Starting phenix.real_space_refine (version: dev) on Tue May 17 16:29:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/05_2022/3ja7_6324.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/05_2022/3ja7_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_6324/05_2022/3ja7_6324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/05_2022/3ja7_6324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/05_2022/3ja7_6324.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja7_6324/05_2022/3ja7_6324.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 15, 'TRANS': 399, 'PCIS': 1} 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: 22.62, per 1000 atoms: 0.55 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: 15.92 Conformation dependent library (CDL) restraints added in 6.1 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: 2.45 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: 15.02 Time building geometry restraints manager: 16.94 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 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. 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.930 Check model and map are aligned: 0.610 Convert atoms to be neutral: 0.310 Process input model: 99.290 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.280 Set refine NCS operators: 0.010 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 1.535 19.291 56760 Z= 0.988 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 : 38.36 Ramachandran Plot: Outliers : 2.12 % Allowed : 11.05 % Favored : 86.83 % Rotamer Outliers : 10.44 % 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 *********************** 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 : 4.876 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 outliers start: 456 outliers final: 100 residues processed: 1428 average time/residue: 0.5991 time to fit residues: 1313.2685 Evaluate side-chains 772 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 672 time to evaluate : 4.891 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 0 residues processed: 100 average time/residue: 0.4787 time to fit residues: 87.0214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 257 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 395 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 457 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 183 GLN A 355 ASN A 358 ASN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** G 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 90 ASN ** I 124 ASN ** 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 ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 124 ASN ** 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: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3771 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= 0.241 Angle : 0.823 13.571 56760 Z= 0.403 Chirality : 0.045 0.159 6228 Planarity : 0.005 0.039 7404 Dihedral : 5.874 26.588 5628 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.86 % Allowed : 3.85 % Favored : 95.28 % Rotamer Outliers : 2.79 % 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: -3.55 (0.10), residues: 5088 helix: -2.59 (0.09), residues: 2220 sheet: -2.09 (0.21), residues: 396 loop : -2.08 (0.11), residues: 2472 *********************** 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 905 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 783 time to evaluate : 4.851 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 outliers start: 122 outliers final: 57 residues processed: 885 average time/residue: 0.5201 time to fit residues: 752.4315 Evaluate side-chains 701 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 644 time to evaluate : 4.888 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.3556 time to fit residues: 45.8544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 380 optimal weight: 1.9990 chunk 311 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 458 optimal weight: 5.9990 chunk 495 optimal weight: 10.0000 chunk 408 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 156 optimal weight: 0.3980 chunk 367 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 90 ASN A 367 GLN A 382 GLN B 85 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN C 85 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN C 382 GLN D 85 ASN D 90 ASN D 367 GLN D 382 GLN E 85 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN F 85 ASN F 367 GLN F 382 GLN G 85 ASN G 90 ASN ** G 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN I 85 ASN I 367 GLN I 382 GLN J 85 ASN J 90 ASN ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN L 85 ASN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN L 382 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 42048 Z= 0.200 Angle : 0.717 11.704 56760 Z= 0.347 Chirality : 0.042 0.165 6228 Planarity : 0.005 0.099 7404 Dihedral : 5.170 23.113 5628 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.09 % Favored : 95.44 % Rotamer Outliers : 2.54 % 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: -2.70 (0.11), residues: 5088 helix: -1.60 (0.10), residues: 2208 sheet: -1.68 (0.24), residues: 384 loop : -1.93 (0.11), residues: 2496 *********************** 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 797 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 686 time to evaluate : 5.074 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 outliers start: 111 outliers final: 31 residues processed: 752 average time/residue: 0.5330 time to fit residues: 655.2857 Evaluate side-chains 630 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 