) REVERT: J 296 LYS cc_start: 0.7708 (ttmm) cc_final: 0.6916 (tmtt) REVERT: J 320 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7492 (ptmt) REVERT: J 401 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8712 (tt) REVERT: J 420 ASP cc_start: 0.7734 (p0) cc_final: 0.7294 (t0) REVERT: J 468 ASN cc_start: 0.8583 (t0) cc_final: 0.8006 (t0) REVERT: J 507 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: K 92 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9256 (t) REVERT: K 221 MET cc_start: 0.5025 (tpt) cc_final: 0.4627 (mtp) REVERT: K 296 LYS cc_start: 0.7657 (ttmm) cc_final: 0.6929 (tmtt) REVERT: K 320 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7580 (ptmt) REVERT: K 361 ASP cc_start: 0.9023 (t0) cc_final: 0.8505 (t0) REVERT: K 371 MET cc_start: 0.8268 (mtp) cc_final: 0.7254 (mtp) REVERT: K 397 THR cc_start: 0.8927 (m) cc_final: 0.8675 (p) REVERT: K 457 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9207 (tt) REVERT: K 468 ASN cc_start: 0.8571 (t0) cc_final: 0.8010 (t0) REVERT: K 507 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7759 (tp30) REVERT: L 83 MET cc_start: 0.8607 (mmm) cc_final: 0.8282 (tpp) REVERT: L 86 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6781 (t80) REVERT: L 176 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7544 (ttt180) REVERT: L 221 MET cc_start: 0.4640 (tpt) cc_final: 0.4324 (mtp) REVERT: L 275 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7409 (ttt180) REVERT: L 296 LYS cc_start: 0.7603 (ttmm) cc_final: 0.6926 (tmtt) REVERT: L 320 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7566 (ptmt) REVERT: L 361 ASP cc_start: 0.9009 (t0) cc_final: 0.8724 (t0) REVERT: L 369 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8838 (tp) REVERT: L 377 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8195 (mt) REVERT: L 397 THR cc_start: 0.9000 (m) cc_final: 0.8788 (p) REVERT: L 420 ASP cc_start: 0.7696 (p0) cc_final: 0.7312 (t0) REVERT: L 468 ASN cc_start: 0.8450 (t0) cc_final: 0.7878 (t0) outliers start: 456 outliers final: 100 residues processed: 1428 average time/residue: 0.6225 time to fit residues: 1353.1935 Evaluate side-chains 856 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 708 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 513 ARG Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 507 GLU Chi-restraints excluded: chain E residue 513 ARG Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 283 ARG Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 467 ILE Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 507 GLU Chi-restraints excluded: chain G residue 513 ARG Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 283 ARG Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 507 GLU Chi-restraints excluded: chain H residue 513 ARG Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 275 ARG Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 513 ARG Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 176 ARG Chi-restraints excluded: chain J residue 254 LEU Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 507 GLU Chi-restraints excluded: chain J residue 513 ARG Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 283 ARG Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 377 LEU Chi-restraints excluded: chain K residue 399 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain K residue 507 GLU Chi-restraints excluded: chain K residue 513 ARG Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 176 ARG Chi-restraints excluded: chain L residue 275 ARG Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 399 ASP Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 513 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 4.9990 chunk 382 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 257 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 395 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 294 optimal weight: 0.9980 chunk 457 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 146 HIS A 183 GLN A 355 ASN A 358 ASN B 90 ASN B 146 HIS B 355 ASN B 358 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 183 GLN C 255 HIS C 355 ASN C 358 ASN C 492 GLN D 84 ASN D 146 HIS D 183 GLN D 355 ASN D 358 ASN E 90 ASN E 146 HIS E 355 ASN E 358 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS F 183 GLN F 255 HIS F 355 ASN F 358 ASN F 492 GLN G 84 ASN G 146 HIS G 183 GLN G 355 ASN G 358 ASN H 90 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 HIS H 355 ASN H 358 ASN ** H 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 HIS I 183 GLN I 255 HIS I 355 ASN I 358 ASN I 492 GLN J 84 ASN J 146 HIS J 183 GLN J 355 ASN J 358 ASN K 90 ASN ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 HIS K 355 ASN K 358 ASN ** K 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 HIS L 183 GLN L 255 HIS L 355 ASN L 358 ASN L 492 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42048 Z= 0.229 Angle : 0.771 9.811 56760 Z= 0.408 Chirality : 0.046 0.243 6228 Planarity : 0.005 0.040 7404 Dihedral : 8.922 57.030 5956 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.94 % Allowed : 3.62 % Favored : 95.44 % Rotamer: Outliers : 4.88 % Allowed : 16.60 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.10), residues: 5088 helix: -2.54 (0.09), residues: 2232 sheet: -1.98 (0.22), residues: 384 loop : -2.20 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 150 HIS 0.004 0.001 HIS K 326 PHE 0.012 0.002 PHE K 365 TYR 0.009 0.001 TYR L 237 ARG 0.005 0.001 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 807 time to evaluate : 5.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8142 (mm) cc_final: 0.7810 (pt) REVERT: A 83 MET cc_start: 0.8246 (mmm) cc_final: 0.8014 (mmm) REVERT: A 221 MET cc_start: 0.4840 (tpt) cc_final: 0.4443 (mtp) REVERT: A 268 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7486 (mt-10) REVERT: A 296 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7114 (tmtt) REVERT: A 301 MET cc_start: 0.8722 (mmm) cc_final: 0.8344 (mmt) REVERT: A 320 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7721 (ptmt) REVERT: A 401 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 438 ASN cc_start: 0.8265 (m-40) cc_final: 0.7859 (m-40) REVERT: A 450 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7707 (mtt90) REVERT: A 464 GLU cc_start: 0.7504 (tt0) cc_final: 0.7226 (tt0) REVERT: A 472 MET cc_start: 0.8566 (ttp) cc_final: 0.8328 (ttp) REVERT: A 513 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: B 72 ILE cc_start: 0.8089 (mm) cc_final: 0.7861 (pt) REVERT: B 221 MET cc_start: 0.4562 (tpt) cc_final: 0.3980 (mtp) REVERT: B 268 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7487 (mt-10) REVERT: B 296 LYS cc_start: 0.7678 (ttmm) cc_final: 0.7031 (tmtt) REVERT: B 320 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7608 (ptmt) REVERT: B 397 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8443 (p) REVERT: B 438 ASN cc_start: 0.7958 (m-40) cc_final: 0.7727 (m-40) REVERT: B 457 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9058 (tt) REVERT: C 72 ILE cc_start: 0.8262 (mm) cc_final: 0.7962 (pt) REVERT: C 136 HIS cc_start: 0.8141 (m90) cc_final: 0.7815 (m-70) REVERT: C 221 MET cc_start: 0.4454 (tpt) cc_final: 0.3959 (mtp) REVERT: C 268 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7261 (mt-10) REVERT: C 296 LYS cc_start: 0.7493 (ttmm) cc_final: 0.6877 (tmtt) REVERT: C 320 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7737 (ptmt) REVERT: C 397 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8575 (p) REVERT: C 468 ASN cc_start: 0.8597 (t0) cc_final: 0.8166 (t0) REVERT: D 72 ILE cc_start: 0.8097 (mm) cc_final: 0.7760 (pt) REVERT: D 83 MET cc_start: 0.8252 (mmm) cc_final: 0.8012 (mmm) REVERT: D 221 MET cc_start: 0.4841 (tpt) cc_final: 0.4444 (mtp) REVERT: D 268 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7485 (mt-10) REVERT: D 296 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7110 (tmtt) REVERT: D 301 MET cc_start: 0.8720 (mmm) cc_final: 0.8355 (mmt) REVERT: D 320 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7722 (ptmt) REVERT: D 401 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8326 (tt) REVERT: D 438 ASN cc_start: 0.8255 (m-40) cc_final: 0.7845 (m-40) REVERT: D 450 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7709 (mtt90) REVERT: D 464 GLU cc_start: 0.7555 (tt0) cc_final: 0.7254 (tt0) REVERT: D 468 ASN cc_start: 0.8589 (t0) cc_final: 0.8381 (t0) REVERT: D 472 MET cc_start: 0.8565 (ttp) cc_final: 0.8328 (ttp) REVERT: D 513 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: E 72 ILE cc_start: 0.8089 (mm) cc_final: 0.7864 (pt) REVERT: E 221 MET cc_start: 0.4559 (tpt) cc_final: 0.3979 (mtp) REVERT: E 268 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7483 (mt-10) REVERT: E 296 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7030 (tmtt) REVERT: E 320 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7607 (ptmt) REVERT: E 397 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8444 (p) REVERT: E 438 ASN cc_start: 0.7953 (m-40) cc_final: 0.7721 (m-40) REVERT: E 457 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9060 (tt) REVERT: F 72 ILE cc_start: 0.8260 (mm) cc_final: 0.7960 (pt) REVERT: F 136 HIS cc_start: 0.8145 (m90) cc_final: 0.7815 (m-70) REVERT: F 221 MET cc_start: 0.4448 (tpt) cc_final: 0.3954 (mtp) REVERT: F 268 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7260 (mt-10) REVERT: F 296 LYS cc_start: 0.7497 (ttmm) cc_final: 0.6880 (tmtt) REVERT: F 320 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7737 (ptmt) REVERT: F 397 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8576 (p) REVERT: F 468 ASN cc_start: 0.8598 (t0) cc_final: 0.8170 (t0) REVERT: G 72 ILE cc_start: 0.8101 (mm) cc_final: 0.7766 (pt) REVERT: G 83 MET cc_start: 0.8249 (mmm) cc_final: 0.8010 (mmm) REVERT: G 221 MET cc_start: 0.4853 (tpt) cc_final: 0.4453 (mtp) REVERT: G 268 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7488 (mt-10) REVERT: G 296 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7112 (tmtt) REVERT: G 301 MET cc_start: 0.8719 (mmm) cc_final: 0.8353 (mmt) REVERT: G 320 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7722 (ptmt) REVERT: G 401 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8329 (tt) REVERT: G 438 ASN cc_start: 0.8252 (m-40) cc_final: 0.7844 (m-40) REVERT: G 450 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7706 (mtt90) REVERT: G 464 GLU cc_start: 0.7556 (tt0) cc_final: 0.7250 (tt0) REVERT: G 468 ASN cc_start: 0.8590 (t0) cc_final: 0.8374 (t0) REVERT: G 472 MET cc_start: 0.8563 (ttp) cc_final: 0.8328 (ttp) REVERT: G 513 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: H 72 ILE cc_start: 0.8087 (mm) cc_final: 0.7861 (pt) REVERT: H 221 MET cc_start: 0.4565 (tpt) cc_final: 0.3985 (mtp) REVERT: H 268 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7480 (mt-10) REVERT: H 296 LYS cc_start: 0.7686 (ttmm) cc_final: 0.7034 (tmtt) REVERT: H 320 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7608 (ptmt) REVERT: H 397 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8444 (p) REVERT: H 438 ASN cc_start: 0.7954 (m-40) cc_final: 0.7722 (m-40) REVERT: H 457 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9058 (tt) REVERT: I 72 ILE cc_start: 0.8257 (mm) cc_final: 0.7958 (pt) REVERT: I 136 HIS cc_start: 0.8142 (m90) cc_final: 0.7814 (m-70) REVERT: I 221 MET cc_start: 0.4442 (tpt) cc_final: 0.3952 (mtp) REVERT: I 268 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7257 (mt-10) REVERT: I 296 LYS cc_start: 0.7502 (ttmm) cc_final: 0.6883 (tmtt) REVERT: I 320 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7737 (ptmt) REVERT: I 397 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8572 (p) REVERT: I 468 ASN cc_start: 0.8600 (t0) cc_final: 0.8170 (t0) REVERT: J 72 ILE cc_start: 0.8096 (mm) cc_final: 0.7760 (pt) REVERT: J 83 MET cc_start: 0.8249 (mmm) cc_final: 0.8013 (mmm) REVERT: J 221 MET cc_start: 0.4854 (tpt) cc_final: 0.4454 (mtp) REVERT: J 268 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7487 (mt-10) REVERT: J 296 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7113 (tmtt) REVERT: J 301 MET cc_start: 0.8722 (mmm) cc_final: 0.8358 (mmt) REVERT: J 320 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7713 (ptmt) REVERT: J 401 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8327 (tt) REVERT: J 438 ASN cc_start: 0.8258 (m-40) cc_final: 0.7851 (m-40) REVERT: J 450 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7706 (mtt90) REVERT: J 464 GLU cc_start: 0.7556 (tt0) cc_final: 0.7254 (tt0) REVERT: J 468 ASN cc_start: 0.8592 (t0) cc_final: 0.8382 (t0) REVERT: J 472 MET cc_start: 0.8567 (ttp) cc_final: 0.8326 (ttp) REVERT: J 513 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: K 72 ILE cc_start: 0.8086 (mm) cc_final: 0.7859 (pt) REVERT: K 221 MET cc_start: 0.4565 (tpt) cc_final: 0.3984 (mtp) REVERT: K 268 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7485 (mt-10) REVERT: K 296 LYS cc_start: 0.7681 (ttmm) cc_final: 0.7030 (tmtt) REVERT: K 320 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7601 (ptmt) REVERT: K 397 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (p) REVERT: K 438 ASN cc_start: 0.7956 (m-40) cc_final: 0.7723 (m-40) REVERT: K 457 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9056 (tt) REVERT: L 72 ILE cc_start: 0.8260 (mm) cc_final: 0.7960 (pt) REVERT: L 136 HIS cc_start: 0.8140 (m90) cc_final: 0.7812 (m-70) REVERT: L 221 MET cc_start: 0.4445 (tpt) cc_final: 0.3957 (mtp) REVERT: L 268 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7263 (mt-10) REVERT: L 296 LYS cc_start: 0.7497 (ttmm) cc_final: 0.6879 (tmtt) REVERT: L 320 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7738 (ptmt) REVERT: L 397 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8573 (p) REVERT: L 468 ASN cc_start: 0.8595 (t0) cc_final: 0.8165 (t0) outliers start: 213 outliers final: 96 residues processed: 1000 average time/residue: 0.5272 time to fit residues: 847.0965 Evaluate side-chains 767 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 651 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 ARG Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 ARG Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 457 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 254 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 513 ARG Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 380 optimal weight: 0.5980 chunk 311 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 458 optimal weight: 5.9990 chunk 495 optimal weight: 1.9990 chunk 408 optimal weight: 7.9990 chunk 454 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 367 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS B 367 GLN B 382 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 GLN E 382 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 412 HIS ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 HIS H 367 GLN H 382 GLN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 412 HIS ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 HIS K 367 GLN K 382 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 42048 Z= 0.231 Angle : 0.683 7.960 56760 Z= 0.360 Chirality : 0.043 0.151 6228 Planarity : 0.004 0.028 7404 Dihedral : 6.745 57.084 5724 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.17 % Favored : 95.36 % Rotamer: Outliers : 5.01 % Allowed : 18.09 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.11), residues: 5088 helix: -1.61 (0.10), residues: 2256 sheet: -1.69 (0.24), residues: 384 loop : -2.01 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 285 HIS 0.003 0.001 HIS C 159 PHE 0.013 0.002 PHE K 365 TYR 0.009 0.001 TYR J 102 ARG 0.005 0.000 ARG K 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 699 time to evaluate : 5.