Starting phenix.real_space_refine on Mon Sep 23 16:21:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/09_2024/8fvg_29486.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/09_2024/8fvg_29486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/09_2024/8fvg_29486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/09_2024/8fvg_29486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/09_2024/8fvg_29486.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/09_2024/8fvg_29486.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 30225 2.51 5 N 8125 2.21 5 O 9503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 158 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 48009 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.97, per 1000 atoms: 0.42 Number of scatterers: 48009 At special positions: 0 Unit cell: (275.52, 273.28, 286.72, 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 156 16.00 O 9503 8.00 N 8125 7.00 C 30225 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 - 3.00 Amino acid : True - 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: 8.78 Conformation dependent library (CDL) restraints added in 4.7 seconds 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11908 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 91 sheets defined 33.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN A 254 " --> pdb=" O TRP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 399 Processing helix chain 'A' and resid 405 through 427 Proline residue: A 418 - end of helix removed outlier: 3.609A pdb=" N ALA A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 149 Processing helix chain 'B' and resid 153 through 158 removed outlier: 4.364A pdb=" N GLN B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN B 254 " --> pdb=" O TRP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.554A pdb=" N THR B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS B 341 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 399 Processing helix chain 'B' and resid 405 through 427 Proline residue: B 418 - end of helix removed outlier: 3.609A pdb=" N ALA B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 149 Processing helix chain 'C' and resid 153 through 158 removed outlier: 4.362A pdb=" N GLN C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN C 254 " --> pdb=" O TRP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 removed outlier: 4.124A pdb=" N GLY C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.554A pdb=" N THR C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS C 341 " --> pdb=" O ASN C 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER C 342 " --> pdb=" O THR C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 399 Processing helix chain 'C' and resid 405 through 427 Proline residue: C 418 - end of helix removed outlier: 3.609A pdb=" N ALA C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN C 455 " --> pdb=" O ARG C 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 149 Processing helix chain 'D' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 254 removed outlier: 3.801A pdb=" N GLN D 254 " --> pdb=" O TRP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 342 removed outlier: 3.617A pdb=" N LYS D 341 " --> pdb=" O ASN D 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER D 342 " --> pdb=" O THR D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 399 Processing helix chain 'D' and resid 405 through 427 Proline residue: D 418 - end of helix removed outlier: 3.609A pdb=" N ALA D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN D 455 " --> pdb=" O ARG D 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'E' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 149 Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN E 158 " --> pdb=" O PRO E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL E 225 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN E 254 " --> pdb=" O TRP E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR E 307 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS E 341 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 342 " --> pdb=" O THR E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 399 Processing helix chain 'E' and resid 405 through 427 Proline residue: E 418 - end of helix removed outlier: 3.608A pdb=" N ALA E 425 " --> pdb=" O ASP E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 447 Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN E 455 " --> pdb=" O ARG E 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 149 Processing helix chain 'F' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN F 158 " --> pdb=" O PRO F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN F 254 " --> pdb=" O TRP F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS F 341 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER F 342 " --> pdb=" O THR F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 399 Processing helix chain 'F' and resid 405 through 427 Proline residue: F 418 - end of helix removed outlier: 3.609A pdb=" N ALA F 425 " --> pdb=" O ASP F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 447 Processing helix chain 'F' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN F 455 " --> pdb=" O ARG F 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 7 Processing helix chain 'G' and resid 48 through 55 Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 Processing helix chain 'G' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL G 225 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER G 226 " --> pdb=" O SER G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN G 254 " --> pdb=" O TRP G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR G 307 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS G 341 " --> pdb=" O ASN G 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER G 342 " --> pdb=" O THR G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 399 Processing helix chain 'G' and resid 405 through 427 Proline residue: G 418 - end of helix removed outlier: 3.609A pdb=" N ALA G 425 " --> pdb=" O ASP G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 447 Processing helix chain 'G' and resid 451 through 456 removed outlier: 3.560A pdb=" N GLN G 455 " --> pdb=" O ARG G 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 7 Processing helix chain 'H' and resid 48 through 55 Processing helix chain 'H' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 149 Processing helix chain 'H' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL H 225 " --> pdb=" O LYS H 221 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 226 " --> pdb=" O SER H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN H 254 " --> pdb=" O TRP H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 272 removed outlier: 4.124A pdb=" N GLY H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 307 removed outlier: 3.556A pdb=" N THR H 307 " --> pdb=" O ILE H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 342 removed outlier: 3.617A pdb=" N LYS H 341 " --> pdb=" O ASN H 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER H 342 " --> pdb=" O THR H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 399 Processing helix chain 'H' and resid 405 through 427 Proline residue: H 418 - end of helix removed outlier: 3.609A pdb=" N ALA H 425 " --> pdb=" O ASP H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 447 Processing helix chain 'H' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN H 455 " --> pdb=" O ARG H 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA I 66 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 149 Processing helix chain 'I' and resid 153 through 158 removed outlier: 4.364A pdb=" N GLN I 158 " --> pdb=" O PRO I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL I 225 " --> pdb=" O LYS I 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER I 226 " --> pdb=" O SER I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 254 removed outlier: 3.801A pdb=" N GLN I 254 " --> pdb=" O TRP I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY I 270 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR I 307 " --> pdb=" O ILE I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS I 341 " --> pdb=" O ASN I 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER I 342 " --> pdb=" O THR I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 399 Processing helix chain 'I' and resid 405 through 427 Proline residue: I 418 - end of helix removed outlier: 3.609A pdb=" N ALA I 425 " --> pdb=" O ASP I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 447 Processing helix chain 'I' and resid 451 through 456 removed outlier: 3.560A pdb=" N GLN I 455 " --> pdb=" O ARG I 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 7 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA J 66 " --> pdb=" O GLN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 149 Processing helix chain 'J' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN J 158 " --> pdb=" O PRO J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL J 225 " --> pdb=" O LYS J 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER J 226 " --> pdb=" O SER J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN J 254 " --> pdb=" O