599 time to evaluate : 4.772 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4041 time to fit residues: 29.2043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 2.9990 chunk 344 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 307 optimal weight: 20.0000 chunk 460 optimal weight: 5.9990 chunk 487 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 436 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS D 255 HIS ** D 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 HIS G 255 HIS G 367 GLN G 382 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 HIS J 255 HIS J 367 GLN J 382 GLN ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 42048 Z= 0.275 Angle : 0.742 11.536 56760 Z= 0.358 Chirality : 0.045 0.228 6228 Planarity : 0.005 0.070 7404 Dihedral : 5.130 21.802 5628 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.27 % Favored : 94.26 % Rotamer Outliers : 2.13 % 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: -2.47 (0.11), residues: 5088 helix: -1.35 (0.10), residues: 2244 sheet: -1.43 (0.26), residues: 396 loop : -1.89 (0.12), residues: 2448 *********************** 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 747 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 654 time to evaluate : 5.401 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 outliers start: 93 outliers final: 46 residues processed: 698 average time/residue: 0.5352 time to fit residues: 607.6640 Evaluate side-chains 640 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 594 time to evaluate : 4.983 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3624 time to fit residues: 38.1369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 362 optimal weight: 0.0370 chunk 201 optimal weight: 0.6980 chunk 415 optimal weight: 0.6980 chunk 336 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 248 optimal weight: 0.7980 chunk 437 optimal weight: 0.9990 chunk 122 optimal weight: 0.0670 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 42048 Z= 0.150 Angle : 0.675 11.307 56760 Z= 0.322 Chirality : 0.041 0.154 6228 Planarity : 0.004 0.060 7404 Dihedral : 4.698 20.286 5628 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.42 % Favored : 95.11 % Rotamer Outliers : 1.17 % 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: -1.97 (0.11), residues: 5088 helix: -0.81 (0.10), residues: 2256 sheet: -1.22 (0.26), residues: 384 loop : -1.77 (0.12), residues: 2448 *********************** 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 716 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 665 time to evaluate : 4.956 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 outliers start: 51 outliers final: 12 residues processed: 691 average time/residue: 0.5166 time to fit residues: 584.7378 Evaluate side-chains 602 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 590 time to evaluate : 4.832 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4476 time to fit residues: 16.0299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 0.8980 chunk 438 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 286 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 487 optimal weight: 5.9990 chunk 404 optimal weight: 0.3980 chunk 225 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 42048 Z= 0.273 Angle : 0.715 11.449 56760 Z= 0.346 Chirality : 0.043 0.153 6228 Planarity : 0.004 0.052 7404 Dihedral : 4.922 22.685 5628 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.72 % Favored : 93.81 % Rotamer Outliers : 2.27 % 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: -1.96 (0.11), residues: 5088 helix: -0.75 (0.10), residues: 2268 sheet: -1.08 (0.26), residues: 384 loop : -1.84 (0.12), residues: 2436 *********************** 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 710 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 611 time to evaluate : 4.880 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 outliers start: 99 outliers final: 51 residues processed: 669 average time/residue: 0.5601 time to fit residues: 610.7628 Evaluate side-chains 643 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 592 time to evaluate : 4.865 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.3806 time to fit residues: 43.4765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 277 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 275 optimal weight: 9.9990 chunk 410 optimal weight: 0.9990 chunk 272 optimal weight: 10.0000 chunk 485 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 296 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 302 GLN D 310 ASN E 302 GLN G 310 ASN H 302 GLN J 310 ASN K 302 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 42048 Z= 0.304 Angle : 0.734 11.504 56760 Z= 0.358 Chirality : 0.044 0.142 6228 Planarity : 0.004 0.122 7404 Dihedral : 5.061 20.607 5628 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.07 % Favored : 93.46 % Rotamer Outliers : 1.63 % 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: -1.93 (0.11), residues: 5088 helix: -0.67 (0.11), residues: 2268 sheet: -1.15 (0.26), residues: 396 loop : -1.87 (0.12), residues: 2424 *********************** 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 681 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 610 time to evaluate : 4.996 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 outliers start: 71 outliers final: 25 residues processed: 658 average time/residue: 0.5411 time to fit residues: 577.2560 Evaluate side-chains 613 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 588 time to evaluate : 5.158 