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8256 (mm) cc_final: 0.7836 (pt) REVERT: A 171 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6023 (tt) REVERT: A 221 MET cc_start: 0.4285 (tpt) cc_final: 0.3959 (mtp) REVERT: A 268 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7584 (mt-10) REVERT: A 296 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7191 (tmtt) REVERT: A 302 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6867 (tt0) REVERT: A 320 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7925 (ptmt) REVERT: A 346 GLU cc_start: 0.8174 (pm20) cc_final: 0.7913 (pm20) REVERT: A 401 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8382 (tt) REVERT: A 416 GLU cc_start: 0.8769 (tt0) cc_final: 0.8565 (tt0) REVERT: A 513 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7532 (mtm-85) REVERT: B 72 ILE cc_start: 0.8117 (mm) cc_final: 0.7824 (pt) REVERT: B 171 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.6100 (tt) REVERT: B 172 LYS cc_start: 0.5710 (mmtm) cc_final: 0.5498 (mmtm) REVERT: B 221 MET cc_start: 0.4660 (tpt) cc_final: 0.3936 (mtp) REVERT: B 268 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7522 (mt-10) REVERT: B 296 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7137 (tmtt) REVERT: B 320 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7759 (ptmt) REVERT: B 328 MET cc_start: 0.5767 (ttt) cc_final: 0.5558 (ttt) REVERT: B 401 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8429 (tt) REVERT: B 408 ARG cc_start: 0.8252 (tpp-160) cc_final: 0.7861 (tpt90) REVERT: B 434 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7430 (tm-30) REVERT: B 438 ASN cc_start: 0.7795 (m-40) cc_final: 0.7566 (m-40) REVERT: C 72 ILE cc_start: 0.8341 (mm) cc_final: 0.7945 (pt) REVERT: C 126 MET cc_start: 0.7478 (mmt) cc_final: 0.7163 (mmm) REVERT: C 221 MET cc_start: 0.4215 (tpt) cc_final: 0.3883 (mtm) REVERT: C 268 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7448 (mt-10) REVERT: C 296 LYS cc_start: 0.7656 (ttmm) cc_final: 0.6997 (tmtt) REVERT: C 320 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7794 (ptmt) REVERT: C 361 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7715 (t0) REVERT: C 397 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8471 (p) REVERT: C 408 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7695 (tpm170) REVERT: C 468 ASN cc_start: 0.8584 (t0) cc_final: 0.8290 (t0) REVERT: D 72 ILE cc_start: 0.8272 (mm) cc_final: 0.7864 (pt) REVERT: D 171 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.6150 (tt) REVERT: D 221 MET cc_start: 0.4299 (tpt) cc_final: 0.3953 (mtp) REVERT: D 268 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7582 (mt-10) REVERT: D 296 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7188 (tmtt) REVERT: D 302 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6871 (tt0) REVERT: D 320 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7923 (ptmt) REVERT: D 346 GLU cc_start: 0.8167 (pm20) cc_final: 0.7916 (pm20) REVERT: D 401 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8382 (tt) REVERT: D 468 ASN cc_start: 0.8815 (t0) cc_final: 0.8464 (t0) REVERT: D 472 MET cc_start: 0.8650 (ttp) cc_final: 0.8444 (ttp) REVERT: D 513 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7533 (mtm-85) REVERT: E 72 ILE cc_start: 0.8122 (mm) cc_final: 0.7836 (pt) REVERT: E 171 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.6102 (tt) REVERT: E 172 LYS cc_start: 0.5706 (mmtm) cc_final: 0.5498 (mmtm) REVERT: E 221 MET cc_start: 0.4663 (tpt) cc_final: 0.3936 (mtp) REVERT: E 268 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7521 (mt-10) REVERT: E 296 LYS cc_start: 0.7873 (ttmm) cc_final: 0.7139 (tmtt) REVERT: E 320 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7756 (ptmt) REVERT: E 328 MET cc_start: 0.5776 (ttt) cc_final: 0.5563 (ttt) REVERT: E 401 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8431 (tt) REVERT: E 408 ARG cc_start: 0.8249 (tpp-160) cc_final: 0.7859 (tpt90) REVERT: E 434 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7430 (tm-30) REVERT: E 438 ASN cc_start: 0.7795 (m-40) cc_final: 0.7564 (m-40) REVERT: F 72 ILE cc_start: 0.8338 (mm) cc_final: 0.7943 (pt) REVERT: F 126 MET cc_start: 0.7476 (mmt) cc_final: 0.7166 (mmm) REVERT: F 221 MET cc_start: 0.4206 (tpt) cc_final: 0.3881 (mtm) REVERT: F 268 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7445 (mt-10) REVERT: F 296 LYS cc_start: 0.7656 (ttmm) cc_final: 0.6999 (tmtt) REVERT: F 320 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7794 (ptmt) REVERT: F 361 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7715 (t0) REVERT: F 397 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8471 (p) REVERT: F 408 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7691 (tpm170) REVERT: F 468 ASN cc_start: 0.8577 (t0) cc_final: 0.8285 (t0) REVERT: G 72 ILE cc_start: 0.8274 (mm) cc_final: 0.7866 (pt) REVERT: G 171 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6145 (tt) REVERT: G 221 MET cc_start: 0.4301 (tpt) cc_final: 0.3957 (mtp) REVERT: G 268 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7580 (mt-10) REVERT: G 296 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7193 (tmtt) REVERT: G 302 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6868 (tt0) REVERT: G 320 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7919 (ptmt) REVERT: G 346 GLU cc_start: 0.8164 (pm20) cc_final: 0.7914 (pm20) REVERT: G 401 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8383 (tt) REVERT: G 468 ASN cc_start: 0.8814 (t0) cc_final: 0.8455 (t0) REVERT: G 472 MET cc_start: 0.8656 (ttp) cc_final: 0.8455 (ttp) REVERT: G 513 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7532 (mtm-85) REVERT: H 72 ILE cc_start: 0.8112 (mm) cc_final: 0.7819 (pt) REVERT: H 172 LYS cc_start: 0.5703 (mmtm) cc_final: 0.5497 (mmtm) REVERT: H 221 MET cc_start: 0.4660 (tpt) cc_final: 0.3941 (mtp) REVERT: H 268 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7517 (mt-10) REVERT: H 296 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7142 (tmtt) REVERT: H 320 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7755 (ptmt) REVERT: H 328 MET cc_start: 0.5771 (ttt) cc_final: 0.5563 (ttt) REVERT: H 401 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8430 (tt) REVERT: H 408 ARG cc_start: 0.8248 (tpp-160) cc_final: 0.7859 (tpt90) REVERT: H 434 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7427 (tm-30) REVERT: H 438 ASN cc_start: 0.7792 (m-40) cc_final: 0.7564 (m-40) REVERT: I 72 ILE cc_start: 0.8336 (mm) cc_final: 0.7941 (pt) REVERT: I 126 MET cc_start: 0.7478 (mmt) cc_final: 0.7169 (mmm) REVERT: I 221 MET cc_start: 0.4203 (tpt) cc_final: 0.3876 (mtm) REVERT: I 268 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7445 (mt-10) REVERT: I 296 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7003 (tmtt) REVERT: I 320 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7795 (ptmt) REVERT: I 361 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7716 (t0) REVERT: I 397 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8470 (p) REVERT: I 408 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7693 (tpm170) REVERT: I 468 ASN cc_start: 0.8582 (t0) cc_final: 0.8291 (t0) REVERT: J 72 ILE cc_start: 0.8275 (mm) cc_final: 0.7866 (pt) REVERT: J 171 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6141 (tt) REVERT: J 221 MET cc_start: 0.4302 (tpt) cc_final: 0.3963 (mtp) REVERT: J 268 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7583 (mt-10) REVERT: J 296 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7193 (tmtt) REVERT: J 302 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6868 (tt0) REVERT: J 320 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7922 (ptmt) REVERT: J 346 GLU cc_start: 0.8160 (pm20) cc_final: 0.7911 (pm20) REVERT: J 401 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8382 (tt) REVERT: J 468 ASN cc_start: 0.8814 (t0) cc_final: 0.8462 (t0) REVERT: J 472 MET cc_start: 0.8659 (ttp) cc_final: 0.8453 (ttp) REVERT: J 513 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7532 (mtm-85) REVERT: K 72 ILE cc_start: 0.8112 (mm) cc_final: 0.7821 (pt) REVERT: K 172 LYS cc_start: 0.5714 (mmtm) cc_final: 0.5504 (mmtm) REVERT: K 221 MET cc_start: 0.4669 (tpt) cc_final: 0.3946 (mtp) REVERT: K 268 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7519 (mt-10) REVERT: K 296 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7138 (tmtt) REVERT: K 320 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7760 (ptmt) REVERT: K 328 MET cc_start: 0.5771 (ttt) cc_final: 0.5564 (ttt) REVERT: K 401 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8428 (tt) REVERT: K 408 ARG cc_start: 0.8248 (tpp-160) cc_final: 0.7860 (tpt90) REVERT: K 434 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7419 (tm-30) REVERT: K 438 ASN cc_start: 0.7791 (m-40) cc_final: 0.7548 (m-40) REVERT: L 72 ILE cc_start: 0.8336 (mm) cc_final: 0.7940 (pt) REVERT: L 126 MET cc_start: 0.7475 (mmt) cc_final: 0.7165 (mmm) REVERT: L 221 MET cc_start: 0.4210 (tpt) cc_final: 0.3881 (mtm) REVERT: L 268 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7445 (mt-10) REVERT: L 296 LYS cc_start: 0.7658 (ttmm) cc_final: 0.6992 (tmtt) REVERT: L 320 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7792 (ptmt) REVERT: L 361 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7713 (t0) REVERT: L 397 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8469 (p) REVERT: L 408 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7693 (tpm170) REVERT: L 468 ASN cc_start: 0.8552 (t0) cc_final: 0.8270 (t0) outliers start: 219 outliers final: 108 residues processed: 878 average time/residue: 0.5189 time to fit residues: 736.7921 Evaluate side-chains 785 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 651 time to evaluate : 4.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 ARG Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 ARG Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 312 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 472 MET Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 457 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 513 ARG Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 472 MET Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 chunk 460 optimal weight: 5.9990 chunk 487 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 436 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 90 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN C 262 ASN D 262 ASN E 90 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 HIS E 262 ASN F 262 ASN G 262 ASN H 90 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN I 262 ASN J 262 ASN K 90 ASN ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN L 262 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 42048 Z= 0.288 Angle : 0.677 8.972 56760 Z= 0.356 Chirality : 0.045 0.215 6228 Planarity : 0.004 0.036 7404 Dihedral : 6.365 57.927 5708 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.40 % Favored : 94.12 % Rotamer: Outliers : 5.01 % Allowed : 19.23 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.11), residues: 5088 helix: -1.33 (0.10), residues: 2280 sheet: -1.22 (0.27), residues: 384 loop : -2.05 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 437 HIS 0.003 0.001 HIS G 159 PHE 0.014 0.002 PHE J 157 TYR 0.012 0.002 TYR D 102 ARG 0.005 0.000 ARG E 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 720 time to evaluate : 5.