Starting phenix.real_space_refine on Mon Nov 18 01:25:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/11_2024/8fvg_29486.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/11_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_29486/11_2024/8fvg_29486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/11_2024/8fvg_29486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/11_2024/8fvg_29486.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/11_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-5513/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: 25.30, per 1000 atoms: 0.53 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: 11.84 Conformation dependent library (CDL) restraints added in 6.0 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: 5.74 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: 18.03 Time building geometry restraints manager: 13.60 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: 3.550 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: 0.100 Extract box with map and model: 2.350 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 98.180 Find NCS groups from input model: 1.810 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.860 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 1203 time to evaluate : 5.270 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: 0.5804 time to fit residues: 1163.2533 Evaluate side-chains 543 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 5.462 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 98 poor density : 606 time to evaluate : 5.350 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: 0.5622 time to fit residues: 640.2753 Evaluate side-chains 564 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 493 time to evaluate : 5.504 ------------------------------------------------------------------------------- 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: 20.0000 chunk 481 optimal weight: 6.9990 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: 6.7990 ------------------------------------------------------------------------------- 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 4 GLN ** 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 48750 Z= 0.256 Angle : 0.582 11.076 66378 Z= 0.317 Chirality : 0.046 0.180 7878 Planarity : 0.004 0.040 8567 Dihedral : 4.932 24.372 6669 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.77 % Allowed : 12.43 % Favored : 84.79 % 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: -0.48 (0.11), residues: 6110 helix: 1.49 (0.11), residues: 2002 sheet: 0.53 (0.19), residues: 910 loop : -1.88 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 163 PHE 0.020 0.002 PHE D 234 TYR 0.019 0.002 TYR H 484 ARG 0.010 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 668 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 527 time to evaluate : 5.505 Fit side-chains REVERT: A 24 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7429 (mtpt) REVERT: A 498 GLU cc_start: 0.6818 (tp30) cc_final: 0.6541 (tp30) REVERT: B 24 LYS cc_start: 0.7527 (mtmt) cc_final: 0.7064 (tmtt) REVERT: B 489 SER cc_start: 0.8333 (p) cc_final: 0.7928 (p) REVERT: C 30 MET cc_start: 0.8278 (mmm) cc_final: 0.7888 (mmm) REVERT: D 1 MET cc_start: 0.3729 (ttt) cc_final: 0.3095 (mmm) REVERT: D 191 GLN cc_start: 0.5745 (mm110) cc_final: 0.5476 (mm110) REVERT: D 381 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5427 (tt0) REVERT: D 409 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5730 (mt-10) REVERT: E 130 ASP cc_start: 0.6786 (OUTLIER) cc_final: 0.6580 (t70) REVERT: E 481 LYS cc_start: 0.7581 (pttp) cc_final: 0.6507 (tptt) REVERT: F 69 LYS cc_start: 0.8178 (pttt) cc_final: 0.6882 (mmtp) REVERT: F 381 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5855 (tt0) REVERT: G 1 MET cc_start: 0.5555 (ttt) cc_final: 0.4961 (tpt) REVERT: G 110 PHE cc_start: 0.8171 (m-10) cc_final: 0.7735 (m-10) REVERT: G 255 ASN cc_start: 0.6056 (p0) cc_final: 0.5768 (t0) REVERT: G 381 GLU cc_start: 0.7205 (tp30) cc_final: 0.6951 (tp30) REVERT: G 481 LYS cc_start: 0.7220 (pttp) cc_final: 0.6414 (tptt) REVERT: H 1 MET cc_start: 0.4198 (ttt) cc_final: 0.2848 (tmm) REVERT: H 315 SER cc_start: 0.6966 (p) cc_final: 0.6520 (m) REVERT: H 481 LYS cc_start: 0.7419 (pttp) cc_final: 0.6015 (mmtp) REVERT: I 118 MET cc_start: 0.7123 (mpp) cc_final: 0.6758 (mpp) REVERT: I 481 LYS cc_start: 0.4011 (tptt) cc_final: 0.3631 (tptt) REVERT: I 490 LYS cc_start: 0.7181 (ptpp) cc_final: 0.6224 (mptt) REVERT: I 503 MET cc_start: 0.5120 (mmt) cc_final: 0.4851 (mmm) REVERT: J 1 MET cc_start: 0.3639 (ttt) cc_final: 0.0756 (tpt) REVERT: J 24 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7512 (tmtt) REVERT: J 165 GLN cc_start: 0.7421 (tp40) cc_final: 0.7173 (tp-100) REVERT: J 203 ASN cc_start: 0.6593 (OUTLIER) cc_final: 0.6357 (p0) REVERT: K 98 ASP cc_start: 0.4774 (OUTLIER) cc_final: 0.4524 (m-30) REVERT: L 148 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7909 (mp) REVERT: L 420 LEU cc_start: 0.8077 (mp) cc_final: 0.7851 (mt) REVERT: L 450 ARG cc_start: 0.6548 (ttp80) cc_final: 0.6299 (ttp-110) REVERT: M 1 MET cc_start: 0.3385 (ttt) cc_final: 0.3006 (ptm) REVERT: M 94 MET cc_start: 0.6971 (mtt) cc_final: 0.6711 (mtp) REVERT: M 271 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8330 (p) REVERT: M 302 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6145 (mt-10) REVERT: M 450 ARG cc_start: 0.5842 (tmm-80) cc_final: 0.5333 (ttp-170) REVERT: M 481 LYS cc_start: 0.7158 (pttp) cc_final: 0.5963 (mmtt) outliers start: 141 outliers final: 101 residues processed: 639 average time/residue: 0.5724 time to fit residues: 618.1507 Evaluate side-chains 571 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 463 time to evaluate : 5.473 ------------------------------------------------------------------------------- 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 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 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 130 ASP 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 