TRP J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY J 270 " --> pdb=" O LEU J 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR J 271 " --> pdb=" O ALA J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR J 307 " --> pdb=" O ILE J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS J 341 " --> pdb=" O ASN J 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER J 342 " --> pdb=" O THR J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 399 Processing helix chain 'J' and resid 405 through 427 Proline residue: J 418 - end of helix removed outlier: 3.609A pdb=" N ALA J 425 " --> pdb=" O ASP J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 447 Processing helix chain 'J' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN J 455 " --> pdb=" O ARG J 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 7 Processing helix chain 'K' and resid 48 through 55 Processing helix chain 'K' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 149 Processing helix chain 'K' and resid 153 through 158 removed outlier: 4.364A pdb=" N GLN K 158 " --> pdb=" O PRO K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL K 225 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER K 226 " --> pdb=" O SER K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN K 254 " --> pdb=" O TRP K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY K 270 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR K 271 " --> pdb=" O ALA K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 307 removed outlier: 3.554A pdb=" N THR K 307 " --> pdb=" O ILE K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 342 removed outlier: 3.617A pdb=" N LYS K 341 " --> pdb=" O ASN K 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER K 342 " --> pdb=" O THR K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 399 Processing helix chain 'K' and resid 405 through 427 Proline residue: K 418 - end of helix removed outlier: 3.610A pdb=" N ALA K 425 " --> pdb=" O ASP K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 447 Processing helix chain 'K' and resid 451 through 456 removed outlier: 3.560A pdb=" N GLN K 455 " --> pdb=" O ARG K 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 7 Processing helix chain 'L' and resid 48 through 55 Processing helix chain 'L' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA L 66 " --> pdb=" O GLN L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 149 Processing helix chain 'L' and resid 153 through 158 removed outlier: 4.364A pdb=" N GLN L 158 " --> pdb=" O PRO L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL L 225 " --> pdb=" O LYS L 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 226 " --> pdb=" O SER L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 254 removed outlier: 3.801A pdb=" N GLN L 254 " --> pdb=" O TRP L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR L 271 " --> pdb=" O ALA L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 removed outlier: 3.554A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 342 removed outlier: 3.617A pdb=" N LYS L 341 " --> pdb=" O ASN L 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER L 342 " --> pdb=" O THR L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 399 Processing helix chain 'L' and resid 405 through 427 Proline residue: L 418 - end of helix removed outlier: 3.609A pdb=" N ALA L 425 " --> pdb=" O ASP L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 447 Processing helix chain 'L' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN L 455 " --> pdb=" O ARG L 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 7 Processing helix chain 'M' and resid 48 through 55 Processing helix chain 'M' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA M 66 " --> pdb=" O GLN M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 149 Processing helix chain 'M' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN M 158 " --> pdb=" O PRO M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER M 226 " --> pdb=" O SER M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN M 254 " --> pdb=" O TRP M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR M 271 " --> pdb=" O ALA M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 307 removed outlier: 3.556A pdb=" N THR M 307 " --> pdb=" O ILE M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS M 341 " --> pdb=" O ASN M 337 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER M 342 " --> pdb=" O THR M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 399 Processing helix chain 'M' and resid 405 through 427 Proline residue: M 418 - end of helix removed outlier: 3.609A pdb=" N ALA M 425 " --> pdb=" O ASP M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 437 through 447 Processing helix chain 'M' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN M 455 " --> pdb=" O ARG M 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL A 29 " --> pdb=" O ALA A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU A 172 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE A 117 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR A 260 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN A 285 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 262 " --> pdb=" O ASN A 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 465 Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.688A pdb=" N TYR A 470 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL B 29 " --> pdb=" O ALA B 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU B 172 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE B 117 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 260 through 264 removed outlier: 6.281A pdb=" N TYR B 260 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN B 285 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 262 " --> pdb=" O ASN B 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AB4, first strand: chain 'B' and resid 461 through 465 Processing sheet with id=AB5, first strand: chain 'B' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR B 470 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL C 29 " --> pdb=" O ALA C 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU C 172 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE C 117 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR C 260 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN C 285 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 262 " --> pdb=" O ASN C 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 347 through 348 Processing sheet with id=AC2, first strand: chain 'C' and resid 461 through 465 Processing sheet with id=AC3, first strand: chain 'C' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR C 470 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL D 29 " --> pdb=" O ALA D 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU D 172 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE D 117 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR D 260 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN D 285 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL D 262 " --> pdb=" O ASN D 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 347 through 348 Processing sheet with id=AC9, first strand: chain 'D' and resid 461 through 465 Processing sheet with id=AD1, first strand: chain 'D' and resid 478 through 479 removed outlier: 3.688A pdb=" N TYR D 470 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL E 29 " --> pdb=" O ALA E 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU E 172 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 123 through 125 removed outlier: 4.715A pdb=" N ILE E 117 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR E 260 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN E 285 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL E 262 " --> pdb=" O ASN E 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 347 through 348 Processing sheet with id=AD7, first strand: chain 'E' and resid 461 through 465 Processing sheet with id=AD8, first strand: chain 'E' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR E 470 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL F 29 " --> pdb=" O ALA F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU F 172 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE F 117 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR F 260 " --> pdb=" O ALA F 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN F 285 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL F 262 " --> pdb=" O ASN F 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 347 through 348 Processing sheet with id=AE5, first strand: chain 'F' and resid 461 through 465 Processing sheet with id=AE6, first strand: chain 'F' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR F 470 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL G 29 " --> pdb=" O ALA G 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU G 172 " --> pdb=" O VAL G 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE G 117 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR G 260 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN G 285 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL G 262 " --> pdb=" O ASN G 