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8359 (mm) cc_final: 0.7973 (pt) REVERT: A 83 MET cc_start: 0.8112 (mmm) cc_final: 0.7654 (mmm) REVERT: A 84 ASN cc_start: 0.8371 (t0) cc_final: 0.8163 (m-40) REVERT: A 171 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6396 (tt) REVERT: A 221 MET cc_start: 0.4067 (tpt) cc_final: 0.3655 (mtp) REVERT: A 268 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7664 (mt-10) REVERT: A 296 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7176 (tmtt) REVERT: A 302 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6637 (tt0) REVERT: A 320 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7940 (ptmt) REVERT: A 401 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 416 GLU cc_start: 0.8854 (tt0) cc_final: 0.8574 (tt0) REVERT: A 438 ASN cc_start: 0.8024 (m-40) cc_final: 0.7744 (m-40) REVERT: A 513 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7558 (mtm-85) REVERT: B 72 ILE cc_start: 0.8309 (mm) cc_final: 0.7996 (pt) REVERT: B 87 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6727 (pt0) REVERT: B 171 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6419 (tt) REVERT: B 221 MET cc_start: 0.3973 (tpt) cc_final: 0.3411 (mtp) REVERT: B 268 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7695 (mt-10) REVERT: B 296 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7087 (tmtt) REVERT: B 302 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6723 (tt0) REVERT: B 320 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7770 (ptmt) REVERT: B 401 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 438 ASN cc_start: 0.7893 (m-40) cc_final: 0.7491 (m-40) REVERT: B 469 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7362 (tpp) REVERT: C 72 ILE cc_start: 0.8381 (mm) cc_final: 0.8004 (pt) REVERT: C 84 ASN cc_start: 0.8222 (m-40) cc_final: 0.7978 (m-40) REVERT: C 221 MET cc_start: 0.4005 (tpt) cc_final: 0.3678 (mtm) REVERT: C 268 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7611 (mt-10) REVERT: C 296 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7018 (tmtt) REVERT: C 302 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6722 (tt0) REVERT: C 320 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7706 (ptmt) REVERT: C 361 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7676 (t0) REVERT: C 397 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8561 (p) REVERT: C 408 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7624 (tpm170) REVERT: C 426 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7750 (tt) REVERT: C 438 ASN cc_start: 0.8040 (m-40) cc_final: 0.7824 (m-40) REVERT: C 468 ASN cc_start: 0.8607 (t0) cc_final: 0.8307 (t0) REVERT: C 508 GLU cc_start: 0.8100 (mp0) cc_final: 0.7628 (mp0) REVERT: D 72 ILE cc_start: 0.8340 (mm) cc_final: 0.7984 (pt) REVERT: D 83 MET cc_start: 0.8107 (mmm) cc_final: 0.7636 (mmm) REVERT: D 84 ASN cc_start: 0.8370 (t0) cc_final: 0.8159 (m-40) REVERT: D 171 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6402 (tt) REVERT: D 221 MET cc_start: 0.4079 (tpt) cc_final: 0.3650 (mtp) REVERT: D 268 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7663 (mt-10) REVERT: D 296 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7194 (tmtt) REVERT: D 302 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6642 (tt0) REVERT: D 320 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7938 (ptmt) REVERT: D 401 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8497 (tt) REVERT: D 416 GLU cc_start: 0.8645 (tt0) cc_final: 0.8405 (tt0) REVERT: D 438 ASN cc_start: 0.8007 (m-40) cc_final: 0.7724 (m-40) REVERT: D 468 ASN cc_start: 0.8800 (t0) cc_final: 0.8460 (t0) REVERT: D 487 MET cc_start: 0.8702 (ttp) cc_final: 0.8289 (ttm) REVERT: D 513 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7564 (mtm-85) REVERT: E 72 ILE cc_start: 0.8311 (mm) cc_final: 0.7997 (pt) REVERT: E 87 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6723 (pt0) REVERT: E 171 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6432 (tt) REVERT: E 221 MET cc_start: 0.3964 (tpt) cc_final: 0.3404 (mtp) REVERT: E 268 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7687 (mt-10) REVERT: E 296 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7087 (tmtt) REVERT: E 302 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6723 (tt0) REVERT: E 320 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7767 (ptmt) REVERT: E 401 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8539 (tt) REVERT: E 438 ASN cc_start: 0.7892 (m-40) cc_final: 0.7488 (m-40) REVERT: E 469 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7363 (tpp) REVERT: F 72 ILE cc_start: 0.8380 (mm) cc_final: 0.8002 (pt) REVERT: F 84 ASN cc_start: 0.8221 (m-40) cc_final: 0.7979 (m-40) REVERT: F 221 MET cc_start: 0.4005 (tpt) cc_final: 0.3683 (mtm) REVERT: F 268 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7610 (mt-10) REVERT: F 296 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7018 (tmtt) REVERT: F 302 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6715 (tt0) REVERT: F 320 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7708 (ptmt) REVERT: F 361 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7677 (t0) REVERT: F 397 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8563 (p) REVERT: F 408 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7624 (tpm170) REVERT: F 426 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7750 (tt) REVERT: F 438 ASN cc_start: 0.8038 (m-40) cc_final: 0.7819 (m-40) REVERT: F 468 ASN cc_start: 0.8606 (t0) cc_final: 0.8303 (t0) REVERT: F 508 GLU cc_start: 0.8098 (mp0) cc_final: 0.7627 (mp0) REVERT: G 72 ILE cc_start: 0.8339 (mm) cc_final: 0.7984 (pt) REVERT: G 83 MET cc_start: 0.8104 (mmm) cc_final: 0.7633 (mmm) REVERT: G 84 ASN cc_start: 0.8367 (t0) cc_final: 0.8158 (m-40) REVERT: G 171 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6401 (tt) REVERT: G 221 MET cc_start: 0.4099 (tpt) cc_final: 0.3668 (mtp) REVERT: G 268 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7663 (mt-10) REVERT: G 296 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7194 (tmtt) REVERT: G 302 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6640 (tt0) REVERT: G 320 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7940 (ptmt) REVERT: G 401 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8499 (tt) REVERT: G 416 GLU cc_start: 0.8644 (tt0) cc_final: 0.8403 (tt0) REVERT: G 438 ASN cc_start: 0.8006 (m-40) cc_final: 0.7722 (m-40) REVERT: G 468 ASN cc_start: 0.8799 (t0) cc_final: 0.8459 (t0) REVERT: G 513 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7556 (mtm-85) REVERT: H 72 ILE cc_start: 0.8306 (mm) cc_final: 0.7993 (pt) REVERT: H 87 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6731 (pt0) REVERT: H 221 MET cc_start: 0.3953 (tpt) cc_final: 0.3410 (mtp) REVERT: H 268 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7686 (mt-10) REVERT: H 296 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7084 (tmtt) REVERT: H 302 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6723 (tt0) REVERT: H 320 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7770 (ptmt) REVERT: H 401 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8541 (tt) REVERT: H 438 ASN cc_start: 0.7891 (m-40) cc_final: 0.7489 (m-40) REVERT: H 469 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7360 (tpp) REVERT: I 72 ILE cc_start: 0.8379 (mm) cc_final: 0.8001 (pt) REVERT: I 84 ASN cc_start: 0.8224 (m-40) cc_final: 0.7979 (m-40) REVERT: I 221 MET cc_start: 0.4001 (tpt) cc_final: 0.3679 (mtm) REVERT: I 268 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7610 (mt-10) REVERT: I 296 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7019 (tmtt) REVERT: I 302 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6720 (tt0) REVERT: I 320 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7706 (ptmt) REVERT: I 361 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7684 (t0) REVERT: I 397 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8561 (p) REVERT: I 408 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7622 (tpm170) REVERT: I 426 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7748 (tt) REVERT: I 438 ASN cc_start: 0.8042 (m-40) cc_final: 0.7821 (m-40) REVERT: I 468 ASN cc_start: 0.8608 (t0) cc_final: 0.8308 (t0) REVERT: I 508 GLU cc_start: 0.8100 (mp0) cc_final: 0.7625 (mp0) REVERT: J 72 ILE cc_start: 0.8343 (mm) cc_final: 0.7987 (pt) REVERT: J 83 MET cc_start: 0.8104 (mmm) cc_final: 0.7634 (mmm) REVERT: J 84 ASN cc_start: 0.8368 (t0) cc_final: 0.8157 (m-40) REVERT: J 171 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6402 (tt) REVERT: J 221 MET cc_start: 0.4094 (tpt) cc_final: 0.3671 (mtp) REVERT: J 268 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7668 (mt-10) REVERT: J 296 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7198 (tmtt) REVERT: J 302 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6642 (tt0) REVERT: J 320 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7938 (ptmt) REVERT: J 401 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8500 (tt) REVERT: J 416 GLU cc_start: 0.8645 (tt0) cc_final: 0.8406 (tt0) REVERT: J 438 ASN cc_start: 0.8006 (m-40) cc_final: 0.7722 (m-40) REVERT: J 468 ASN cc_start: 0.8800 (t0) cc_final: 0.8459 (t0) REVERT: J 513 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7559 (mtm-85) REVERT: K 72 ILE cc_start: 0.8304 (mm) cc_final: 0.7993 (pt) REVERT: K 87 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6726 (pt0) REVERT: K 221 MET cc_start: 0.3967 (tpt) cc_final: 0.3418 (mtp) REVERT: K 268 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7691 (mt-10) REVERT: K 296 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7083 (tmtt) REVERT: K 302 GLN cc_start: 0.7143 (mm-40) cc_final: 0.6725 (tt0) REVERT: K 320 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7771 (ptmt) REVERT: K 401 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8540 (tt) REVERT: K 438 ASN cc_start: 0.7887 (m-40) cc_final: 0.7483 (m-40) REVERT: K 469 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7366 (tpp) REVERT: L 72 ILE cc_start: 0.8372 (mm) cc_final: 0.7998 (pt) REVERT: L 84 ASN cc_start: 0.8225 (m-40) cc_final: 0.7982 (m-40) REVERT: L 221 MET cc_start: 0.4003 (tpt) cc_final: 0.3678 (mtm) REVERT: L 268 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7605 (mt-10) REVERT: L 296 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7017 (tmtt) REVERT: L 302 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6693 (tt0) REVERT: L 320 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7703 (ptmt) REVERT: L 361 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7659 (t0) REVERT: L 397 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8559 (p) REVERT: L 408 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7624 (tpm170) REVERT: L 426 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7750 (tt) REVERT: L 438 ASN cc_start: 0.8041 (m-40) cc_final: 0.7823 (m-40) REVERT: L 468 ASN cc_start: 0.8597 (t0) cc_final: 0.8315 (t0) REVERT: L 508 GLU cc_start: 0.8101 (mp0) cc_final: 0.7626 (mp0) outliers start: 219 outliers final: 104 residues processed: 895 average time/residue: 0.5266 time to fit residues: 760.8179 Evaluate side-chains 810 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 668 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 ARG Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 ARG Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 312 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 469 MET Chi-restraints excluded: chain H residue 472 MET Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 513 ARG Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 144 SER Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 469 MET Chi-restraints excluded: chain K residue 472 MET Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 362 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 415 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 248 optimal weight: 0.0170 chunk 437 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN ** I 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 42048 Z= 0.158 Angle : 0.603 8.911 56760 Z= 0.318 Chirality : 0.041 0.137 6228 Planarity : 0.003 0.030 7404 Dihedral : 5.921 59.961 5700 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.82 % Favored : 94.71 % Rotamer: Outliers : 3.87 % Allowed : 19.71 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.11), residues: 5088 helix: -0.82 (0.10), residues: 2292 sheet: -1.11 (0.26), residues: 384 loop : -1.91 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 285 HIS 0.003 0.001 HIS K 159 PHE 0.010 0.001 PHE J 365 TYR 0.005 0.001 TYR J 314 ARG 0.004 0.000 ARG H 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 704 time to evaluate : 5.