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4609 time to fit residues: 26.7392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 5.9990 chunk 193 optimal weight: 0.2980 chunk 290 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 308 optimal weight: 0.9990 chunk 330 optimal weight: 4.9990 chunk 240 optimal weight: 0.0970 chunk 45 optimal weight: 0.3980 chunk 381 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS C 310 ASN F 310 ASN I 310 ASN L 310 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.107 42048 Z= 0.177 Angle : 0.682 11.421 56760 Z= 0.332 Chirality : 0.041 0.139 6228 Planarity : 0.005 0.134 7404 Dihedral : 4.663 20.597 5628 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.40 % Favored : 94.12 % Rotamer Outliers : 0.78 % 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: -1.57 (0.11), residues: 5088 helix: -0.26 (0.11), residues: 2256 sheet: -0.94 (0.27), residues: 384 loop : -1.80 (0.12), residues: 2448 *********************** 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 636 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 602 time to evaluate : 5.063 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 outliers start: 34 outliers final: 21 residues processed: 618 average time/residue: 0.5631 time to fit residues: 554.4813 Evaluate side-chains 600 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 579 time to evaluate : 4.729 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3888 time to fit residues: 21.5114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 9.9990 chunk 465 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 452 optimal weight: 5.9990 chunk 272 optimal weight: 0.1980 chunk 197 optimal weight: 0.0000 chunk 355 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 409 optimal weight: 1.9990 chunk 428 optimal weight: 3.9990 chunk 451 optimal weight: 0.6980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 HIS G 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.111 42048 Z= 0.209 Angle : 0.689 11.484 56760 Z= 0.340 Chirality : 0.041 0.141 6228 Planarity : 0.006 0.135 7404 Dihedral : 4.558 19.679 5628 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.27 % Favored : 94.18 % Rotamer Outliers : 0.46 % 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: -1.40 (0.11), residues: 5088 helix: -0.11 (0.11), residues: 2256 sheet: -0.90 (0.27), residues: 384 loop : -1.71 (0.12), residues: 2448 *********************** 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 624 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 604 time to evaluate : 6.602 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 outliers start: 20 outliers final: 17 residues processed: 608 average time/residue: 0.5741 time to fit residues: 557.2744 Evaluate side-chains 593 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 576 time to evaluate : 4.849 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4378 time to fit residues: 19.8491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 5.9990 chunk 478 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 227 optimal weight: 0.6980 chunk 332 optimal weight: 0.9990 chunk 502 optimal weight: 4.9990 chunk 462 optimal weight: 1.9990 chunk 399 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 chunk 308 optimal weight: 0.7980 chunk 245 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 42048 Z= 0.191 Angle : 0.678 11.534 56760 Z= 0.331 Chirality : 0.041 0.143 6228 Planarity : 0.005 0.114 7404 Dihedral : 4.424 19.064 5628 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.64 % Favored : 94.65 % Rotamer Outliers : 0.23 % 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: -1.23 (0.11), residues: 5088 helix: 0.10 (0.11), residues: 2256 sheet: -0.82 (0.26), residues: 384 loop : -1.70 (0.12), residues: 2448 ********************** 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 611 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 601 time to evaluate : 4.887 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 outliers start: 10 outliers final: 8 residues processed: 607 average time/residue: 0.5683 time to fit residues: 548.6287 Evaluate side-chains 564 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 556 time to evaluate : 4.811 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4667 time to fit residues: 13.0079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 10.0000 chunk 425 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 368 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 chunk 400 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 411 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.177903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138849 restraints weight = 53796.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135918 restraints weight = 54117.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137906 restraints weight = 53535.646| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.133 42048 Z= 0.231 Angle : 0.700 12.119 56760 Z= 0.346 Chirality : 0.042 0.136 6228 Planarity : 0.006 0.148 7404 Dihedral : 4.477 18.654 5628 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.23 % Favored : 94.06 % Rotamer Outliers : 0.32 % 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: -1.18 (0.11), residues: 5088 helix: 0.18 (0.11), residues: 2244 sheet: -0.79 (0.26), residues: 384 loop : -1.72 (0.12), residues: 2460 =============================================================================== Job complete usr+sys time: 10332.84 seconds wall clock time: 186 minutes 47.28 seconds (11207.28 seconds total)