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 347 through 348 Processing sheet with id=AF3, first strand: chain 'G' and resid 461 through 465 Processing sheet with id=AF4, first strand: chain 'G' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR G 470 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL H 29 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU H 172 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE H 117 " --> pdb=" O ALA H 185 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 260 through 264 removed outlier: 6.281A pdb=" N TYR H 260 " --> pdb=" O ALA H 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN H 285 " --> pdb=" O TYR H 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL H 262 " --> pdb=" O ASN H 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'H' and resid 347 through 348 Processing sheet with id=AG1, first strand: chain 'H' and resid 461 through 465 Processing sheet with id=AG2, first strand: chain 'H' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR H 470 " --> pdb=" O GLU H 479 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.443A pdb=" N VAL I 29 " --> pdb=" O ALA I 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'I' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU I 172 " --> pdb=" O VAL I 95 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE I 117 " --> pdb=" O ALA I 185 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR I 260 " --> pdb=" O ALA I 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN I 285 " --> pdb=" O TYR I 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL I 262 " --> pdb=" O ASN I 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'I' and resid 347 through 348 Processing sheet with id=AG8, first strand: chain 'I' and resid 461 through 465 Processing sheet with id=AG9, first strand: chain 'I' and resid 478 through 479 removed outlier: 3.688A pdb=" N TYR I 470 " --> pdb=" O GLU I 479 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL J 29 " --> pdb=" O ALA J 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'J' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU J 172 " --> pdb=" O VAL J 95 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 123 through 125 removed outlier: 4.715A pdb=" N ILE J 117 " --> pdb=" O ALA J 185 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 260 through 264 removed outlier: 6.281A pdb=" N TYR J 260 " --> pdb=" O ALA J 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN J 285 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL J 262 " --> pdb=" O ASN J 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'J' and resid 347 through 348 Processing sheet with id=AH6, first strand: chain 'J' and resid 461 through 465 Processing sheet with id=AH7, first strand: chain 'J' and resid 478 through 479 removed outlier: 3.688A pdb=" N TYR J 470 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL K 29 " --> pdb=" O ALA K 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'K' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU K 172 " --> pdb=" O VAL K 95 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE K 117 " --> pdb=" O ALA K 185 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 260 through 264 removed outlier: 6.281A pdb=" N TYR K 260 " --> pdb=" O ALA K 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN K 285 " --> pdb=" O TYR K 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL K 262 " --> pdb=" O ASN K 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'K' and resid 347 through 348 Processing sheet with id=AI4, first strand: chain 'K' and resid 461 through 465 Processing sheet with id=AI5, first strand: chain 'K' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR K 470 " --> pdb=" O GLU K 479 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 28 through 31 removed outlier: 6.443A pdb=" N VAL L 29 " --> pdb=" O ALA L 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'L' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU L 172 " --> pdb=" O VAL L 95 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 123 through 125 removed outlier: 4.717A pdb=" N ILE L 117 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR L 260 " --> pdb=" O ALA L 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN L 285 " --> pdb=" O TYR L 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL L 262 " --> pdb=" O ASN L 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'L' and resid 347 through 348 Processing sheet with id=AJ2, first strand: chain 'L' and resid 461 through 465 Processing sheet with id=AJ3, first strand: chain 'L' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR L 470 " --> pdb=" O GLU L 479 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL M 29 " --> pdb=" O ALA M 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'M' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU M 172 " --> pdb=" O VAL M 95 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 123 through 125 removed outlier: 4.717A pdb=" N ILE M 117 " --> pdb=" O ALA M 185 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR M 260 " --> pdb=" O ALA M 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN M 285 " --> pdb=" O TYR M 260 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL M 262 " --> pdb=" O ASN M 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'M' and resid 347 through 348 Processing sheet with id=AJ9, first strand: chain 'M' and resid 461 through 465 Processing sheet with id=AK1, first strand: chain 'M' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR M 470 " --> pdb=" O GLU M 479 " (cutoff:3.500A) 1560 hydrogen bonds defined for protein. 4329 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: 17.22 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15885 1.34 - 1.46: 10424 1.46 - 1.58: 22155 1.58 - 1.69: 0 1.69 - 1.81: 286 Bond restraints: 48750 Sorted by residual: bond pdb=" CA GLY C 22 " pdb=" C GLY C 22 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 1.84e+00 bond pdb=" CB MET J 137 " pdb=" CG MET J 137 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CB MET L 137 " pdb=" CG MET L 137 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB MET F 137 " pdb=" CG MET F 137 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB MET A 137 " pdb=" CG MET A 137 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.62e+00 ... (remaining 48745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 63220 1.33 - 2.66: 2404 2.66 - 3.99: 595 3.99 - 5.32: 133 5.32 - 6.65: 26 Bond angle restraints: 66378 Sorted by residual: angle pdb=" C SER E 74 " pdb=" N VAL E 75 " pdb=" CA VAL E 75 " ideal model delta sigma weight residual 121.70 126.93 -5.23 1.80e+00 3.09e-01 8.45e+00 angle pdb=" C SER I 74 " pdb=" N VAL I 75 " pdb=" CA VAL I 75 " ideal model delta sigma weight residual 121.70 126.87 -5.17 1.80e+00 3.09e-01 8.25e+00 angle pdb=" C SER K 74 " pdb=" N VAL K 75 " pdb=" CA VAL K 75 " ideal model delta sigma weight residual 121.70 126.87 -5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" C SER G 74 " pdb=" N VAL G 75 " pdb=" CA VAL G 75 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.22e+00 angle pdb=" C SER C 74 " pdb=" N VAL C 75 " pdb=" CA VAL C 75 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.21e+00 ... (remaining 66373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 26156 17.71 - 35.43: 2067 35.43 - 53.14: 285 53.14 - 70.86: 131 70.86 - 88.57: 52 Dihedral angle restraints: 28691 sinusoidal: 10296 harmonic: 18395 Sorted by residual: dihedral pdb=" CA ALA M 196 " pdb=" C ALA M 196 " pdb=" N LEU M 197 " pdb=" CA LEU M 197 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA J 196 " pdb=" C ALA J 196 " pdb=" N LEU J 197 " pdb=" CA LEU J 197 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA G 196 " pdb=" C ALA G 196 " pdb=" N LEU G 197 " pdb=" CA LEU G 197 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 28688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 4141 0.029 - 0.058: 2249 0.058 - 0.087: 703 0.087 - 0.116: 613 0.116 - 0.144: 172 Chirality restraints: 7878 Sorted by residual: chirality pdb=" CB VAL J 456 " pdb=" CA VAL J 456 " pdb=" CG1 VAL J 456 " pdb=" CG2 VAL J 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CB VAL I 456 " pdb=" CA VAL I 456 " pdb=" CG1 VAL I 456 " pdb=" CG2 VAL I 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CB VAL B 456 " pdb=" CA VAL B 456 " pdb=" CG1 VAL B 456 " pdb=" CG2 VAL B 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 7875 not shown) Planarity restraints: 8567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 153 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO J 154 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 154 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 154 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 37 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO E 38 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 153 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 154 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.018 5.00e-02 4.00e+02 ... (remaining 8564 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 712 2.66 - 3.22: 45991 3.22 - 3.78: 68771 3.78 - 4.34: 91678 4.34 - 4.90: 154362 Nonbonded interactions: 361514 Sorted by model distance: nonbonded pdb=" OD1 ASP B 394 " pdb=" ND2 ASN B 398 " model vdw 2.106 3.120 nonbonded pdb=" OD1 ASP D 394 " pdb=" ND2 ASN D 398 " model vdw 2.106 3.120 nonbonded pdb=" OD1 ASP C 394 " pdb=" ND2 ASN C 398 " model vdw 2.106 3.120 nonbonded pdb=" OD1 ASP J 394 " pdb=" ND2 ASN J 398 " model vdw 2.106 3.120 nonbonded pdb=" OD1 ASP E 394 " pdb=" ND2 ASN E 398 " model vdw 2.106 3.120 ... (remaining 361509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.560 Check model and map are aligned: 0.270 Set scattering table: 0.360 Process input model: 82.040 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.004 0.039 48750 Z= 0.279 Angle : 0.657 6.647 66378 Z= 0.372 Chirality : 0.047 0.144 7878 Planarity : 0.004 0.033 8567 Dihedral : 14.205 88.571 16783 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 6110 helix: 1.38 (0.12), residues: 2041 sheet: 0.25 (0.19), residues: 936 loop : -1.96 (0.10), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 480 PHE 0.012 0.002 PHE K 258 TYR 0.020 0.002 TYR K 321 ARG 0.004 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1203 time to evaluate : 3.