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8337 (mm) cc_final: 0.7983 (pt) REVERT: A 221 MET cc_start: 0.3504 (tpt) cc_final: 0.3198 (mtp) REVERT: A 268 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7531 (mt-10) REVERT: A 296 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7140 (tmtt) REVERT: A 302 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6739 (tt0) REVERT: A 320 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7874 (ptmt) REVERT: A 401 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 416 GLU cc_start: 0.8831 (tt0) cc_final: 0.8598 (tt0) REVERT: A 438 ASN cc_start: 0.8019 (m-40) cc_final: 0.7674 (m-40) REVERT: B 72 ILE cc_start: 0.8297 (mm) cc_final: 0.7971 (pt) REVERT: B 77 ASP cc_start: 0.8433 (t0) cc_final: 0.8218 (t0) REVERT: B 87 GLU cc_start: 0.7318 (pt0) cc_final: 0.6383 (pt0) REVERT: B 171 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.6165 (tt) REVERT: B 221 MET cc_start: 0.3750 (tpt) cc_final: 0.3286 (mtp) REVERT: B 236 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8195 (p) REVERT: B 268 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7593 (mt-10) REVERT: B 296 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7030 (tmtt) REVERT: B 302 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6716 (tt0) REVERT: B 320 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7741 (ptmt) REVERT: B 330 MET cc_start: 0.8426 (ttp) cc_final: 0.8125 (ttm) REVERT: B 408 ARG cc_start: 0.8173 (tpp-160) cc_final: 0.7857 (tpt90) REVERT: B 438 ASN cc_start: 0.7952 (m-40) cc_final: 0.7736 (m-40) REVERT: C 72 ILE cc_start: 0.8349 (mm) cc_final: 0.7967 (pt) REVERT: C 87 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: C 126 MET cc_start: 0.7726 (mmm) cc_final: 0.7335 (mmm) REVERT: C 171 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6273 (tt) REVERT: C 221 MET cc_start: 0.3969 (tpt) cc_final: 0.3690 (mtm) REVERT: C 268 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7545 (mt-10) REVERT: C 296 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7078 (tmtt) REVERT: C 302 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6609 (tt0) REVERT: C 320 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7614 (ptmt) REVERT: C 361 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7531 (t0) REVERT: C 397 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8312 (p) REVERT: C 408 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7703 (tpm170) REVERT: C 438 ASN cc_start: 0.8071 (m-40) cc_final: 0.7825 (m-40) REVERT: C 508 GLU cc_start: 0.8132 (mp0) cc_final: 0.7670 (mp0) REVERT: D 72 ILE cc_start: 0.8391 (mm) cc_final: 0.8032 (pt) REVERT: D 171 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6434 (tt) REVERT: D 221 MET cc_start: 0.3514 (tpt) cc_final: 0.3176 (mtp) REVERT: D 268 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7518 (mt-10) REVERT: D 296 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7140 (tmtt) REVERT: D 302 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6741 (tt0) REVERT: D 320 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7873 (ptmt) REVERT: D 401 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8420 (tt) REVERT: D 416 GLU cc_start: 0.8596 (tt0) cc_final: 0.8327 (tt0) REVERT: D 426 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7775 (tt) REVERT: D 438 ASN cc_start: 0.8022 (m-40) cc_final: 0.7698 (m-40) REVERT: D 468 ASN cc_start: 0.8762 (t0) cc_final: 0.8432 (t0) REVERT: D 487 MET cc_start: 0.8559 (ttp) cc_final: 0.8214 (ttm) REVERT: D 508 GLU cc_start: 0.8296 (mp0) cc_final: 0.7811 (mp0) REVERT: E 72 ILE cc_start: 0.8272 (mm) cc_final: 0.7968 (pt) REVERT: E 77 ASP cc_start: 0.8427 (t0) cc_final: 0.8211 (t0) REVERT: E 87 GLU cc_start: 0.7322 (pt0) cc_final: 0.6385 (pt0) REVERT: E 171 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6186 (tt) REVERT: E 221 MET cc_start: 0.3748 (tpt) cc_final: 0.3278 (mtp) REVERT: E 236 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8201 (p) REVERT: E 268 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7577 (mt-10) REVERT: E 296 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7030 (tmtt) REVERT: E 302 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6719 (tt0) REVERT: E 320 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7741 (ptmt) REVERT: E 330 MET cc_start: 0.8428 (ttp) cc_final: 0.8125 (ttm) REVERT: E 408 ARG cc_start: 0.8176 (tpp-160) cc_final: 0.7865 (tpt90) REVERT: E 438 ASN cc_start: 0.7950 (m-40) cc_final: 0.7736 (m-40) REVERT: F 72 ILE cc_start: 0.8351 (mm) cc_final: 0.7969 (pt) REVERT: F 87 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6961 (pt0) REVERT: F 126 MET cc_start: 0.7728 (mmm) cc_final: 0.7340 (mmm) REVERT: F 171 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6272 (tt) REVERT: F 221 MET cc_start: 0.3965 (tpt) cc_final: 0.3690 (mtm) REVERT: F 268 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7545 (mt-10) REVERT: F 296 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7078 (tmtt) REVERT: F 302 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6604 (tt0) REVERT: F 320 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7612 (ptmt) REVERT: F 361 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7533 (t0) REVERT: F 397 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8313 (p) REVERT: F 408 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7703 (tpm170) REVERT: F 438 ASN cc_start: 0.8068 (m-40) cc_final: 0.7823 (m-40) REVERT: F 508 GLU cc_start: 0.8128 (mp0) cc_final: 0.7673 (mp0) REVERT: G 72 ILE cc_start: 0.8392 (mm) cc_final: 0.8032 (pt) REVERT: G 171 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6441 (tt) REVERT: G 221 MET cc_start: 0.3528 (tpt) cc_final: 0.3188 (mtp) REVERT: G 268 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7533 (mt-10) REVERT: G 296 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7136 (tmtt) REVERT: G 302 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6743 (tt0) REVERT: G 320 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7873 (ptmt) REVERT: G 401 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8422 (tt) REVERT: G 416 GLU cc_start: 0.8595 (tt0) cc_final: 0.8327 (tt0) REVERT: G 426 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7775 (tt) REVERT: G 438 ASN cc_start: 0.8017 (m-40) cc_final: 0.7690 (m-40) REVERT: G 468 ASN cc_start: 0.8753 (t0) cc_final: 0.8420 (t0) REVERT: G 508 GLU cc_start: 0.8285 (mp0) cc_final: 0.7806 (mp0) REVERT: H 72 ILE cc_start: 0.8297 (mm) cc_final: 0.7970 (pt) REVERT: H 77 ASP cc_start: 0.8434 (t0) cc_final: 0.8215 (t0) REVERT: H 87 GLU cc_start: 0.7328 (pt0) cc_final: 0.6389 (pt0) REVERT: H 221 MET cc_start: 0.3741 (tpt) cc_final: 0.3294 (mtp) REVERT: H 236 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8203 (p) REVERT: H 268 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7573 (mt-10) REVERT: H 296 LYS cc_start: 0.7942 (ttmm) cc_final: 0.7033 (tmtt) REVERT: H 302 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6719 (tt0) REVERT: H 320 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7742 (ptmt) REVERT: H 330 MET cc_start: 0.8430 (ttp) cc_final: 0.8124 (ttm) REVERT: H 408 ARG cc_start: 0.8177 (tpp-160) cc_final: 0.7865 (tpt90) REVERT: H 438 ASN cc_start: 0.7953 (m-40) cc_final: 0.7739 (m-40) REVERT: I 72 ILE cc_start: 0.8352 (mm) cc_final: 0.7973 (pt) REVERT: I 87 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: I 126 MET cc_start: 0.7726 (mmm) cc_final: 0.7339 (mmm) REVERT: I 171 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.6280 (tt) REVERT: I 221 MET cc_start: 0.3969 (tpt) cc_final: 0.3692 (mtm) REVERT: I 268 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7546 (mt-10) REVERT: I 296 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7078 (tmtt) REVERT: I 302 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6602 (tt0) REVERT: I 320 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7618 (ptmt) REVERT: I 361 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7535 (t0) REVERT: I 397 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8309 (p) REVERT: I 408 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7705 (tpm170) REVERT: I 438 ASN cc_start: 0.8072 (m-40) cc_final: 0.7824 (m-40) REVERT: I 508 GLU cc_start: 0.8129 (mp0) cc_final: 0.7671 (mp0) REVERT: J 72 ILE cc_start: 0.8392 (mm) cc_final: 0.8035 (pt) REVERT: J 171 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6437 (tt) REVERT: J 221 MET cc_start: 0.3533 (tpt) cc_final: 0.3196 (mtp) REVERT: J 268 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7534 (mt-10) REVERT: J 296 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7139 (tmtt) REVERT: J 302 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6742 (tt0) REVERT: J 320 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7872 (ptmt) REVERT: J 401 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8422 (tt) REVERT: J 416 GLU cc_start: 0.8593 (tt0) cc_final: 0.8328 (tt0) REVERT: J 426 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7773 (tt) REVERT: J 438 ASN cc_start: 0.8019 (m-40) cc_final: 0.7692 (m-40) REVERT: J 468 ASN cc_start: 0.8751 (t0) cc_final: 0.8430 (t0) REVERT: J 508 GLU cc_start: 0.8290 (mp0) cc_final: 0.7811 (mp0) REVERT: K 72 ILE cc_start: 0.8293 (mm) cc_final: 0.7968 (pt) REVERT: K 77 ASP cc_start: 0.8433 (t0) cc_final: 0.8217 (t0) REVERT: K 87 GLU cc_start: 0.7322 (pt0) cc_final: 0.6384 (pt0) REVERT: K 221 MET cc_start: 0.3752 (tpt) cc_final: 0.3296 (mtp) REVERT: K 236 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8203 (p) REVERT: K 268 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7580 (mt-10) REVERT: K 296 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7029 (tmtt) REVERT: K 302 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6718 (tt0) REVERT: K 320 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7738 (ptmt) REVERT: K 330 MET cc_start: 0.8428 (ttp) cc_final: 0.8124 (ttm) REVERT: K 408 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7861 (tpt90) REVERT: K 438 ASN cc_start: 0.7948 (m-40) cc_final: 0.7734 (m-40) REVERT: L 72 ILE cc_start: 0.8344 (mm) cc_final: 0.7965 (pt) REVERT: L 87 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6953 (pt0) REVERT: L 126 MET cc_start: 0.7730 (mmm) cc_final: 0.7339 (mmm) REVERT: L 171 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6285 (tt) REVERT: L 221 MET cc_start: 0.3966 (tpt) cc_final: 0.3688 (mtm) REVERT: L 268 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7558 (mt-10) REVERT: L 296 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7041 (tmtt) REVERT: L 302 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6535 (tt0) REVERT: L 320 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7610 (ptmt) REVERT: L 361 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7512 (t0) REVERT: L 397 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8308 (p) REVERT: L 408 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7702 (tpm170) REVERT: L 438 ASN cc_start: 0.8077 (m-40) cc_final: 0.7841 (m-40) REVERT: L 508 GLU cc_start: 0.8131 (mp0) cc_final: 0.7671 (mp0) outliers start: 169 outliers final: 95 residues processed: 845 average time/residue: 0.5225 time to fit residues: 716.8916 Evaluate side-chains 765 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 638 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 303 HIS Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 469 MET Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 3.9990 chunk 438 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 286 optimal weight: 0.0670 chunk 120 optimal weight: 0.7980 chunk 487 optimal weight: 0.8980 chunk 404 optimal weight: 6.9990 chunk 225 optimal weight: 20.0000 chunk 40 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 256 optimal weight: 8.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN A 382 GLN ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 367 GLN D 382 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 367 GLN G 382 GLN J 367 GLN J 382 GLN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 42048 Z= 0.153 Angle : 0.591 9.353 56760 Z= 0.313 Chirality : 0.041 0.133 6228 Planarity : 0.003 0.032 7404 Dihedral : 5.195 57.022 5676 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.17 % Favored : 94.36 % Rotamer: Outliers : 3.78 % Allowed : 20.26 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.11), residues: 5088 helix: -0.31 (0.11), residues: 2304 sheet: -0.95 (0.26), residues: 384 loop : -1.80 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 285 HIS 0.003 0.001 HIS D 136 PHE 0.011 0.001 PHE I 365 TYR 0.005 0.001 TYR I 314 ARG 0.003 0.000 ARG E 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 700 time to evaluate : 4.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8362 (mm) cc_final: 0.8002 (pt) REVERT: A 77 ASP cc_start: 0.8461 (t0) cc_final: 0.8159 (t0) REVERT: A 83 MET cc_start: 0.8050 (tpp) cc_final: 0.7782 (mmm) REVERT: A 87 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6769 (pt0) REVERT: A 221 MET cc_start: 0.3530 (tpt) cc_final: 0.3082 (mtp) REVERT: A 268 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7430 (mt-10) REVERT: A 296 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7484 (pttt) REVERT: A 302 GLN cc_start: 0.7098 (mm-40) cc_final: 0.6727 (tt0) REVERT: A 320 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7910 (ptmt) REVERT: A 330 MET cc_start: 0.8321 (ttp) cc_final: 0.8045 (ttp) REVERT: A 416 GLU cc_start: 0.8856 (tt0) cc_final: 0.8605 (tt0) REVERT: A 426 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 438 ASN cc_start: 0.8046 (m-40) cc_final: 0.7683 (m-40) REVERT: A 504 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 508 GLU cc_start: 0.8202 (mp0) cc_final: 0.7682 (mp0) REVERT: B 72 ILE cc_start: 0.8309 (mm) cc_final: 0.7984 (pt) REVERT: B 77 ASP cc_start: 0.8432 (t0) cc_final: 0.8213 (t0) REVERT: B 87 GLU cc_start: 0.7128 (pt0) cc_final: 0.6286 (pt0) REVERT: B 221 MET cc_start: 0.3495 (tpt) cc_final: 0.3028 (mtp) REVERT: B 236 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 268 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7653 (mt-10) REVERT: B 296 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7000 (tmtt) REVERT: B 302 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6699 (tt0) REVERT: B 320 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7728 (ptmt) REVERT: B 330 MET cc_start: 0.8432 (ttp) cc_final: 0.8124 (ttm) REVERT: B 438 ASN cc_start: 0.7955 (m-40) cc_final: 0.7698 (m-40) REVERT: B 469 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7344 (tpp) REVERT: C 72 ILE cc_start: 0.8345 (mm) cc_final: 0.7937 (pt) REVERT: C 87 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6719 (pt0) REVERT: C 171 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6287 (tt) REVERT: C 221 MET cc_start: 0.3850 (tpt) cc_final: 0.3451 (mtp) REVERT: C 284 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8408 (m) REVERT: C 296 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7061 (tmtt) REVERT: C 302 GLN cc_start: 0.7024 (mm-40) cc_final: 0.6610 (tt0) REVERT: C 320 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7549 (ptmt) REVERT: C 361 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7308 (t70) REVERT: C 397 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8177 (p) REVERT: C 508 GLU cc_start: 0.8154 (mp0) cc_final: 0.7725 (mp0) REVERT: D 72 ILE cc_start: 0.8375 (mm) cc_final: 0.8019 (pt) REVERT: D 83 MET cc_start: 0.8065 (tpp) cc_final: 0.7775 (mmm) REVERT: D 87 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6765 (pt0) REVERT: D 221 MET cc_start: 0.3501 (tpt) cc_final: 0.3075 (mtp) REVERT: D 268 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7441 (mt-10) REVERT: D 296 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7475 (pttt) REVERT: D 302 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6681 (tt0) REVERT: D 320 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7905 (ptmt) REVERT: D 426 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7578 (tt) REVERT: D 434 GLU cc_start: 0.7719 (tm-30) cc_final: 0.6903 (tm-30) REVERT: D 438 ASN cc_start: 0.8039 (m-40) cc_final: 0.7043 (m-40) REVERT: D 468 ASN cc_start: 0.8714 (t0) cc_final: 0.8421 (t0) REVERT: D 487 MET cc_start: 0.8441 (ttp) cc_final: 0.8190 (ttm) REVERT: D 504 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7878 (tm-30) REVERT: D 508 GLU cc_start: 0.8212 (mp0) cc_final: 0.7681 (mp0) REVERT: E 72 ILE cc_start: 0.8311 (mm) cc_final: 0.7984 (pt) REVERT: E 77 ASP cc_start: 0.8432 (t0) cc_final: 0.8205 (t0) REVERT: E 87 GLU cc_start: 0.7129 (pt0) cc_final: 0.6319 (pt0) REVERT: E 221 MET cc_start: 0.3493 (tpt) cc_final: 0.3036 (mtp) REVERT: E 236 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8260 (p) REVERT: E 268 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7643 (mt-10) REVERT: E 296 LYS cc_start: 0.7950 (ttmm) cc_final: 0.6999 (tmtt) REVERT: E 302 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6696 (tt0) REVERT: E 320 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7729 (ptmt) REVERT: E 330 MET cc_start: 0.8435 (ttp) cc_final: 0.8126 (ttm) REVERT: E 438 ASN cc_start: 0.7953 (m-40) cc_final: 0.7698 (m-40) REVERT: E 469 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7341 (tpp) REVERT: F 72 ILE cc_start: 0.8347 (mm) cc_final: 0.7942 (pt) REVERT: F 87 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6671 (pt0) REVERT: F 171 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6282 (tt) REVERT: F 221 MET cc_start: 0.3845 (tpt) cc_final: 0.3448 (mtp) REVERT: F 284 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8403 (m) REVERT: F 296 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7057 (tmtt) REVERT: F 302 GLN cc_start: 0.7025 (mm-40) cc_final: 0.6614 (tt0) REVERT: F 320 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7546 (ptmt) REVERT: F 361 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7310 (t70) REVERT: F 397 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8177 (p) REVERT: F 508 GLU cc_start: 0.8153 (mp0) cc_final: 0.7729 (mp0) REVERT: G 72 ILE cc_start: 0.8377 (mm) cc_final: 0.8031 (pt) REVERT: G 83 MET cc_start: 0.8071 (tpp) cc_final: 0.7798 (mmm) REVERT: G 87 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6762 (pt0) REVERT: G 221 MET cc_start: 0.3512 (tpt) cc_final: 0.3086 (mtp) REVERT: G 268 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7434 (mt-10) REVERT: G 296 LYS cc_start: 0.7943 (ttmm) cc_final: 0.7477 (pttt) REVERT: G 302 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6682 (tt0) REVERT: G 320 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7906 (ptmt) REVERT: G 426 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7576 (tt) REVERT: G 438 ASN cc_start: 0.8033 (m-40) cc_final: 0.7662 (m-40) REVERT: G 468 ASN cc_start: 0.8706 (t0) cc_final: 0.8422 (t0) REVERT: G 504 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7913 (tm-30) REVERT: G 508 GLU cc_start: 0.8197 (mp0) cc_final: 0.7678 (mp0) REVERT: H 72 ILE cc_start: 0.8310 (mm) cc_final: 0.7983 (pt) REVERT: H 77 ASP cc_start: 0.8435 (t0) cc_final: 0.8209 (t0) REVERT: H 87 GLU cc_start: 0.7137 (pt0) cc_final: 0.6324 (pt0) REVERT: H 221 MET cc_start: 0.3492 (tpt) cc_final: 0.3039 (mtp) REVERT: H 236 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8263 (p) REVERT: H 268 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7642 (mt-10) REVERT: H 296 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7005 (tmtt) REVERT: H 302 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6695 (tt0) REVERT: H 320 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7732 (ptmt) REVERT: H 330 MET cc_start: 0.8433 (ttp) cc_final: 0.8123 (ttm) REVERT: H 438 ASN cc_start: 0.7957 (m-40) cc_final: 0.7702 (m-40) REVERT: H 469 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7340 (tpp) REVERT: I 72 ILE cc_start: 0.8345 (mm) cc_final: 0.7944 (pt) REVERT: I 87 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6670 (pt0) REVERT: I 171 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6279 (tt) REVERT: I 221 MET cc_start: 0.3852 (tpt) cc_final: 0.3451 (mtp) REVERT: I 284 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8409 (m) REVERT: I 296 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7059 (tmtt) REVERT: I 302 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6610 (tt0) REVERT: I 320 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7557 (ptmt) REVERT: I 361 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7314 (t70) REVERT: I 397 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8175 (p) REVERT: I 508 GLU cc_start: 0.8156 (mp0) cc_final: 0.7727 (mp0) REVERT: J 72 ILE cc_start: 0.8377 (mm) cc_final: 0.8033 (pt) REVERT: J 83 MET cc_start: 0.8070 (tpp) cc_final: 0.7798 (mmm) REVERT: J 87 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6765 (pt0) REVERT: J 221 MET cc_start: 0.3518 (tpt) cc_final: 0.3095 (mtp) REVERT: J 268 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7436 (mt-10) REVERT: J 296 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7479 (pttt) REVERT: J 302 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6682 (tt0) REVERT: J 320 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7907 (ptmt) REVERT: J 426 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7581 (tt) REVERT: J 438 ASN cc_start: 0.8035 (m-40) cc_final: 0.7663 (m-40) REVERT: J 468 ASN cc_start: 0.8708 (t0) cc_final: 0.8421 (t0) REVERT: J 504 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7915 (tm-30) REVERT: J 508 GLU cc_start: 0.8200 (mp0) cc_final: 0.7681 (mp0) REVERT: K 72 ILE cc_start: 0.8310 (mm) cc_final: 0.7986 (pt) REVERT: K 77 ASP cc_start: 0.8437 (t0) cc_final: 0.8215 (t0) REVERT: K 87 GLU cc_start: 0.7132 (pt0) cc_final: 0.6286 (pt0) REVERT: K 221 MET cc_start: 0.3492 (tpt) cc_final: 0.3040 (mtp) REVERT: K 236 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8264 (p) REVERT: K 268 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7656 (mt-10) REVERT: K 296 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7005 (tmtt) REVERT: K 302 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6697 (tt0) REVERT: K 320 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7725 (ptmt) REVERT: K 330 MET cc_start: 0.8432 (ttp) cc_final: 0.8122 (ttm) REVERT: K 438 ASN cc_start: 0.7952 (m-40) cc_final: 0.7703 (m-40) REVERT: K 469 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7346 (tpp) REVERT: L 72 ILE cc_start: 0.8336 (mm) cc_final: 0.7933 (pt) REVERT: L 87 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6709 (pt0) REVERT: L 126 MET cc_start: 0.7769 (mmm) cc_final: 0.7566 (mmm) REVERT: L 171 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6288 (tt) REVERT: L 221 MET cc_start: 0.3844 (tpt) cc_final: 0.3448 (mtp) REVERT: L 296 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7066 (tmtt) REVERT: L 302 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6543 (tt0) REVERT: L 320 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7528 (ptmt) REVERT: L 361 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7319 (t70) REVERT: L 397 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8175 (p) REVERT: L 438 ASN cc_start: 0.8014 (m-40) cc_final: 0.7794 (m-40) REVERT: L 508 GLU cc_start: 0.8154 (mp0) cc_final: 0.7722 (mp0) outliers start: 165 outliers final: 84 residues processed: 826 average time/residue: 0.5340 time to fit residues: 714.0825 Evaluate side-chains 785 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 666 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 TYR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain H residue 359 MET Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 469 MET Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 303 HIS Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 165 LYS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 328 MET Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 469 MET Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 237 TYR Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 303 HIS Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 469 MET Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 4.9990 chunk 54 optimal weight: 0.0020 chunk 277 optimal weight: 2.9990 chunk 356 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 410 optimal weight: 5.9990 chunk 272 optimal weight: 0.0030 chunk 485 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN C 382 GLN D 85 ASN ** D 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN F 85 ASN F 382 GLN ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN I 85 ASN I 382 GLN J 90 ASN ** J 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 382 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 42048 Z= 0.177 Angle : 0.612 9.004 56760 Z= 0.322 Chirality : 0.042 0.137 6228 Planarity : 0.003 0.030 7404 Dihedral : 4.859 50.362 5655 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.44 % Favored : 94.08 % Rotamer: Outliers : 4.56 % Allowed : 19.41 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.11), residues: 5088 helix: -0.09 (0.11), residues: 2304 sheet: -0.85 (0.26), residues: 384 loop : -1.74 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 285 HIS 0.003 0.001 HIS A 136 PHE 0.010 0.001 PHE J 365 TYR 0.008 0.001 TYR D 86 ARG 0.006 0.000 ARG L 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 700 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8355 (mm) cc_final: 0.8016 (pt) REVERT: A 77 ASP cc_start: 0.8516 (t0) cc_final: 0.8201 (t0) REVERT: A 221 MET cc_start: 0.3289 (tpt) cc_final: 0.3018 (mtp) REVERT: A 268 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7487 (mt-10) REVERT: A 296 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7250 (tmtt) REVERT: A 302 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6627 (tt0) REVERT: A 320 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7892 (ptmt) REVERT: A 330 MET cc_start: 0.8312 (ttp) cc_final: 0.8056 (ttp) REVERT: A 416 GLU cc_start: 0.8834 (tt0) cc_final: 0.8584 (tt0) REVERT: A 426 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7614 (tt) REVERT: A 438 ASN cc_start: 0.8051 (m-40) cc_final: 0.7689 (m-40) REVERT: A 504 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 72 ILE cc_start: 0.8327 (mm) cc_final: 0.7987 (pt) REVERT: B 77 ASP cc_start: 0.8448 (t0) cc_final: 0.8209 (t0) REVERT: B 221 MET cc_start: 0.3450 (tpt) cc_final: 0.3045 (mtp) REVERT: B 236 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 268 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7654 (mt-10) REVERT: B 296 LYS cc_start: 0.7871 (ttmm) cc_final: 0.6966 (tmtt) REVERT: B 302 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6563 (tt0) REVERT: B 320 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7657 (ptmt) REVERT: B 330 MET cc_start: 0.8408 (ttp) cc_final: 0.8122 (ttm) REVERT: B 346 GLU cc_start: 0.7900 (pm20) cc_final: 0.7407 (pm20) REVERT: B 438 ASN cc_start: 0.7943 (m-40) cc_final: 0.7680 (m-40) REVERT: B 469 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7380 (tpp) REVERT: C 72 ILE cc_start: 0.8360 (mm) cc_final: 0.7945 (pt) REVERT: C 87 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6720 (pt0) REVERT: C 221 MET cc_start: 0.3670 (tpt) cc_final: 0.3311 (mtp) REVERT: C 268 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7447 (mt-10) REVERT: C 296 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7230 (tmtt) REVERT: C 302 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6520 (tt0) REVERT: C 320 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7586 (ptmt) REVERT: C 397 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8198 (p) REVERT: C 426 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7670 (tt) REVERT: C 504 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7883 (tm-30) REVERT: D 72 ILE cc_start: 0.8385 (mm) cc_final: 0.8049 (pt) REVERT: D 77 ASP cc_start: 0.8465 (t0) cc_final: 0.8174 (t0) REVERT: D 172 LYS cc_start: 0.6172 (mmtm) cc_final: 0.5869 (mmtm) REVERT: D 221 MET cc_start: 0.3302 (tpt) cc_final: 0.3003 (mtp) REVERT: D 268 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7499 (mt-10) REVERT: D 296 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7237 (tmtt) REVERT: D 302 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6629 (tt0) REVERT: D 320 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7894 (ptmt) REVERT: D 438 ASN cc_start: 0.8005 (m-40) cc_final: 0.7606 (m-40) REVERT: D 468 ASN cc_start: 0.8727 (t0) cc_final: 0.8427 (t0) REVERT: D 487 MET cc_start: 0.8555 (ttp) cc_final: 0.8178 (ttm) REVERT: D 504 GLN cc_start: 0.8468 (tm-30) cc_final: 0.7870 (tm-30) REVERT: E 72 ILE cc_start: 0.8330 (mm) cc_final: 0.7988 (pt) REVERT: E 77 ASP cc_start: 0.8440 (t0) cc_final: 0.8218 (t0) REVERT: E 221 MET cc_start: 0.3459 (tpt) cc_final: 0.3046 (mtp) REVERT: E 236 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8324 (p) REVERT: E 268 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7631 (mt-10) REVERT: E 296 LYS cc_start: 0.7875 (ttmm) cc_final: 0.6971 (tmtt) REVERT: E 302 GLN cc_start: 0.7072 (mm-40) cc_final: 0.6567 (tt0) REVERT: E 320 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7661 (ptmt) REVERT: E 346 GLU cc_start: 0.7896 (pm20) cc_final: 0.7396 (pm20) REVERT: E 438 ASN cc_start: 0.7944 (m-40) cc_final: 0.7680 (m-40) REVERT: E 469 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7349 (tpp) REVERT: F 72 ILE cc_start: 0.8359 (mm) cc_final: 0.7952 (pt) REVERT: F 87 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6725 (pt0) REVERT: F 221 MET cc_start: 0.3654 (tpt) cc_final: 0.3315 (mtp) REVERT: F 268 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7446 (mt-10) REVERT: F 296 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7225 (tmtt) REVERT: F 302 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6516 (tt0) REVERT: F 320 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7612 (ptmt) REVERT: F 397 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8198 (p) REVERT: F 426 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7674 (tt) REVERT: F 504 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7885 (tm-30) REVERT: G 72 ILE cc_start: 0.8402 (mm) cc_final: 0.8053 (pt) REVERT: G 77 ASP cc_start: 0.8514 (t0) cc_final: 0.8214 (t0) REVERT: G 172 LYS cc_start: 0.6168 (mmtm) cc_final: 0.5859 (mmtm) REVERT: G 221 MET cc_start: 0.3303 (tpt) cc_final: 0.3005 (mtp) REVERT: G 268 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7483 (mt-10) REVERT: G 296 LYS cc_start: 0.7894 (ttmm) cc_final: 0.7240 (tmtt) REVERT: G 302 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6630 (tt0) REVERT: G 320 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7881 (ptmt) REVERT: G 438 ASN cc_start: 0.8004 (m-40) cc_final: 0.7602 (m-40) REVERT: G 468 ASN cc_start: 0.8718 (t0) cc_final: 0.8425 (t0) REVERT: G 504 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7842 (tm-30) REVERT: H 72 ILE cc_start: 0.8328 (mm) cc_final: 0.7983 (pt) REVERT: H 77 ASP cc_start: 0.8441 (t0) cc_final: 0.8206 (t0) REVERT: H 221 MET cc_start: 0.3453 (tpt) cc_final: 0.3046 (mtp) REVERT: H 236 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8322 (p) REVERT: H 268 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7634 (mt-10) REVERT: H 296 LYS cc_start: 0.7875 (ttmm) cc_final: 0.6975 (tmtt) REVERT: H 302 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6562 (tt0) REVERT: H 320 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7661 (ptmt) REVERT: H 330 MET cc_start: 0.8411 (ttp) cc_final: 0.8117 (ttm) REVERT: H 346 GLU cc_start: 0.7893 (pm20) cc_final: 0.7405 (pm20) REVERT: H 438 ASN cc_start: 0.7949 (m-40) cc_final: 0.7683 (m-40) REVERT: H 469 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7349 (tpp) REVERT: I 72 ILE cc_start: 0.8357 (mm) cc_final: 0.7953 (pt) REVERT: I 87 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6716 (pt0) REVERT: I 221 MET cc_start: 0.3661 (tpt) cc_final: 0.3322 (mtp) REVERT: I 268 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7449 (mt-10) REVERT: I 296 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7231 (tmtt) REVERT: I 302 GLN cc_start: 0.7047 (mm-40) cc_final: 0.6509 (tt0) REVERT: I 320 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7584 (ptmt) REVERT: I 397 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8195 (p) REVERT: I 426 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7671 (tt) REVERT: I 504 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7886 (tm-30) REVERT: J 72 ILE cc_start: 0.8402 (mm) cc_final: 0.8052 (pt) REVERT: J 77 ASP cc_start: 0.8517 (t0) cc_final: 0.8216 (t0) REVERT: J 172 LYS cc_start: 0.6178 (mmtm) cc_final: 0.5868 (mmtm) REVERT: J 221 MET cc_start: 0.3317 (tpt) cc_final: 0.3014 (mtp) REVERT: J 268 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7485 (mt-10) REVERT: J 296 LYS cc_start: 0.7894 (ttmm) cc_final: 0.7233 (tmtt) REVERT: J 302 GLN cc_start: 0.7047 (mm-40) cc_final: 0.6628 (tt0) REVERT: J 320 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7885 (ptmt) REVERT: J 438 ASN cc_start: 0.8000 (m-40) cc_final: 0.7600 (m-40) REVERT: J 468 ASN cc_start: 0.8720 (t0) cc_final: 0.8425 (t0) REVERT: J 504 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7839 (tm-30) REVERT: K 72 ILE cc_start: 0.8333 (mm) cc_final: 0.7989 (pt) REVERT: K 77 ASP cc_start: 0.8449 (t0) cc_final: 0.8213 (t0) REVERT: K 221 MET cc_start: 0.3464 (tpt) cc_final: 0.3049 (mtp) REVERT: K 236 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8323 (p) REVERT: K 268 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7636 (mt-10) REVERT: K 296 LYS cc_start: 0.7878 (ttmm) cc_final: 0.6973 (tmtt) REVERT: K 302 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6567 (tt0) REVERT: K 320 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7650 (ptmt) REVERT: K 330 MET cc_start: 0.8409 (ttp) cc_final: 0.8117 (ttm) REVERT: K 346 GLU cc_start: 0.7910 (pm20) cc_final: 0.7402 (pm20) REVERT: K 438 ASN cc_start: 0.7950 (m-40) cc_final: 0.7680 (m-40) REVERT: K 469 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7347 (tpp) REVERT: L 72 ILE cc_start: 0.8346 (mm) cc_final: 0.7937 (pt) REVERT: L 87 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6760 (pt0) REVERT: L 221 MET cc_start: 0.3653 (tpt) cc_final: 0.3319 (mtp) REVERT: L 268 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7460 (mt-10) REVERT: L 296 LYS cc_start: 0.7823 (ttmm) cc_final: 0.7220 (tmtt) REVERT: L 302 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6484 (tt0) REVERT: L 320 LYS cc_start: 0.7815 (mtmt) cc_final: 0.7553 (ptmt) REVERT: L 397 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8196 (p) REVERT: L 408 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7695 (tpm170) REVERT: L 426 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7660 (tt) REVERT: L 438 ASN cc_start: 0.7971 (m-40) cc_final: 0.7760 (m-40) REVERT: L 504 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7882 (tm-30) outliers start: 199 outliers final: 131 residues processed: 847 average time/residue: 0.5447 time to fit residues: 744.4679 Evaluate side-chains 830 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 678 time to evaluate : 5.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 237 TYR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain H residue 359 MET Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 469 MET Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 237 TYR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 165 LYS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 283 ARG Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 328 MET Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 469 MET Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 237 TYR Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 330 MET Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 415 GLU Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 330 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 381 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN F 85 ASN H 500 GLN I 85 ASN L 310 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 42048 Z= 0.254 Angle : 0.650 9.948 56760 Z= 0.343 Chirality : 0.043 0.139 6228 Planarity : 0.004 0.046 7404 Dihedral : 5.057 48.384 5655 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.05 % Favored : 93.40 % Rotamer: Outliers : 4.35 % Allowed : 19.80 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 5088 helix: -0.07 (0.11), residues: 2280 sheet: -0.95 (0.26), residues: 384 loop : -1.79 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 437 HIS 0.003 0.001 HIS E 136 PHE 0.012 0.001 PHE G 157 TYR 0.013 0.001 TYR F 86 ARG 0.012 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 662 time to evaluate : 5.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8422 (mm) cc_final: 0.8073 (pt) REVERT: A 77 ASP cc_start: 0.8551 (t0) cc_final: 0.8218 (t0) REVERT: A 221 MET cc_start: 0.3493 (tpt) cc_final: 0.2997 (mtp) REVERT: A 268 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7488 (mt-10) REVERT: A 296 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7123 (tmtt) REVERT: A 302 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6641 (tt0) REVERT: A 320 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7918 (ptmt) REVERT: A 330 MET cc_start: 0.8285 (ttp) cc_final: 0.8019 (ttp) REVERT: A 416 GLU cc_start: 0.8768 (tt0) cc_final: 0.8520 (tt0) REVERT: A 426 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7699 (tt) REVERT: A 438 ASN cc_start: 0.8043 (m-40) cc_final: 0.7662 (m-40) REVERT: A 508 GLU cc_start: 0.8272 (mp0) cc_final: 0.7858 (mp0) REVERT: B 72 ILE cc_start: 0.8335 (mm) cc_final: 0.7986 (pt) REVERT: B 221 MET cc_start: 0.3467 (tpt) cc_final: 0.3048 (mtp) REVERT: B 268 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7666 (mt-10) REVERT: B 296 LYS cc_start: 0.7891 (ttmm) cc_final: 0.6962 (tmtt) REVERT: B 320 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7622 (ptmt) REVERT: B 346 GLU cc_start: 0.7963 (pm20) cc_final: 0.7498 (pm20) REVERT: B 438 ASN cc_start: 0.7948 (m-40) cc_final: 0.7681 (m-40) REVERT: B 469 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7364 (tpp) REVERT: C 72 ILE cc_start: 0.8291 (mm) cc_final: 0.7898 (pt) REVERT: C 83 MET cc_start: 0.8250 (tpp) cc_final: 0.8022 (tpp) REVERT: C 87 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6935 (pt0) REVERT: C 268 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7589 (mt-10) REVERT: C 296 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7171 (tmtt) REVERT: C 302 GLN cc_start: 0.7088 (mm-40) cc_final: 0.6613 (tt0) REVERT: C 320 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7656 (ptmt) REVERT: C 397 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8338 (p) REVERT: C 408 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7671 (tpm170) REVERT: C 426 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7730 (tt) REVERT: C 508 GLU cc_start: 0.8186 (mp0) cc_final: 0.7646 (mp0) REVERT: D 72 ILE cc_start: 0.8435 (mm) cc_final: 0.8098 (pt) REVERT: D 77 ASP cc_start: 0.8575 (t0) cc_final: 0.8236 (t0) REVERT: D 172 LYS cc_start: 0.6409 (mmtm) cc_final: 0.6151 (mmtm) REVERT: D 221 MET cc_start: 0.3469 (tpt) cc_final: 0.2984 (mtp) REVERT: D 268 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7498 (mt-10) REVERT: D 289 THR cc_start: 0.6534 (OUTLIER) cc_final: 0.6254 (p) REVERT: D 296 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7172 (tmtt) REVERT: D 302 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6765 (tt0) REVERT: D 320 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7910 (ptmt) REVERT: D 438 ASN cc_start: 0.8046 (m-40) cc_final: 0.7664 (m-40) REVERT: D 468 ASN cc_start: 0.8728 (t0) cc_final: 0.8425 (t0) REVERT: D 487 MET cc_start: 0.8726 (ttp) cc_final: 0.8512 (ttm) REVERT: D 508 GLU cc_start: 0.8276 (mp0) cc_final: 0.7844 (mp0) REVERT: E 72 ILE cc_start: 0.8339 (mm) cc_final: 0.7993 (pt) REVERT: E 221 MET cc_start: 0.3401 (tpt) cc_final: 0.2941 (mtp) REVERT: E 268 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7759 (mt-10) REVERT: E 296 LYS cc_start: 0.7899 (ttmm) cc_final: 0.6965 (tmtt) REVERT: E 320 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7623 (ptmt) REVERT: E 346 GLU cc_start: 0.7967 (pm20) cc_final: 0.7500 (pm20) REVERT: E 438 ASN cc_start: 0.7950 (m-40) cc_final: 0.7681 (m-40) REVERT: E 469 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7351 (tpp) REVERT: F 72 ILE cc_start: 0.8291 (mm) cc_final: 0.7897 (pt) REVERT: F 268 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7595 (mt-10) REVERT: F 296 LYS cc_start: 0.7796 (ttmm) cc_final: 0.7161 (tmtt) REVERT: F 302 GLN cc_start: 0.7088 (mm-40) cc_final: 0.6614 (tt0) REVERT: F 320 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7666 (ptmt) REVERT: F 397 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8333 (p) REVERT: F 408 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7671 (tpm170) REVERT: F 426 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7734 (tt) REVERT: F 508 GLU cc_start: 0.8189 (mp0) cc_final: 0.7650 (mp0) REVERT: G 72 ILE cc_start: 0.8443 (mm) cc_final: 0.8105 (pt) REVERT: G 77 ASP cc_start: 0.8580 (t0) cc_final: 0.8252 (t0) REVERT: G 172 LYS cc_start: 0.6413 (mmtm) cc_final: 0.6150 (mmtm) REVERT: G 221 MET cc_start: 0.3478 (tpt) cc_final: 0.2991 (mtp) REVERT: G 268 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7468 (mt-10) REVERT: G 289 THR cc_start: 0.6531 (OUTLIER) cc_final: 0.6263 (p) REVERT: G 296 LYS cc_start: 0.7857 (ttmm) cc_final: 0.7176 (tmtt) REVERT: G 302 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6763 (tt0) REVERT: G 320 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7914 (ptmt) REVERT: G 438 ASN cc_start: 0.8045 (m-40) cc_final: 0.7660 (m-40) REVERT: G 468 ASN cc_start: 0.8718 (t0) cc_final: 0.8422 (t0) REVERT: G 508 GLU cc_start: 0.8266 (mp0) cc_final: 0.7856 (mp0) REVERT: H 72 ILE cc_start: 0.8336 (mm) cc_final: 0.7992 (pt) REVERT: H 221 MET cc_start: 0.3473 (tpt) cc_final: 0.3062 (mtp) REVERT: H 268 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7748 (mt-10) REVERT: H 296 LYS cc_start: 0.7902 (ttmm) cc_final: 0.6965 (tmtt) REVERT: H 320 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7656 (ptmt) REVERT: H 346 GLU cc_start: 0.7960 (pm20) cc_final: 0.7494 (pm20) REVERT: H 438 ASN cc_start: 0.7951 (m-40) cc_final: 0.7686 (m-40) REVERT: H 469 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7354 (tpp) REVERT: I 72 ILE cc_start: 0.8297 (mm) cc_final: 0.7903 (pt) REVERT: I 268 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7602 (mt-10) REVERT: I 296 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7167 (tmtt) REVERT: I 302 GLN cc_start: 0.7083 (mm-40) cc_final: 0.6617 (tt0) REVERT: I 320 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7662 (ptmt) REVERT: I 361 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7268 (t70) REVERT: I 397 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8330 (p) REVERT: I 408 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7673 (tpm170) REVERT: I 426 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7734 (tt) REVERT: I 508 GLU cc_start: 0.8198 (mp0) cc_final: 0.7653 (mp0) REVERT: J 72 ILE cc_start: 0.8443 (mm) cc_final: 0.8104 (pt) REVERT: J 77 ASP cc_start: 0.8576 (t0) cc_final: 0.8254 (t0) REVERT: J 172 LYS cc_start: 0.6414 (mmtm) cc_final: 0.6147 (mmtm) REVERT: J 221 MET cc_start: 0.3489 (tpt) cc_final: 0.3003 (mtp) REVERT: J 268 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7469 (mt-10) REVERT: J 289 THR cc_start: 0.6505 (OUTLIER) cc_final: 0.6236 (p) REVERT: J 296 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7173 (tmtt) REVERT: J 302 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6819 (tt0) REVERT: J 320 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7920 (ptmt) REVERT: J 438 ASN cc_start: 0.8045 (m-40) cc_final: 0.7654 (m-40) REVERT: J 468 ASN cc_start: 0.8722 (t0) cc_final: 0.8425 (t0) REVERT: J 508 GLU cc_start: 0.8270 (mp0) cc_final: 0.7859 (mp0) REVERT: K 72 ILE cc_start: 0.8336 (mm) cc_final: 0.7993 (pt) REVERT: K 221 MET cc_start: 0.3466 (tpt) cc_final: 0.3058 (mtp) REVERT: K 268 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7744 (mt-10) REVERT: K 296 LYS cc_start: 0.7897 (ttmm) cc_final: 0.6967 (tmtt) REVERT: K 320 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7651 (ptmt) REVERT: K 346 GLU cc_start: 0.7978 (pm20) cc_final: 0.7503 (pm20) REVERT: K 438 ASN cc_start: 0.7945 (m-40) cc_final: 0.7681 (m-40) REVERT: K 469 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7358 (tpp) REVERT: L 72 ILE cc_start: 0.8281 (mm) cc_final: 0.7889 (pt) REVERT: L 83 MET cc_start: 0.8256 (tpp) cc_final: 0.8029 (tpp) REVERT: L 87 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6968 (pt0) REVERT: L 268 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7575 (mt-10) REVERT: L 296 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7183 (tmtt) REVERT: L 302 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6574 (tt0) REVERT: L 320 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7634 (ptmt) REVERT: L 397 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8336 (p) REVERT: L 408 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7671 (tpm170) REVERT: L 426 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7683 (tt) REVERT: L 438 ASN cc_start: 0.8035 (m-40) cc_final: 0.7768 (m-40) REVERT: L 508 GLU cc_start: 0.8189 (mp0) cc_final: 0.7647 (mp0) outliers start: 190 outliers final: 135 residues processed: 798 average time/residue: 0.5542 time to fit residues: 706.8776 Evaluate side-chains 809 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 655 time to evaluate : 5.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 TYR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 472 MET Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 469 MET Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 472 MET Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 165 LYS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 328 MET Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 469 MET Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 237 TYR Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 310 ASN Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 415 GLU Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 4.9990 chunk 465 optimal weight: 8.9990 chunk 424 optimal weight: 1.9990 chunk 452 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 409 optimal weight: 0.9990 chunk 428 optimal weight: 2.9990 chunk 451 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN E 302 GLN F 310 ASN H 302 GLN I 310 ASN K 302 GLN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 310 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 42048 Z= 0.208 Angle : 0.631 9.970 56760 Z= 0.333 Chirality : 0.042 0.135 6228 Planarity : 0.004 0.058 7404 Dihedral : 4.872 47.466 5647 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.50 % Favored : 93.87 % Rotamer: Outliers : 4.10 % Allowed : 19.71 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 5088 helix: 0.02 (0.11), residues: 2280 sheet: -0.88 (0.26), residues: 384 loop : -1.76 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 285 HIS 0.003 0.001 HIS K 136 PHE 0.010 0.001 PHE G 157 TYR 0.008 0.001 TYR L 314 ARG 0.013 0.001 ARG F 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 650 time to evaluate : 5.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8370 (mm) cc_final: 0.8048 (pt) REVERT: A 77 ASP cc_start: 0.8577 (t0) cc_final: 0.8270 (t0) REVERT: A 126 MET cc_start: 0.7709 (mmt) cc_final: 0.7489 (mmm) REVERT: A 221 MET cc_start: 0.3355 (tpt) cc_final: 0.3020 (mtp) REVERT: A 268 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7528 (mt-10) REVERT: A 296 LYS cc_start: 0.7809 (ttmm) cc_final: 0.7087 (tmtt) REVERT: A 302 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6778 (tt0) REVERT: A 320 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7741 (ptmt) REVERT: A 416 GLU cc_start: 0.8783 (tt0) cc_final: 0.8529 (tt0) REVERT: A 426 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7660 (tt) REVERT: A 438 ASN cc_start: 0.8028 (m-40) cc_final: 0.7658 (m-40) REVERT: A 464 GLU cc_start: 0.7473 (tt0) cc_final: 0.7174 (tt0) REVERT: A 508 GLU cc_start: 0.8234 (mp0) cc_final: 0.7903 (mp0) REVERT: B 72 ILE cc_start: 0.8318 (mm) cc_final: 0.7983 (pt) REVERT: B 221 MET cc_start: 0.3331 (tpt) cc_final: 0.2931 (mtp) REVERT: B 268 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7614 (mt-10) REVERT: B 296 LYS cc_start: 0.7885 (ttmm) cc_final: 0.6968 (tmtt) REVERT: B 320 LYS cc_start: 0.7869 (mtmt) cc_final: 0.7563 (ptmt) REVERT: B 346 GLU cc_start: 0.7947 (pm20) cc_final: 0.7432 (pm20) REVERT: B 438 ASN cc_start: 0.7948 (m-40) cc_final: 0.7694 (m-40) REVERT: B 469 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7353 (tpp) REVERT: B 508 GLU cc_start: 0.7965 (mp0) cc_final: 0.7515 (mp0) REVERT: C 72 ILE cc_start: 0.8285 (mm) cc_final: 0.7890 (pt) REVERT: C 83 MET cc_start: 0.8237 (tpp) cc_final: 0.8032 (tpp) REVERT: C 87 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: C 268 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7561 (mt-10) REVERT: C 296 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7042 (tmtt) REVERT: C 302 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6672 (tt0) REVERT: C 320 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7647 (ptmt) REVERT: C 397 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8279 (p) REVERT: C 408 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7663 (tpm170) REVERT: C 426 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7777 (tt) REVERT: C 508 GLU cc_start: 0.8198 (mp0) cc_final: 0.7725 (mp0) REVERT: D 72 ILE cc_start: 0.8377 (mm) cc_final: 0.7974 (pt) REVERT: D 77 ASP cc_start: 0.8552 (t0) cc_final: 0.8269 (t0) REVERT: D 221 MET cc_start: 0.3372 (tpt) cc_final: 0.2984 (mtp) REVERT: D 268 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7554 (mt-10) REVERT: D 289 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6401 (p) REVERT: D 296 LYS cc_start: 0.7831 (ttmm) cc_final: 0.7132 (tmtt) REVERT: D 302 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6818 (tt0) REVERT: D 320 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7793 (ptmt) REVERT: D 438 ASN cc_start: 0.8031 (m-40) cc_final: 0.7658 (m-40) REVERT: D 464 GLU cc_start: 0.7473 (tt0) cc_final: 0.7169 (tt0) REVERT: D 468 ASN cc_start: 0.8715 (t0) cc_final: 0.8450 (t0) REVERT: D 508 GLU cc_start: 0.8235 (mp0) cc_final: 0.7898 (mp0) REVERT: E 72 ILE cc_start: 0.8324 (mm) cc_final: 0.7980 (pt) REVERT: E 221 MET cc_start: 0.3351 (tpt) cc_final: 0.2941 (mtp) REVERT: E 268 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7597 (mt-10) REVERT: E 296 LYS cc_start: 0.7890 (ttmm) cc_final: 0.6970 (tmtt) REVERT: E 320 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7567 (ptmt) REVERT: E 346 GLU cc_start: 0.7943 (pm20) cc_final: 0.7427 (pm20) REVERT: E 438 ASN cc_start: 0.7945 (m-40) cc_final: 0.7688 (m-40) REVERT: E 469 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7407 (tpp) REVERT: E 508 GLU cc_start: 0.8078 (mp0) cc_final: 0.7861 (mt-10) REVERT: F 72 ILE cc_start: 0.8280 (mm) cc_final: 0.7887 (pt) REVERT: F 87 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6628 (pt0) REVERT: F 268 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7581 (mt-10) REVERT: F 296 LYS cc_start: 0.7809 (ttmm) cc_final: 0.7038 (tmtt) REVERT: F 302 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6674 (tt0) REVERT: F 320 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7653 (ptmt) REVERT: F 397 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8277 (p) REVERT: F 408 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7664 (tpm170) REVERT: F 426 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7777 (tt) REVERT: F 508 GLU cc_start: 0.8201 (mp0) cc_final: 0.7736 (mp0) REVERT: G 72 ILE cc_start: 0.8383 (mm) cc_final: 0.7987 (pt) REVERT: G 77 ASP cc_start: 0.8544 (t0) cc_final: 0.8271 (t0) REVERT: G 221 MET cc_start: 0.3377 (tpt) cc_final: 0.2993 (mtp) REVERT: G 268 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7526 (mt-10) REVERT: G 289 THR cc_start: 0.6682 (OUTLIER) cc_final: 0.6439 (p) REVERT: G 296 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7135 (tmtt) REVERT: G 302 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6784 (tt0) REVERT: G 320 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7792 (ptmt) REVERT: G 438 ASN cc_start: 0.8032 (m-40) cc_final: 0.7661 (m-40) REVERT: G 464 GLU cc_start: 0.7477 (tt0) cc_final: 0.7171 (tt0) REVERT: G 468 ASN cc_start: 0.8705 (t0) cc_final: 0.8446 (t0) REVERT: G 508 GLU cc_start: 0.8229 (mp0) cc_final: 0.7902 (mp0) REVERT: H 72 ILE cc_start: 0.8320 (mm) cc_final: 0.7981 (pt) REVERT: H 221 MET cc_start: 0.3339 (tpt) cc_final: 0.2941 (mtp) REVERT: H 268 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7595 (mt-10) REVERT: H 296 LYS cc_start: 0.7893 (ttmm) cc_final: 0.6974 (tmtt) REVERT: H 320 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7582 (ptmt) REVERT: H 346 GLU cc_start: 0.7940 (pm20) cc_final: 0.7427 (pm20) REVERT: H 438 ASN cc_start: 0.7948 (m-40) cc_final: 0.7690 (m-40) REVERT: H 469 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7356 (tpp) REVERT: H 508 GLU cc_start: 0.7980 (mp0) cc_final: 0.7517 (mp0) REVERT: I 72 ILE cc_start: 0.8281 (mm) cc_final: 0.7888 (pt) REVERT: I 87 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6623 (pt0) REVERT: I 268 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7572 (mt-10) REVERT: I 296 LYS cc_start: 0.7815 (ttmm) cc_final: 0.7040 (tmtt) REVERT: I 302 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6675 (tt0) REVERT: I 320 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7649 (ptmt) REVERT: I 397 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8276 (p) REVERT: I 408 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7665 (tpm170) REVERT: I 426 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7777 (tt) REVERT: I 508 GLU cc_start: 0.8209 (mp0) cc_final: 0.7738 (mp0) REVERT: J 72 ILE cc_start: 0.8389 (mm) cc_final: 0.7992 (pt) REVERT: J 77 ASP cc_start: 0.8544 (t0) cc_final: 0.8273 (t0) REVERT: J 221 MET cc_start: 0.3385 (tpt) cc_final: 0.3006 (mtp) REVERT: J 268 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7524 (mt-10) REVERT: J 289 THR cc_start: 0.6668 (OUTLIER) cc_final: 0.6416 (p) REVERT: J 296 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7105 (tmtt) REVERT: J 302 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6775 (tt0) REVERT: J 320 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7791 (ptmt) REVERT: J 438 ASN cc_start: 0.8029 (m-40) cc_final: 0.7657 (m-40) REVERT: J 464 GLU cc_start: 0.7469 (tt0) cc_final: 0.7163 (tt0) REVERT: J 468 ASN cc_start: 0.8709 (t0) cc_final: 0.8448 (t0) REVERT: J 508 GLU cc_start: 0.8231 (mp0) cc_final: 0.7903 (mp0) REVERT: K 72 ILE cc_start: 0.8319 (mm) cc_final: 0.7985 (pt) REVERT: K 221 MET cc_start: 0.3337 (tpt) cc_final: 0.2942 (mtp) REVERT: K 268 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7607 (mt-10) REVERT: K 296 LYS cc_start: 0.7892 (ttmm) cc_final: 0.6973 (tmtt) REVERT: K 320 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7580 (ptmt) REVERT: K 346 GLU cc_start: 0.7952 (pm20) cc_final: 0.7438 (pm20) REVERT: K 438 ASN cc_start: 0.7947 (m-40) cc_final: 0.7694 (m-40) REVERT: K 469 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7410 (tpp) REVERT: K 508 GLU cc_start: 0.8105 (mp0) cc_final: 0.7563 (mp0) REVERT: L 72 ILE cc_start: 0.8277 (mm) cc_final: 0.7888 (pt) REVERT: L 83 MET cc_start: 0.8242 (tpp) cc_final: 0.8034 (tpp) REVERT: L 87 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6963 (pt0) REVERT: L 268 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7544 (mt-10) REVERT: L 296 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7053 (tmtt) REVERT: L 302 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6679 (tt0) REVERT: L 320 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7634 (ptmt) REVERT: L 397 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8278 (p) REVERT: L 408 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7664 (tpm170) REVERT: L 426 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7779 (tt) REVERT: L 438 ASN cc_start: 0.7992 (m-40) cc_final: 0.7731 (m-40) REVERT: L 508 GLU cc_start: 0.8200 (mp0) cc_final: 0.7729 (mp0) outliers start: 179 outliers final: 133 residues processed: 779 average time/residue: 0.5809 time to fit residues: 730.4641 Evaluate side-chains 795 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 642 time to evaluate : 5.