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4909 (ttt) cc_final: 0.4452 (ttt) REVERT: A 24 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7542 (mtpt) REVERT: A 332 ASP cc_start: 0.6401 (m-30) cc_final: 0.6140 (m-30) REVERT: B 9 ARG cc_start: 0.6434 (ttt180) cc_final: 0.6209 (pmt-80) REVERT: B 24 LYS cc_start: 0.7228 (mtmt) cc_final: 0.6972 (tmtt) REVERT: B 69 LYS cc_start: 0.7980 (pttt) cc_final: 0.7537 (mmtp) REVERT: B 162 THR cc_start: 0.8012 (t) cc_final: 0.7792 (p) REVERT: B 211 SER cc_start: 0.7394 (p) cc_final: 0.7094 (t) REVERT: B 332 ASP cc_start: 0.6751 (m-30) cc_final: 0.6304 (t0) REVERT: B 481 LYS cc_start: 0.7635 (pttp) cc_final: 0.6528 (tppt) REVERT: B 489 SER cc_start: 0.7968 (p) cc_final: 0.7758 (t) REVERT: B 490 LYS cc_start: 0.7819 (ptpp) cc_final: 0.6581 (mptt) REVERT: C 30 MET cc_start: 0.8065 (mmm) cc_final: 0.7641 (mmm) REVERT: C 311 GLU cc_start: 0.4407 (mt-10) cc_final: 0.4092 (mt-10) REVERT: D 1 MET cc_start: 0.4703 (ttt) cc_final: 0.4266 (mmt) REVERT: D 69 LYS cc_start: 0.7587 (pttt) cc_final: 0.7082 (mmmt) REVERT: D 115 LEU cc_start: 0.7947 (mm) cc_final: 0.7524 (tt) REVERT: D 287 LEU cc_start: 0.7635 (mt) cc_final: 0.7412 (tp) REVERT: D 398 ASN cc_start: 0.7941 (m-40) cc_final: 0.7658 (m-40) REVERT: D 481 LYS cc_start: 0.7977 (pttp) cc_final: 0.6643 (tptt) REVERT: D 490 LYS cc_start: 0.7270 (ptpp) cc_final: 0.5649 (mptt) REVERT: E 1 MET cc_start: 0.5052 (ttt) cc_final: 0.4462 (ttt) REVERT: E 69 LYS cc_start: 0.8024 (pttt) cc_final: 0.7304 (mmtt) REVERT: E 221 LYS cc_start: 0.8584 (mttm) cc_final: 0.8364 (mmpt) REVERT: E 481 LYS cc_start: 0.7673 (pttp) cc_final: 0.6317 (tptt) REVERT: F 12 SER cc_start: 0.8026 (t) cc_final: 0.7813 (m) REVERT: F 69 LYS cc_start: 0.8160 (pttt) cc_final: 0.6685 (mmtt) REVERT: F 465 ILE cc_start: 0.7490 (mm) cc_final: 0.7168 (mp) REVERT: G 69 LYS cc_start: 0.8107 (pttt) cc_final: 0.7556 (mmtt) REVERT: G 117 ILE cc_start: 0.8121 (mt) cc_final: 0.7524 (tt) REVERT: G 255 ASN cc_start: 0.5961 (p0) cc_final: 0.5529 (t0) REVERT: G 481 LYS cc_start: 0.7314 (pttp) cc_final: 0.6484 (tptp) REVERT: G 492 ASP cc_start: 0.6181 (m-30) cc_final: 0.5807 (m-30) REVERT: H 24 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7715 (mtmt) REVERT: H 69 LYS cc_start: 0.8551 (pttt) cc_final: 0.7226 (mttt) REVERT: H 117 ILE cc_start: 0.8294 (mt) cc_final: 0.8043 (tp) REVERT: H 213 ASP cc_start: 0.6281 (t70) cc_final: 0.5960 (t0) REVERT: H 295 PHE cc_start: 0.6045 (p90) cc_final: 0.5340 (p90) REVERT: H 315 SER cc_start: 0.6839 (p) cc_final: 0.6448 (m) REVERT: H 481 LYS cc_start: 0.7508 (pttp) cc_final: 0.5639 (mmtp) REVERT: H 503 MET cc_start: 0.7190 (mmt) cc_final: 0.6851 (mmm) REVERT: I 481 LYS cc_start: 0.6970 (pttp) cc_final: 0.6649 (tptt) REVERT: I 490 LYS cc_start: 0.7293 (ptpp) cc_final: 0.6353 (mptt) REVERT: I 503 MET cc_start: 0.5448 (mmt) cc_final: 0.5163 (mmm) REVERT: J 24 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7290 (tmtt) REVERT: J 69 LYS cc_start: 0.8277 (pttt) cc_final: 0.7194 (mmtp) REVERT: J 165 GLN cc_start: 0.7435 (tp40) cc_final: 0.7143 (tp-100) REVERT: J 328 ILE cc_start: 0.8674 (mm) cc_final: 0.8412 (tp) REVERT: J 449 ASP cc_start: 0.5988 (t70) cc_final: 0.5774 (t0) REVERT: J 474 ASN cc_start: 0.6248 (m-40) cc_final: 0.5867 (m110) REVERT: J 481 LYS cc_start: 0.6828 (pttp) cc_final: 0.5399 (tptt) REVERT: K 194 SER cc_start: 0.8528 (m) cc_final: 0.8148 (p) REVERT: K 203 ASN cc_start: 0.5897 (p0) cc_final: 0.5610 (p0) REVERT: K 299 CYS cc_start: 0.7124 (m) cc_final: 0.6815 (m) REVERT: L 30 MET cc_start: 0.7200 (mmm) cc_final: 0.6824 (mmt) REVERT: L 181 VAL cc_start: 0.7488 (t) cc_final: 0.7195 (p) REVERT: L 332 ASP cc_start: 0.5532 (m-30) cc_final: 0.5288 (m-30) REVERT: L 479 GLU cc_start: 0.3245 (tp30) cc_final: 0.2990 (tt0) REVERT: L 503 MET cc_start: 0.6551 (mmt) cc_final: 0.6191 (mmt) REVERT: M 1 MET cc_start: 0.3318 (ttt) cc_final: 0.2856 (ptm) REVERT: M 9 ARG cc_start: 0.6911 (ttt180) cc_final: 0.6609 (pmt-80) REVERT: M 69 LYS cc_start: 0.7654 (pttt) cc_final: 0.7441 (mmtp) REVERT: M 94 MET cc_start: 0.6678 (mtt) cc_final: 0.6466 (mtp) REVERT: M 195 THR cc_start: 0.7038 (m) cc_final: 0.6589 (m) REVERT: M 409 GLU cc_start: 0.7156 (mp0) cc_final: 0.6946 (mp0) REVERT: M 481 LYS cc_start: 0.7097 (pttp) cc_final: 0.5363 (mmtt) REVERT: M 490 LYS cc_start: 0.7518 (ptpp) cc_final: 0.7094 (mptt) REVERT: M 503 MET cc_start: 0.6267 (mmt) cc_final: 0.5985 (mmm) outliers start: 0 outliers final: 0 residues processed: 1203 average time/residue: 0.4933 time to fit residues: 998.7250 Evaluate side-chains 543 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 537 optimal weight: 7.9990 chunk 482 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 325 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 chunk 499 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 303 optimal weight: 8.9990 chunk 371 optimal weight: 6.9990 chunk 578 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 4 GLN B 139 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN C 4 GLN C 48 ASN C 124 GLN C 155 GLN C 165 GLN C 191 GLN C 361 GLN D 99 ASN D 124 GLN D 125 ASN D 191 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN G 293 ASN G 322 GLN H 4 GLN H 361 GLN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN I 124 GLN I 166 ASN I 361 GLN ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN J 440 GLN J 441 GLN K 33 ASN K 243 GLN K 251 ASN L 4 GLN L 361 GLN M 257 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 48750 Z= 0.235 Angle : 0.585 10.686 66378 Z= 0.320 Chirality : 0.047 0.170 7878 Planarity : 0.004 0.042 8567 Dihedral : 4.872 23.096 6669 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.93 % Allowed : 9.13 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 6110 helix: 1.31 (0.11), residues: 2093 sheet: 0.42 (0.19), residues: 936 loop : -1.79 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 383 PHE 0.019 0.002 PHE F 295 TYR 0.019 0.002 TYR H 360 ARG 0.009 0.001 ARG K 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 606 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7637 (mtpt) REVERT: A 186 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6500 (tmtm) REVERT: A 498 GLU cc_start: 0.6835 (tp30) cc_final: 0.6555 (tp30) REVERT: B 9 ARG cc_start: 0.6818 (ttt180) cc_final: 0.6385 (pmt-80) REVERT: B 24 LYS cc_start: 0.7440 (mtmt) cc_final: 0.6954 (tmtt) REVERT: B 69 LYS cc_start: 0.7944 (pttt) cc_final: 0.7491 (mmtp) REVERT: B 162 THR cc_start: 0.7855 (t) cc_final: 0.7575 (p) REVERT: B 481 LYS cc_start: 0.7631 (pttp) cc_final: 0.6567 (tptt) REVERT: B 489 SER cc_start: 0.8223 (p) cc_final: 0.7808 (p) REVERT: C 30 MET cc_start: 0.8140 (mmm) cc_final: 0.7716 (mmm) REVERT: D 1 MET cc_start: 0.4178 (ttt) cc_final: 0.3387 (mmm) REVERT: D 69 LYS cc_start: 0.7620 (pttt) cc_final: 0.7034 (mmtt) REVERT: D 179 THR cc_start: 0.6806 (m) cc_final: 0.6560 (p) REVERT: D 287 LEU cc_start: 0.7641 (mt) cc_final: 0.7283 (tp) REVERT: D 381 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5475 (tt0) REVERT: D 409 GLU cc_start: 0.5903 (mt-10) cc_final: 0.5481 (mt-10) REVERT: E 1 MET cc_start: 0.5142 (ttt) cc_final: 0.4793 (ttt) REVERT: E 147 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7332 (mm-30) REVERT: E 374 ASP cc_start: 0.5316 (t0) cc_final: 0.5068 (t0) REVERT: E 481 LYS cc_start: 0.7588 (pttp) cc_final: 0.6416 (tptt) REVERT: F 69 LYS cc_start: 0.8257 (pttt) cc_final: 0.6917 (mmtp) REVERT: G 1 MET cc_start: 0.5515 (ttt) cc_final: 0.4731 (tpt) REVERT: G 69 LYS cc_start: 0.8164 (pttt) cc_final: 0.7494 (mmtm) REVERT: G 255 ASN cc_start: 0.5847 (p0) cc_final: 0.5469 (t0) REVERT: G 481 LYS cc_start: 0.7050 (pttp) cc_final: 0.6381 (tptp) REVERT: H 1 MET cc_start: 0.4279 (ttt) cc_final: 0.3493 (tmm) REVERT: H 24 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7726 (mtmt) REVERT: H 315 SER cc_start: 0.6864 (p) cc_final: 0.6418 (m) REVERT: H 481 LYS cc_start: 0.7227 (pttp) cc_final: 0.5643 (mmtp) REVERT: I 311 GLU cc_start: 0.4576 (mt-10) cc_final: 0.4286 (mt-10) REVERT: I 490 LYS cc_start: 0.7274 (ptpp) cc_final: 0.6012 (mptt) REVERT: I 503 MET cc_start: 0.5352 (mmt) cc_final: 0.4926 (mmm) REVERT: J 24 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7370 (tmtt) REVERT: J 165 GLN cc_start: 0.7401 (tp40) cc_final: 0.7137 (tp-100) REVERT: J 474 ASN cc_start: 0.6318 (m-40) cc_final: 0.5983 (m-40) REVERT: K 319 MET cc_start: 0.7248 (ttt) cc_final: 0.6961 (ttt) REVERT: L 181 VAL cc_start: 0.7855 (t) cc_final: 0.7574 (p) REVERT: L 420 LEU cc_start: 0.8127 (mp) cc_final: 0.7888 (mt) REVERT: M 1 MET cc_start: 0.3144 (ttt) cc_final: 0.2899 (ptm) REVERT: M 9 ARG cc_start: 0.7045 (ttt180) cc_final: 0.6563 (pmt-80) REVERT: M 94 MET cc_start: 0.6826 (mtt) cc_final: 0.6588 (mtp) REVERT: M 271 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8058 (p) REVERT: M 302 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6004 (mt-10) REVERT: M 355 GLN cc_start: 0.6536 (mm110) cc_final: 0.6289 (mt0) REVERT: M 481 LYS cc_start: 0.7122 (pttp) cc_final: 0.5964 (mmtt) REVERT: M 503 MET cc_start: 0.6170 (mmt) cc_final: 0.5905 (mmm) outliers start: 98 outliers final: 68 residues processed: 676 average time/residue: 0.4901 time to fit residues: 562.5163 Evaluate side-chains 564 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 493 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 288 SER Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 456 VAL Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 321 optimal weight: 30.0000 chunk 179 optimal weight: 9.9990 chunk 481 optimal weight: 5.9990 chunk 393 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 579 optimal weight: 6.9990 chunk 626 optimal weight: 10.0000 chunk 516 optimal weight: 20.0000 chunk 574 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 464 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 293 ASN B 139 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 298 GLN C 441 GLN D 191 GLN D 398 ASN E 293 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN G 125 ASN G 151 ASN H 398 ASN ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN K 33 ASN K 191 GLN K 251 ASN K 426 ASN L 165 GLN L 426 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 48750 Z= 0.249 Angle : 0.575 9.908 66378 Z= 0.314 Chirality : 0.046 0.190 7878 Planarity : 0.004 0.040 8567 Dihedral : 4.896 24.159 6669 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.64 % Allowed : 12.37 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 6110 helix: 1.51 (0.11), residues: 2002 sheet: 0.55 (0.19), residues: 910 loop : -1.87 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 383 PHE 0.020 0.002 PHE D 234 TYR 0.018 0.002 TYR H 484 ARG 0.009 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 522 time to evaluate : 3.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7694 (mtmt) cc_final: 0.7456 (mtpt) REVERT: A 498 GLU cc_start: 0.6816 (tp30) cc_final: 0.6538 (tp30) REVERT: B 24 LYS cc_start: 0.7522 (mtmt) cc_final: 0.7062 (tmtt) REVERT: B 489 SER cc_start: 0.8330 (p) cc_final: 0.7924 (p) REVERT: C 30 MET cc_start: 0.8273 (mmm) cc_final: 0.7884 (mmm) REVERT: D 1 MET cc_start: 0.3676 (ttt) cc_final: 0.3067 (mmm) REVERT: D 191 GLN cc_start: 0.5790 (mm110) cc_final: 0.5513 (mm110) REVERT: D 381 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5428 (tt0) REVERT: D 409 GLU cc_start: 0.6115 (mt-10) cc_final: 0.5726 (mt-10) REVERT: E 1 MET cc_start: 0.5247 (ttt) cc_final: 0.4767 (ttt) REVERT: E 481 LYS cc_start: 0.7637 (pttp) cc_final: 0.6535 (tptt) REVERT: F 69 LYS cc_start: 0.8172 (pttt) cc_final: 0.6877 (mmtp) REVERT: F 381 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5850 (tt0) REVERT: G 1 MET cc_start: 0.5610 (ttt) cc_final: 0.5015 (tpt) REVERT: G 110 PHE cc_start: 0.8159 (m-10) cc_final: 0.7734 (m-10) REVERT: G 255 ASN cc_start: 0.5994 (p0) cc_final: 0.5695 (t0) REVERT: G 381 GLU cc_start: 0.7196 (tp30) cc_final: 0.6944 (tp30) REVERT: G 481 LYS cc_start: 0.7193 (pttp) cc_final: 0.6534 (tptt) REVERT: H 1 MET cc_start: 0.4418 (ttt) cc_final: 0.3114 (tmm) REVERT: H 315 SER cc_start: 0.6966 (p) cc_final: 0.6518 (m) REVERT: H 481 LYS cc_start: 0.7403 (pttp) cc_final: 0.6001 (mmtp) REVERT: I 118 MET cc_start: 0.7115 (mpp) cc_final: 0.6747 (mpp) REVERT: I 481 LYS cc_start: 0.4007 (tptt) cc_final: 0.3625 (tptt) REVERT: I 490 LYS cc_start: 0.7183 (ptpp) cc_final: 0.6224 (mptt) REVERT: I 503 MET cc_start: 0.5107 (mmt) cc_final: 0.4840 (mmm) REVERT: J 1 MET cc_start: 0.3624 (ttt) cc_final: 0.0742 (tpt) REVERT: J 24 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7477 (tmtt) REVERT: J 165 GLN cc_start: 0.7449 (tp40) cc_final: 0.7189 (tp-100) REVERT: J 203 ASN cc_start: 0.6561 (OUTLIER) cc_final: 0.6352 (p0) REVERT: K 98 ASP cc_start: 0.4613 (m-30) cc_final: 0.4372 (m-30) REVERT: L 148 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7917 (mp) REVERT: L 420 LEU cc_start: 0.8076 (mp) cc_final: 0.7851 (mt) REVERT: L 450 ARG cc_start: 0.6551 (ttp80) cc_final: 0.6295 (ttp-110) REVERT: M 1 MET cc_start: 0.3371 (ttt) cc_final: 0.3005 (ptm) REVERT: M 94 MET cc_start: 0.6979 (mtt) cc_final: 0.6726 (mtp) REVERT: M 271 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8275 (p) REVERT: M 302 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6048 (mt-10) REVERT: M 450 ARG cc_start: 0.5835 (tmm-80) cc_final: 0.5328 (ttp-170) REVERT: M 481 LYS cc_start: 0.7017 (pttp) cc_final: 0.5893 (mmtt) REVERT: M 503 MET cc_start: 0.5943 (mmt) cc_final: 0.5504 (mmm) outliers start: 134 outliers final: 96 residues processed: 631 average time/residue: 0.4571 time to fit residues: 489.2642 Evaluate side-chains 561 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 460 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain J residue 430 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 572 optimal weight: 30.0000 chunk 435 optimal weight: 8.9990 chunk 300 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 276 optimal weight: 10.0000 chunk 389 optimal weight: 9.9990 chunk 581 optimal weight: 20.0000 chunk 615 optimal weight: 50.0000 chunk 303 optimal weight: 10.0000 chunk 551 optimal weight: 8.9990 chunk 165 optimal weight: 40.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 4 GLN E 257 GLN E 398 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 GLN G 293 ASN H 48 ASN H 361 GLN I 361 GLN I 398 ASN K 151 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 GLN L 426 ASN M 298 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 48750 Z= 0.331 Angle : 0.638 7.488 66378 Z= 0.351 Chirality : 0.048 0.192 7878 Planarity : 0.004 0.045 8567 Dihedral : 5.383 24.189 6669 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.64 % Allowed : 13.73 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 6110 helix: 1.27 (0.11), residues: 1976 sheet: 0.18 (0.19), residues: 910 loop : -1.94 (0.10), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 480 PHE 0.026 0.002 PHE D 234 TYR 0.019 0.002 TYR H 360 ARG 0.009 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 482 time to evaluate : 4.051 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7148 (ttpp) REVERT: A 321 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: A 498 GLU cc_start: 0.6950 (tp30) cc_final: 0.6678 (tp30) REVERT: B 24 LYS cc_start: 0.7507 (mtmt) cc_final: 0.7104 (tmtt) REVERT: B 321 TYR cc_start: 0.4426 (t80) cc_final: 0.3940 (t80) REVERT: C 30 MET cc_start: 0.8387 (mmm) cc_final: 0.8024 (mmm) REVERT: D 1 MET cc_start: 0.3730 (ttt) cc_final: 0.3207 (mmm) REVERT: D 88 ASN cc_start: 0.7800 (t0) cc_final: 0.7545 (t0) REVERT: D 381 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5472 (tt0) REVERT: D 409 GLU cc_start: 0.6430 (mt-10) cc_final: 0.6098 (mt-10) REVERT: E 194 SER cc_start: 0.7640 (m) cc_final: 0.7155 (p) REVERT: E 481 LYS cc_start: 0.7829 (pttp) cc_final: 0.6628 (tptt) REVERT: G 1 MET cc_start: 0.5756 (ttt) cc_final: 0.5016 (tpt) REVERT: G 295 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.4984 (p90) REVERT: G 481 LYS cc_start: 0.7237 (pttp) cc_final: 0.6366 (tptt) REVERT: H 1 MET cc_start: 0.4531 (ttt) cc_final: 0.2946 (tmm) REVERT: H 228 ASN cc_start: 0.6250 (m-40) cc_final: 0.5857 (t0) REVERT: H 461 TYR cc_start: 0.8697 (p90) cc_final: 0.8232 (p90) REVERT: I 118 MET cc_start: 0.7207 (mpp) cc_final: 0.6897 (mpp) REVERT: I 396 PHE cc_start: 0.8009 (m-10) cc_final: 0.7108 (t80) REVERT: I 481 LYS cc_start: 0.4254 (tptt) cc_final: 0.3908 (tptt) REVERT: I 490 LYS cc_start: 0.7113 (ptpp) cc_final: 0.6072 (mptt) REVERT: I 503 MET cc_start: 0.5414 (mmt) cc_final: 0.5141 (mmm) REVERT: J 1 MET cc_start: 0.3493 (ttt) cc_final: 0.0462 (tpt) REVERT: J 24 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7379 (tmtt) REVERT: J 203 ASN cc_start: 0.7073 (OUTLIER) cc_final: 0.6813 (p0) REVERT: K 295 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.5716 (p90) REVERT: L 24 LYS cc_start: 0.5638 (tttp) cc_final: 0.5383 (ttpp) REVERT: L 148 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7998 (mp) REVERT: L 337 ASN cc_start: 0.6205 (m-40) cc_final: 0.5818 (m110) REVERT: L 420 LEU cc_start: 0.8040 (mp) cc_final: 0.7829 (mt) REVERT: M 1 MET cc_start: 0.3101 (ttt) cc_final: 0.2701 (ptm) REVERT: M 240 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6236 (t0) REVERT: M 295 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.4229 (p90) REVERT: M 450 ARG cc_start: 0.5955 (tmm-80) cc_final: 0.5445 (ttp-170) REVERT: M 481 LYS cc_start: 0.7309 (pttp) cc_final: 0.5825 (mmtt) outliers start: 185 outliers final: 126 residues processed: 633 average time/residue: 0.4577 time to fit residues: 499.3104 Evaluate side-chains 559 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 425 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 456 VAL Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 433 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 195 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 465 ILE Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 512 optimal weight: 2.9990 chunk 349 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 458 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 chunk 525 optimal weight: 7.9990 chunk 425 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 0.0270 chunk 552 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN B 4 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN H 361 GLN I 316 GLN I 361 GLN I 398 ASN ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 ASN M 298 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 48750 Z= 0.140 Angle : 0.509 7.535 66378 Z= 0.277 Chirality : 0.044 0.161 7878 Planarity : 0.003 0.041 8567 Dihedral : 4.718 23.099 6669 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.48 % Allowed : 16.17 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 6110 helix: 1.53 (0.12), residues: 2002 sheet: 0.38 (0.19), residues: 910 loop : -1.89 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 383 PHE 0.014 0.001 PHE K 396 TYR 0.024 0.001 TYR H 484 ARG 0.006 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 475 time to evaluate : 3.948 Fit side-chains REVERT: A 24 LYS cc_start: 0.7603 (mtmt) cc_final: 0.7121 (ttpp) REVERT: A 498 GLU cc_start: 0.6722 (tp30) cc_final: 0.6469 (tp30) REVERT: B 24 LYS cc_start: 0.7559 (mtmt) cc_final: 0.7247 (tmtt) REVERT: B 321 TYR cc_start: 0.4300 (t80) cc_final: 0.3898 (t80) REVERT: C 30 MET cc_start: 0.8276 (mmm) cc_final: 0.7940 (mmm) REVERT: C 467 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7051 (t80) REVERT: D 1 MET cc_start: 0.3618 (ttt) cc_final: 0.3106 (mmm) REVERT: D 30 MET cc_start: 0.7472 (mmm) cc_final: 0.7159 (mmm) REVERT: D 88 ASN cc_start: 0.7789 (t0) cc_final: 0.7551 (t0) REVERT: D 242 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6935 (p0) REVERT: D 381 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5434 (tt0) REVERT: D 409 GLU cc_start: 0.6426 (mt-10) cc_final: 0.6164 (mt-10) REVERT: E 394 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7238 (t70) REVERT: E 481 LYS cc_start: 0.7606 (pttp) cc_final: 0.6545 (tptt) REVERT: F 69 LYS cc_start: 0.7936 (pttt) cc_final: 0.6862 (mmtp) REVERT: F 381 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5988 (tt0) REVERT: F 481 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.5455 (tptt) REVERT: G 193 MET cc_start: 0.8025 (mtm) cc_final: 0.7557 (mtm) REVERT: G 295 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.4395 (p90) REVERT: G 316 GLN cc_start: 0.6726 (tt0) cc_final: 0.6462 (tt0) REVERT: G 481 LYS cc_start: 0.7078 (pttp) cc_final: 0.6304 (tptt) REVERT: H 1 MET cc_start: 0.4288 (ttt) cc_final: 0.2543 (mmm) REVERT: H 295 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.4948 (p90) REVERT: H 316 GLN cc_start: 0.6376 (tt0) cc_final: 0.5986 (tt0) REVERT: H 461 TYR cc_start: 0.8626 (p90) cc_final: 0.8215 (p90) REVERT: I 118 MET cc_start: 0.7165 (mpp) cc_final: 0.6908 (mpp) REVERT: I 396 PHE cc_start: 0.7998 (m-10) cc_final: 0.7202 (t80) REVERT: I 481 LYS cc_start: 0.4145 (tptt) cc_final: 0.3761 (tptt) REVERT: I 490 LYS cc_start: 0.7216 (ptpp) cc_final: 0.6212 (mptt) REVERT: J 1 MET cc_start: 0.3572 (ttt) cc_final: 0.0523 (tpt) REVERT: J 24 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7467 (tmtt) REVERT: J 203 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6662 (p0) REVERT: L 148 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7950 (mp) REVERT: L 337 ASN cc_start: 0.6036 (m-40) cc_final: 0.5705 (m110) REVERT: M 1 MET cc_start: 0.2922 (ttt) cc_final: 0.2585 (ptm) REVERT: M 242 ASP cc_start: 0.7471 (p0) cc_final: 0.6992 (p0) REVERT: M 295 PHE cc_start: 0.5879 (OUTLIER) cc_final: 0.4205 (p90) REVERT: M 450 ARG cc_start: 0.5879 (tmm-80) cc_final: 0.5358 (ttp-170) REVERT: M 481 LYS cc_start: 0.7307 (pttp) cc_final: 0.5959 (mmtt) outliers start: 126 outliers final: 89 residues processed: 572 average time/residue: 0.4592 time to fit residues: 448.9219 Evaluate side-chains 534 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 434 time to evaluate : 3.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 467 PHE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 424 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 207 optimal weight: 7.9990 chunk 554 optimal weight: 50.0000 chunk 121 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 616 optimal weight: 30.0000 chunk 511 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 203 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 124 GLN B 4 GLN C 169 GLN C 285 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN H 169 GLN I 398 ASN K 169 GLN K 426 ASN M 298 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 48750 Z= 0.278 Angle : 0.596 8.292 66378 Z= 0.326 Chirality : 0.047 0.184 7878 Planarity : 0.004 0.044 8567 Dihedral : 5.106 23.896 6669 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.64 % Allowed : 16.33 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.11), residues: 6110 helix: 1.39 (0.12), residues: 1989 sheet: 0.18 (0.19), residues: 910 loop : -1.95 (0.10), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 383 PHE 0.023 0.002 PHE B 234 TYR 0.015 0.002 TYR H 360 ARG 0.009 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 443 time to evaluate : 4.649 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7153 (ttpp) REVERT: A 498 GLU cc_start: 0.6920 (tp30) cc_final: 0.6661 (tp30) REVERT: B 24 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7252 (tmtt) REVERT: B 71 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6561 (mt) REVERT: B 189 ASP cc_start: 0.6306 (OUTLIER) cc_final: 0.5878 (m-30) REVERT: B 321 TYR cc_start: 0.4423 (t80) cc_final: 0.3816 (t80) REVERT: B 381 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6423 (tt0) REVERT: C 30 MET cc_start: 0.8401 (mmm) cc_final: 0.8031 (mmm) REVERT: C 193 MET cc_start: 0.7782 (mtt) cc_final: 0.7132 (mtm) REVERT: C 467 PHE cc_start: 0.7575 (m-80) cc_final: 0.7131 (t80) REVERT: D 1 MET cc_start: 0.3952 (ttt) cc_final: 0.3314 (mmm) REVERT: D 30 MET cc_start: 0.7519 (mmm) cc_final: 0.6856 (mmm) REVERT: D 88 ASN cc_start: 0.7803 (t0) cc_final: 0.7552 (t0) REVERT: D 295 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.5783 (p90) REVERT: D 381 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5407 (tt0) REVERT: D 434 GLU cc_start: 0.5533 (pm20) cc_final: 0.5299 (pm20) REVERT: E 394 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7324 (t70) REVERT: E 481 LYS cc_start: 0.7775 (pttp) cc_final: 0.6619 (tptt) REVERT: F 189 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7035 (t70) REVERT: G 295 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.4752 (p90) REVERT: G 481 LYS cc_start: 0.7237 (pttp) cc_final: 0.6300 (tptp) REVERT: H 1 MET cc_start: 0.4219 (ttt) cc_final: 0.2544 (mmm) REVERT: H 124 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7192 (tp40) REVERT: H 295 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.5168 (p90) REVERT: H 461 TYR cc_start: 0.8687 (p90) cc_final: 0.8251 (p90) REVERT: I 118 MET cc_start: 0.7200 (mpp) cc_final: 0.6689 (mpp) REVERT: I 340 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: I 396 PHE cc_start: 0.8045 (m-10) cc_final: 0.7173 (t80) REVERT: I 490 LYS cc_start: 0.7070 (ptpp) cc_final: 0.6016 (mptt) REVERT: J 1 MET cc_start: 0.3592 (ttt) cc_final: 0.0542 (tpt) REVERT: J 501 ASP cc_start: 0.6348 (p0) cc_final: 0.6056 (p0) REVERT: K 98 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6405 (m-30) REVERT: K 114 VAL cc_start: 0.6652 (t) cc_final: 0.6389 (m) REVERT: K 295 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.5799 (p90) REVERT: K 395 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8172 (tp) REVERT: L 148 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7918 (mp) REVERT: L 337 ASN cc_start: 0.6210 (m-40) cc_final: 0.5858 (m110) REVERT: M 1 MET cc_start: 0.3136 (ttt) cc_final: 0.2683 (ptm) REVERT: M 295 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.4240 (p90) REVERT: M 450 ARG cc_start: 0.6039 (tmm-80) cc_final: 0.5503 (ttp-170) REVERT: M 481 LYS cc_start: 0.7238 (pttp) cc_final: 0.5817 (mmtt) outliers start: 185 outliers final: 135 residues processed: 600 average time/residue: 0.4481 time to fit residues: 464.0079 Evaluate side-chains 566 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 415 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain J residue 467 PHE Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 395 LEU Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 195 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 594 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 450 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 518 optimal weight: 0.4980 chunk 344 optimal weight: 20.0000 chunk 613 optimal weight: 10.0000 chunk 384 optimal weight: 6.9990 chunk 374 optimal weight: 20.0000 chunk 283 optimal weight: 6.9990 overall best weight: 6.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 255 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 398 ASN J 203 ASN L 4 GLN L 206 ASN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48750 Z= 0.224 Angle : 0.554 6.940 66378 Z= 0.303 Chirality : 0.045 0.166 7878 Planarity : 0.003 0.042 8567 Dihedral : 4.950 22.989 6669 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.66 % Allowed : 16.64 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.11), residues: 6110 helix: 1.44 (0.12), residues: 1989 sheet: 0.16 (0.19), residues: 910 loop : -1.94 (0.10), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 383 PHE 0.015 0.001 PHE B 234 TYR 0.012 0.001 TYR C 431 ARG 0.007 0.001 ARG K 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 431 time to evaluate : 3.948 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7613 (mtmt) cc_final: 0.7134 (ttpp) REVERT: A 498 GLU cc_start: 0.6917 (tp30) cc_final: 0.6649 (tp30) REVERT: B 24 LYS cc_start: 0.7576 (mtmt) cc_final: 0.7291 (tmtt) REVERT: B 189 ASP cc_start: 0.6312 (OUTLIER) cc_final: 0.5883 (m-30) REVERT: B 321 TYR cc_start: 0.4329 (t80) cc_final: 0.3628 (t80) REVERT: B 381 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6415 (tt0) REVERT: C 30 MET cc_start: 0.8419 (mmm) cc_final: 0.8097 (mmm) REVERT: C 467 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.7110 (t80) REVERT: D 1 MET cc_start: 0.4309 (ttt) cc_final: 0.3099 (mmm) REVERT: D 30 MET cc_start: 0.7476 (mmm) cc_final: 0.6963 (mmm) REVERT: D 88 ASN cc_start: 0.7773 (t0) cc_final: 0.7535 (t0) REVERT: D 242 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6885 (p0) REVERT: D 295 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.5704 (p90) REVERT: D 381 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5343 (tt0) REVERT: D 434 GLU cc_start: 0.5632 (pm20) cc_final: 0.5334 (pm20) REVERT: E 1 MET cc_start: 0.5034 (OUTLIER) cc_final: 0.4276 (ttt) REVERT: E 394 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7295 (t70) REVERT: E 481 LYS cc_start: 0.7690 (pttp) cc_final: 0.6580 (tptt) REVERT: F 189 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7038 (t70) REVERT: G 295 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.4463 (p90) REVERT: G 481 LYS cc_start: 0.7222 (pttp) cc_final: 0.6238 (tptp) REVERT: H 1 MET cc_start: 0.4153 (OUTLIER) cc_final: 0.2075 (mmm) REVERT: H 124 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7198 (tp40) REVERT: H 295 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.5152 (p90) REVERT: H 461 TYR cc_start: 0.8674 (p90) cc_final: 0.8247 (p90) REVERT: I 118 MET cc_start: 0.7091 (mpp) cc_final: 0.6642 (mpp) REVERT: I 340 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: I 396 PHE cc_start: 0.8054 (m-10) cc_final: 0.7222 (t80) REVERT: I 490 LYS cc_start: 0.7058 (ptpp) cc_final: 0.6015 (mptt) REVERT: J 1 MET cc_start: 0.3581 (ttt) cc_final: 0.0425 (tpt) REVERT: K 295 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.5718 (p90) REVERT: K 395 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8120 (tp) REVERT: L 148 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7877 (mp) REVERT: L 337 ASN cc_start: 0.6074 (m-40) cc_final: 0.5718 (m110) REVERT: M 1 MET cc_start: 0.3185 (ttt) cc_final: 0.2738 (ptm) REVERT: M 137 MET cc_start: 0.4265 (mmp) cc_final: 0.3812 (mmp) REVERT: M 295 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.4260 (p90) REVERT: M 370 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7564 (t) REVERT: M 450 ARG cc_start: 0.6014 (tmm-80) cc_final: 0.5448 (ttp-170) REVERT: M 481 LYS cc_start: 0.7292 (pttp) cc_final: 0.5921 (mmtt) outliers start: 186 outliers final: 144 residues processed: 582 average time/residue: 0.4543 time to fit residues: 452.6484 Evaluate side-chains 578 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 415 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 467 PHE Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 395 LEU Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 379 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 366 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 390 optimal weight: 0.8980 chunk 418 optimal weight: 30.0000 chunk 303 optimal weight: 30.0000 chunk 57 optimal weight: 0.7980 chunk 482 optimal weight: 6.9990 overall best weight: 3.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 48750 Z= 0.160 Angle : 0.512 7.546 66378 Z= 0.278 Chirality : 0.044 0.177 7878 Planarity : 0.003 0.041 8567 Dihedral : 4.639 22.281 6669 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.97 % Allowed : 17.39 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 6110 helix: 1.60 (0.12), residues: 1989 sheet: 0.51 (0.17), residues: 1040 loop : -1.95 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 383 PHE 0.010 0.001 PHE G 234 TYR 0.012 0.001 TYR C 431 ARG 0.007 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 441 time to evaluate : 3.948 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7115 (ttpp) REVERT: A 498 GLU cc_start: 0.6740 (tp30) cc_final: 0.6490 (tp30) REVERT: B 24 LYS cc_start: 0.7566 (mtmt) cc_final: 0.7335 (tmtt) REVERT: B 189 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5831 (m-30) REVERT: B 321 TYR cc_start: 0.4195 (t80) cc_final: 0.3526 (t80) REVERT: B 381 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6340 (tt0) REVERT: C 30 MET cc_start: 0.8378 (mmm) cc_final: 0.8053 (mmm) REVERT: C 467 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7059 (t80) REVERT: D 1 MET cc_start: 0.4388 (ttt) cc_final: 0.3158 (mmm) REVERT: D 30 MET cc_start: 0.7457 (mmm) cc_final: 0.6976 (mmm) REVERT: D 88 ASN cc_start: 0.7788 (t0) cc_final: 0.7554 (t0) REVERT: D 242 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6909 (p0) REVERT: D 295 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.5722 (p90) REVERT: D 381 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5275 (tt0) REVERT: E 1 MET cc_start: 0.4930 (OUTLIER) cc_final: 0.4156 (ttt) REVERT: E 394 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7249 (t70) REVERT: E 481 LYS cc_start: 0.7663 (pttp) cc_final: 0.6551 (tptt) REVERT: F 189 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6961 (t70) REVERT: F 381 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5843 (tt0) REVERT: G 295 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.4265 (p90) REVERT: G 481 LYS cc_start: 0.7205 (pttp) cc_final: 0.6210 (tptp) REVERT: H 1 MET cc_start: 0.4113 (OUTLIER) cc_final: 0.2061 (mmm) REVERT: H 124 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7186 (tp40) REVERT: H 295 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.4969 (p90) REVERT: H 461 TYR cc_start: 0.8637 (p90) cc_final: 0.8236 (p90) REVERT: I 118 MET cc_start: 0.7140 (mpp) cc_final: 0.6694 (mpp) REVERT: I 222 SER cc_start: 0.8251 (t) cc_final: 0.8008 (p) REVERT: I 340 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: I 396 PHE cc_start: 0.8026 (m-10) cc_final: 0.7255 (t80) REVERT: I 413 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8717 (tt) REVERT: I 490 LYS cc_start: 0.7028 (ptpp) cc_final: 0.6009 (mptt) REVERT: J 1 MET cc_start: 0.3601 (ttt) cc_final: 0.0529 (tpt) REVERT: K 295 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.5776 (p90) REVERT: L 148 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7834 (mp) REVERT: L 337 ASN cc_start: 0.6064 (m-40) cc_final: 0.5705 (m110) REVERT: L 451 ARG cc_start: 0.6486 (mtp-110) cc_final: 0.6247 (mtp85) REVERT: M 1 MET cc_start: 0.3068 (ttt) cc_final: 0.2645 (ptm) REVERT: M 137 MET cc_start: 0.4234 (mmp) cc_final: 0.3764 (mmp) REVERT: M 295 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.4267 (p90) REVERT: M 370 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7613 (t) REVERT: M 450 ARG cc_start: 0.5930 (tmm-80) cc_final: 0.5399 (ttp-170) REVERT: M 481 LYS cc_start: 0.7303 (pttp) cc_final: 0.5952 (mmtt) outliers start: 151 outliers final: 115 residues processed: 557 average time/residue: 0.4553 time to fit residues: 436.2781 Evaluate side-chains 557 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 422 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 467 PHE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 558 optimal weight: 20.0000 chunk 588 optimal weight: 20.0000 chunk 536 optimal weight: 30.0000 chunk 572 optimal weight: 20.0000 chunk 344 optimal weight: 6.9990 chunk 249 optimal weight: 20.0000 chunk 449 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 517 optimal weight: 0.9980 chunk 541 optimal weight: 40.0000 chunk 570 optimal weight: 20.