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 TYR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 310 ASN Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 237 TYR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain H residue 359 MET Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 469 MET Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 310 ASN Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 237 TYR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 165 LYS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 328 MET Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 469 MET Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 237 TYR Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 310 ASN Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 330 MET Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 415 GLU Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 9.9990 chunk 478 optimal weight: 2.9990 chunk 292 optimal weight: 0.0870 chunk 227 optimal weight: 0.6980 chunk 332 optimal weight: 0.9980 chunk 502 optimal weight: 3.9990 chunk 462 optimal weight: 6.9990 chunk 399 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 308 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN B 500 GLN C 85 ASN C 310 ASN ** D 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN F 310 ASN G 85 ASN H 302 GLN I 310 ASN K 302 GLN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 310 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 42048 Z= 0.197 Angle : 0.633 9.964 56760 Z= 0.335 Chirality : 0.042 0.134 6228 Planarity : 0.004 0.067 7404 Dihedral : 4.745 47.354 5641 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.66 % Favored : 93.63 % Rotamer: Outliers : 3.87 % Allowed : 20.26 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 5088 helix: 0.11 (0.11), residues: 2280 sheet: -0.87 (0.26), residues: 384 loop : -1.75 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 437 HIS 0.004 0.001 HIS E 136 PHE 0.010 0.001 PHE J 365 TYR 0.007 0.001 TYR K 314 ARG 0.014 0.001 ARG A 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 637 time to evaluate : 4.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8352 (mm) cc_final: 0.8053 (pt) REVERT: A 77 ASP cc_start: 0.8596 (t0) cc_final: 0.8232 (t0) REVERT: A 126 MET cc_start: 0.7709 (mmt) cc_final: 0.7482 (mmm) REVERT: A 221 MET cc_start: 0.3345 (tpt) cc_final: 0.2985 (mtp) REVERT: A 268 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7513 (mt-10) REVERT: A 296 LYS cc_start: 0.7818 (ttmm) cc_final: 0.7087 (tmtt) REVERT: A 302 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6819 (tt0) REVERT: A 320 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7690 (ptmt) REVERT: A 416 GLU cc_start: 0.8769 (tt0) cc_final: 0.8526 (tt0) REVERT: A 426 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7585 (tt) REVERT: A 438 ASN cc_start: 0.8057 (m-40) cc_final: 0.7682 (m-40) REVERT: A 508 GLU cc_start: 0.8196 (mp0) cc_final: 0.7889 (mp0) REVERT: B 72 ILE cc_start: 0.8319 (mm) cc_final: 0.7975 (pt) REVERT: B 221 MET cc_start: 0.3279 (tpt) cc_final: 0.2934 (mtp) REVERT: B 268 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7589 (mt-10) REVERT: B 296 LYS cc_start: 0.7833 (ttmm) cc_final: 0.6934 (tmtt) REVERT: B 320 LYS cc_start: 0.7802 (mtmt) cc_final: 0.7476 (ptmt) REVERT: B 346 GLU cc_start: 0.7921 (pm20) cc_final: 0.7401 (pm20) REVERT: B 438 ASN cc_start: 0.7960 (m-40) cc_final: 0.7682 (m-40) REVERT: B 469 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7360 (tpp) REVERT: B 508 GLU cc_start: 0.7938 (mp0) cc_final: 0.7533 (mp0) REVERT: C 72 ILE cc_start: 0.8282 (mm) cc_final: 0.7887 (pt) REVERT: C 87 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6791 (pt0) REVERT: C 268 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7575 (mt-10) REVERT: C 296 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7028 (tmtt) REVERT: C 302 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6651 (tt0) REVERT: C 320 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7637 (ptmt) REVERT: C 397 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8252 (p) REVERT: C 408 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7686 (tpm170) REVERT: C 426 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7803 (tt) REVERT: C 508 GLU cc_start: 0.8227 (mp0) cc_final: 0.7750 (mp0) REVERT: D 72 ILE cc_start: 0.8356 (mm) cc_final: 0.7979 (pt) REVERT: D 77 ASP cc_start: 0.8557 (t0) cc_final: 0.8274 (t0) REVERT: D 221 MET cc_start: 0.3337 (tpt) cc_final: 0.3035 (mtp) REVERT: D 268 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7529 (mt-10) REVERT: D 289 THR cc_start: 0.6817 (OUTLIER) cc_final: 0.6582 (p) REVERT: D 296 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7117 (tmtt) REVERT: D 302 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6801 (tt0) REVERT: D 320 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7695 (ptmt) REVERT: D 438 ASN cc_start: 0.8060 (m-40) cc_final: 0.7661 (m-40) REVERT: D 468 ASN cc_start: 0.8712 (t0) cc_final: 0.8445 (t0) REVERT: D 508 GLU cc_start: 0.8210 (mp0) cc_final: 0.7892 (mp0) REVERT: E 72 ILE cc_start: 0.8329 (mm) cc_final: 0.7985 (pt) REVERT: E 221 MET cc_start: 0.3299 (tpt) cc_final: 0.2942 (mtp) REVERT: E 268 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7672 (mt-10) REVERT: E 296 LYS cc_start: 0.7834 (ttmm) cc_final: 0.6937 (tmtt) REVERT: E 320 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7525 (ptmt) REVERT: E 346 GLU cc_start: 0.7914 (pm20) cc_final: 0.7390 (pm20) REVERT: E 438 ASN cc_start: 0.7960 (m-40) cc_final: 0.7685 (m-40) REVERT: E 469 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7358 (tpp) REVERT: F 72 ILE cc_start: 0.8278 (mm) cc_final: 0.7882 (pt) REVERT: F 87 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: F 268 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7569 (mt-10) REVERT: F 296 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7020 (tmtt) REVERT: F 302 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6653 (tt0) REVERT: F 320 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7646 (ptmt) REVERT: F 397 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8247 (p) REVERT: F 408 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7686 (tpm170) REVERT: F 426 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7802 (tt) REVERT: F 508 GLU cc_start: 0.8227 (mp0) cc_final: 0.7755 (mp0) REVERT: G 72 ILE cc_start: 0.8368 (mm) cc_final: 0.7989 (pt) REVERT: G 77 ASP cc_start: 0.8563 (t0) cc_final: 0.8275 (t0) REVERT: G 221 MET cc_start: 0.3348 (tpt) cc_final: 0.3042 (mtp) REVERT: G 268 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7523 (mt-10) REVERT: G 289 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6574 (p) REVERT: G 296 LYS cc_start: 0.7824 (ttmm) cc_final: 0.7120 (tmtt) REVERT: G 302 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6800 (tt0) REVERT: G 320 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7692 (ptmt) REVERT: G 438 ASN cc_start: 0.8061 (m-40) cc_final: 0.7660 (m-40) REVERT: G 468 ASN cc_start: 0.8706 (t0) cc_final: 0.8435 (t0) REVERT: G 508 GLU cc_start: 0.8196 (mp0) cc_final: 0.7891 (mp0) REVERT: H 72 ILE cc_start: 0.8318 (mm) cc_final: 0.7973 (pt) REVERT: H 221 MET cc_start: 0.3290 (tpt) cc_final: 0.2935 (mtp) REVERT: H 268 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7668 (mt-10) REVERT: H 296 LYS cc_start: 0.7835 (ttmm) cc_final: 0.6939 (tmtt) REVERT: H 320 LYS cc_start: 0.7872 (mtmt) cc_final: 0.7528 (ptmt) REVERT: H 346 GLU cc_start: 0.7912 (pm20) cc_final: 0.7393 (pm20) REVERT: H 438 ASN cc_start: 0.7961 (m-40) cc_final: 0.7684 (m-40) REVERT: H 469 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7362 (tpp) REVERT: I 72 ILE cc_start: 0.8278 (mm) cc_final: 0.7881 (pt) REVERT: I 87 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6742 (pt0) REVERT: I 268 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7568 (mt-10) REVERT: I 296 LYS cc_start: 0.7805 (ttmm) cc_final: 0.7025 (tmtt) REVERT: I 302 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6651 (tt0) REVERT: I 320 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7639 (ptmt) REVERT: I 397 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8248 (p) REVERT: I 408 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7688 (tpm170) REVERT: I 426 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7802 (tt) REVERT: I 508 GLU cc_start: 0.8236 (mp0) cc_final: 0.7759 (mp0) REVERT: J 72 ILE cc_start: 0.8374 (mm) cc_final: 0.7993 (pt) REVERT: J 77 ASP cc_start: 0.8572 (t0) cc_final: 0.8265 (t0) REVERT: J 221 MET cc_start: 0.3357 (tpt) cc_final: 0.3047 (mtp) REVERT: J 268 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7513 (mt-10) REVERT: J 289 THR cc_start: 0.6792 (OUTLIER) cc_final: 0.6558 (p) REVERT: J 296 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7114 (tmtt) REVERT: J 302 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6743 (tt0) REVERT: J 320 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7696 (ptmt) REVERT: J 438 ASN cc_start: 0.8063 (m-40) cc_final: 0.7660 (m-40) REVERT: J 468 ASN cc_start: 0.8710 (t0) cc_final: 0.8437 (t0) REVERT: J 508 GLU cc_start: 0.8198 (mp0) cc_final: 0.7893 (mp0) REVERT: K 72 ILE cc_start: 0.8317 (mm) cc_final: 0.7973 (pt) REVERT: K 221 MET cc_start: 0.3285 (tpt) cc_final: 0.2939 (mtp) REVERT: K 268 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7677 (mt-10) REVERT: K 296 LYS cc_start: 0.7835 (ttmm) cc_final: 0.6939 (tmtt) REVERT: K 320 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7527 (ptmt) REVERT: K 346 GLU cc_start: 0.7935 (pm20) cc_final: 0.7426 (pm20) REVERT: K 438 ASN cc_start: 0.7960 (m-40) cc_final: 0.7684 (m-40) REVERT: K 469 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7357 (tpp) REVERT: K 508 GLU cc_start: 0.8101 (mp0) cc_final: 0.7867 (mt-10) REVERT: L 72 ILE cc_start: 0.8279 (mm) cc_final: 0.7883 (pt) REVERT: L 83 MET cc_start: 0.8234 (tpp) cc_final: 0.8028 (tpp) REVERT: L 87 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: L 268 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7557 (mt-10) REVERT: L 296 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7040 (tmtt) REVERT: L 302 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6944 (mt0) REVERT: L 320 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7636 (ptmt) REVERT: L 397 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8253 (p) REVERT: L 408 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7686 (tpm170) REVERT: L 426 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7835 (tt) REVERT: L 438 ASN cc_start: 0.7971 (m-40) cc_final: 0.7667 (m-40) REVERT: L 508 GLU cc_start: 0.8228 (mp0) cc_final: 0.7752 (mp0) outliers start: 169 outliers final: 135 residues processed: 763 average time/residue: 0.5656 time to fit residues: 680.8889 Evaluate side-chains 786 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 631 time to evaluate : 4.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 TYR Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 310 ASN Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 237 TYR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 472 MET Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 283 ARG Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 469 MET Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 310 ASN Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 237 TYR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 472 MET Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 165 LYS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 328 MET Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 469 MET Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 237 TYR Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 310 ASN Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 330 MET Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 9.9990 chunk 425 optimal weight: 0.0870 chunk 122 optimal weight: 0.5980 chunk 368 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 400 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 411 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN C 85 ASN C 310 ASN E 302 GLN F 310 ASN G 85 ASN H 302 GLN I 310 ASN J 85 ASN K 302 GLN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.178347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140473 restraints weight = 53541.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137818 restraints weight = 57310.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139639 restraints weight = 55146.588| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 42048 Z= 0.168 Angle : 0.621 10.107 56760 Z= 0.329 Chirality : 0.041 0.135 6228 Planarity : 0.004 0.066 7404 Dihedral : 4.619 47.730 5641 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.15 % Favored : 94.14 % Rotamer: Outliers : 3.50 % Allowed : 20.70 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 5088 helix: 0.26 (0.11), residues: 2280 sheet: -0.81 (0.26), residues: 384 loop : -1.73 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 285 HIS 0.004 0.001 HIS B 136 PHE 0.010 0.001 PHE L 365 TYR 0.014 0.001 TYR G 86 ARG 0.014 0.001 ARG A 339 =============================================================================== Job complete usr+sys time: 11805.86 seconds wall clock time: 211 minutes 4.63 seconds (12664.63 seconds total)