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 285 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 398 ASN H 139 ASN H 298 GLN I 398 ASN J 203 ASN M 298 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 48750 Z= 0.342 Angle : 0.639 8.793 66378 Z= 0.350 Chirality : 0.048 0.242 7878 Planarity : 0.004 0.044 8567 Dihedral : 5.328 24.800 6669 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.50 % Allowed : 17.33 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.11), residues: 6110 helix: 1.28 (0.11), residues: 1976 sheet: 0.14 (0.17), residues: 1040 loop : -2.06 (0.10), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 383 PHE 0.024 0.002 PHE B 234 TYR 0.018 0.002 TYR I 67 ARG 0.010 0.001 ARG L 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 417 time to evaluate : 4.046 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7145 (ttpp) REVERT: A 498 GLU cc_start: 0.6930 (tp30) cc_final: 0.6659 (tp30) REVERT: B 24 LYS cc_start: 0.7539 (mtmt) cc_final: 0.7307 (tmtt) REVERT: B 118 MET cc_start: 0.7460 (mtp) cc_final: 0.6979 (mtp) REVERT: B 189 ASP cc_start: 0.6463 (OUTLIER) cc_final: 0.6089 (m-30) REVERT: B 321 TYR cc_start: 0.4509 (t80) cc_final: 0.3587 (t80) REVERT: B 381 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6521 (tt0) REVERT: B 489 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.7961 (t) REVERT: C 30 MET cc_start: 0.8405 (mmm) cc_final: 0.8037 (mmm) REVERT: D 30 MET cc_start: 0.7498 (mmm) cc_final: 0.6840 (mmm) REVERT: D 88 ASN cc_start: 0.7804 (t0) cc_final: 0.7559 (t0) REVERT: D 104 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6278 (mp) REVERT: D 295 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.5675 (p90) REVERT: D 321 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.6677 (t80) REVERT: D 381 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5394 (tt0) REVERT: E 1 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.4129 (ttt) REVERT: E 394 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7337 (t70) REVERT: E 481 LYS cc_start: 0.7821 (pttp) cc_final: 0.6655 (tptt) REVERT: F 189 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6948 (t70) REVERT: G 295 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.4851 (p90) REVERT: G 481 LYS cc_start: 0.7360 (pttp) cc_final: 0.6289 (tptp) REVERT: H 1 MET cc_start: 0.4101 (OUTLIER) cc_final: 0.2016 (mmm) REVERT: H 124 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7172 (tp40) REVERT: H 295 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.5211 (p90) REVERT: H 461 TYR cc_start: 0.8732 (p90) cc_final: 0.8272 (p90) REVERT: I 118 MET cc_start: 0.7111 (mpp) cc_final: 0.6685 (mpp) REVERT: I 340 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: I 396 PHE cc_start: 0.8038 (m-10) cc_final: 0.7163 (t80) REVERT: I 413 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8746 (tt) REVERT: I 484 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7782 (p90) REVERT: I 490 LYS cc_start: 0.7116 (ptpp) cc_final: 0.6004 (mptt) REVERT: J 1 MET cc_start: 0.3497 (ttt) cc_final: 0.0517 (tpt) REVERT: K 295 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.5597 (p90) REVERT: L 148 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7847 (mp) REVERT: L 337 ASN cc_start: 0.6249 (m-40) cc_final: 0.5860 (m110) REVERT: M 1 MET cc_start: 0.3362 (ttt) cc_final: 0.2615 (ptm) REVERT: M 69 LYS cc_start: 0.7866 (pttt) cc_final: 0.7621 (mmtp) REVERT: M 137 MET cc_start: 0.4418 (mmp) cc_final: 0.3908 (mmp) REVERT: M 295 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.4304 (p90) REVERT: M 341 LYS cc_start: 0.4481 (mmtt) cc_final: 0.4255 (mptt) REVERT: M 370 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7617 (t) REVERT: M 450 ARG cc_start: 0.6009 (tmm-80) cc_final: 0.5454 (ttp-170) REVERT: M 481 LYS cc_start: 0.7182 (pttp) cc_final: 0.5768 (mmtt) outliers start: 178 outliers final: 141 residues processed: 565 average time/residue: 0.4578 time to fit residues: 443.8235 Evaluate side-chains 560 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 398 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 375 optimal weight: 6.9990 chunk 605 optimal weight: 30.0000 chunk 369 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 chunk 420 optimal weight: 7.9990 chunk 634 optimal weight: 8.9990 chunk 584 optimal weight: 3.9990 chunk 505 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 390 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 99 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 191 GLN E 398 ASN I 398 ASN ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48750 Z= 0.197 Angle : 0.549 11.271 66378 Z= 0.298 Chirality : 0.045 0.197 7878 Planarity : 0.003 0.043 8567 Dihedral : 4.932 24.556 6669 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.09 % Allowed : 17.78 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 6110 helix: 1.43 (0.12), residues: 1989 sheet: 0.23 (0.17), residues: 1040 loop : -2.02 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 383 PHE 0.012 0.001 PHE G 234 TYR 0.015 0.001 TYR A 360 ARG 0.009 0.001 ARG L 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 420 time to evaluate : 4.050 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7113 (ttpp) REVERT: A 498 GLU cc_start: 0.6774 (tp30) cc_final: 0.6513 (tp30) REVERT: B 186 LYS cc_start: 0.6215 (tptp) cc_final: 0.5114 (ttmm) REVERT: B 321 TYR cc_start: 0.4531 (t80) cc_final: 0.3766 (t80) REVERT: B 381 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6339 (tt0) REVERT: B 489 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7942 (t) REVERT: C 30 MET cc_start: 0.8330 (mmm) cc_final: 0.8024 (mmm) REVERT: C 467 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7221 (t80) REVERT: D 30 MET cc_start: 0.7456 (mmm) cc_final: 0.6973 (mmm) REVERT: D 88 ASN cc_start: 0.7781 (t0) cc_final: 0.7543 (t0) REVERT: D 242 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6898 (p0) REVERT: D 295 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.5494 (p90) REVERT: D 321 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6723 (t80) REVERT: D 381 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5322 (tt0) REVERT: E 1 MET cc_start: 0.5013 (OUTLIER) cc_final: 0.4243 (ttt) REVERT: E 355 GLN cc_start: 0.6794 (mm-40) cc_final: 0.6488 (mm-40) REVERT: E 394 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7289 (t70) REVERT: E 481 LYS cc_start: 0.7697 (pttp) cc_final: 0.6611 (tptt) REVERT: F 189 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7001 (t70) REVERT: G 295 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.4532 (p90) REVERT: G 481 LYS cc_start: 0.7218 (pttp) cc_final: 0.6209 (tptp) REVERT: H 1 MET cc_start: 0.3975 (OUTLIER) cc_final: 0.1942 (mmm) REVERT: H 124 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7185 (tp40) REVERT: H 295 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.4972 (p90) REVERT: H 461 TYR cc_start: 0.8690 (p90) cc_final: 0.8253 (p90) REVERT: I 118 MET cc_start: 0.7145 (mpp) cc_final: 0.6711 (mpp) REVERT: I 222 SER cc_start: 0.8344 (t) cc_final: 0.8100 (p) REVERT: I 340 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: I 396 PHE cc_start: 0.8032 (m-10) cc_final: 0.7220 (t80) REVERT: I 413 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8745 (tt) REVERT: I 484 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7711 (p90) REVERT: I 490 LYS cc_start: 0.7080 (ptpp) cc_final: 0.6008 (mptt) REVERT: J 1 MET cc_start: 0.3582 (ttt) cc_final: 0.0566 (tpt) REVERT: J 245 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7512 (mttm) REVERT: K 295 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.5681 (p90) REVERT: L 148 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7819 (mp) REVERT: L 337 ASN cc_start: 0.6218 (m-40) cc_final: 0.5840 (m110) REVERT: M 1 MET cc_start: 0.3262 (ttt) cc_final: 0.2584 (ptm) REVERT: M 137 MET cc_start: 0.4525 (mmp) cc_final: 0.3997 (mmp) REVERT: M 295 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.4313 (p90) REVERT: M 341 LYS cc_start: 0.4284 (mmtt) cc_final: 0.3986 (mptt) REVERT: M 370 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7597 (t) REVERT: M 450 ARG cc_start: 0.6031 (tmm-80) cc_final: 0.5480 (ttp-170) REVERT: M 481 LYS cc_start: 0.7237 (pttp) cc_final: 0.5883 (mmtt) outliers start: 157 outliers final: 129 residues processed: 551 average time/residue: 0.4501 time to fit residues: 424.9103 Evaluate side-chains 561 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 411 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 467 PHE Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 401 optimal weight: 20.0000 chunk 538 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 465 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 506 optimal weight: 0.9980 chunk 211 optimal weight: 20.0000 chunk 519 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN J 203 ASN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.109699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.098909 restraints weight = 133950.597| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.52 r_work: 0.3427 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 48750 Z= 0.208 Angle : 0.639 59.195 66378 Z= 0.364 Chirality : 0.045 0.636 7878 Planarity : 0.003 0.080 8567 Dihedral : 4.927 24.533 6669 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.11 % Allowed : 17.92 % Favored : 78.97 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 6110 helix: 1.44 (0.12), residues: 1989 sheet: 0.23 (0.17), residues: 1040 loop : -2.01 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 383 PHE 0.011 0.001 PHE G 234 TYR 0.014 0.001 TYR A 360 ARG 0.022 0.000 ARG B 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10305.27 seconds wall clock time: 180 minutes 28.68 seconds (10828.68 seconds total)