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 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 33 ASN Chi-restraints excluded: chain K residue 98 ASP 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 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 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 201 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: 20.0000 chunk 435 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 276 optimal weight: 10.0000 chunk 389 optimal weight: 5.9990 chunk 581 optimal weight: 20.0000 chunk 615 optimal weight: 50.0000 chunk 303 optimal weight: 6.9990 chunk 551 optimal weight: 6.9990 chunk 165 optimal weight: 40.0000 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 316 GLN B 4 GLN E 139 ASN 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 ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 151 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 GLN L 426 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 48750 Z= 0.283 Angle : 0.597 6.755 66378 Z= 0.327 Chirality : 0.047 0.185 7878 Planarity : 0.004 0.043 8567 Dihedral : 5.129 23.932 6669 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.40 % Allowed : 14.07 % Favored : 82.53 % 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: -0.62 (0.11), residues: 6110 helix: 1.38 (0.11), residues: 1989 sheet: 0.29 (0.19), residues: 910 loop : -1.89 (0.10), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 383 PHE 0.023 0.002 PHE B 234 TYR 0.017 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 650 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 477 time to evaluate : 5.504 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7647 (mtmt) cc_final: 0.7127 (ttpp) REVERT: A 321 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: A 498 GLU cc_start: 0.6928 (tp30) cc_final: 0.6650 (tp30) REVERT: B 24 LYS cc_start: 0.7480 (mtmt) cc_final: 0.7180 (tmtt) REVERT: B 321 TYR cc_start: 0.4302 (t80) cc_final: 0.3900 (t80) REVERT: C 30 MET cc_start: 0.8373 (mmm) cc_final: 0.8005 (mmm) REVERT: D 1 MET cc_start: 0.3716 (ttt) cc_final: 0.3199 (mmm) REVERT: D 88 ASN cc_start: 0.7794 (t0) cc_final: 0.7539 (t0) REVERT: D 381 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5423 (tt0) REVERT: D 409 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6092 (mt-10) REVERT: E 481 LYS cc_start: 0.7703 (pttp) cc_final: 0.6583 (tptt) REVERT: F 69 LYS cc_start: 0.8151 (pttt) cc_final: 0.6796 (mmtp) REVERT: G 1 MET cc_start: 0.5562 (ttt) cc_final: 0.4943 (tpt) REVERT: G 295 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.4877 (p90) REVERT: G 481 LYS cc_start: 0.7192 (pttp) cc_final: 0.6355 (tptt) REVERT: H 1 MET cc_start: 0.4391 (ttt) cc_final: 0.2930 (tmm) REVERT: H 228 ASN cc_start: 0.6580 (m-40) cc_final: 0.6168 (t0) REVERT: H 461 TYR cc_start: 0.8675 (p90) cc_final: 0.8234 (p90) REVERT: I 118 MET cc_start: 0.7183 (mpp) cc_final: 0.6879 (mpp) REVERT: I 396 PHE cc_start: 0.7996 (m-10) cc_final: 0.7122 (t80) REVERT: I 490 LYS cc_start: 0.7180 (ptpp) cc_final: 0.6144 (mptt) REVERT: I 503 MET cc_start: 0.5225 (mmt) cc_final: 0.4966 (mmm) REVERT: J 1 MET cc_start: 0.3522 (ttt) cc_final: 0.0571 (tpt) REVERT: J 24 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7445 (tmtt) REVERT: J 203 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6741 (p0) REVERT: L 24 LYS cc_start: 0.5589 (tttp) cc_final: 0.5346 (ttpp) REVERT: L 148 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8010 (mp) REVERT: L 337 ASN cc_start: 0.6113 (m-40) cc_final: 0.5769 (m110) REVERT: L 420 LEU cc_start: 0.8042 (mp) cc_final: 0.7833 (mt) REVERT: M 1 MET cc_start: 0.3067 (ttt) cc_final: 0.2683 (ptm) REVERT: M 94 MET cc_start: 0.7130 (mtt) cc_final: 0.6884 (mtp) REVERT: M 240 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6395 (t0) REVERT: M 295 PHE cc_start: 0.5982 (OUTLIER) cc_final: 0.4237 (p90) REVERT: M 450 ARG cc_start: 0.5862 (tmm-80) cc_final: 0.5367 (ttp-170) REVERT: M 481 LYS cc_start: 0.7179 (pttp) cc_final: 0.5871 (mmtt) outliers start: 173 outliers final: 121 residues processed: 617 average time/residue: 0.5443 time to fit residues: 574.8698 Evaluate side-chains 556 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 428 time to evaluate : 5.415 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain C residue 2 ILE 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 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 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 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 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 481 LYS 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 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 370 THR 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 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 33 ASN 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 444 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 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: 7.9990 chunk 349 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 458 optimal weight: 20.0000 chunk 254 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 425 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 552 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 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 ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN ** F 57 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 33 ASN K 169 GLN K 251 ASN ** K 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 48750 Z= 0.196 Angle : 0.535 6.862 66378 Z= 0.292 Chirality : 0.045 0.177 7878 Planarity : 0.003 0.042 8567 Dihedral : 4.842 23.189 6669 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.19 % Allowed : 15.62 % Favored : 81.19 % 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: -0.59 (0.11), residues: 6110 helix: 1.47 (0.12), residues: 2002 sheet: 0.24 (0.18), residues: 936 loop : -1.92 (0.10), residues: 3172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 383 PHE 0.015 0.001 PHE K 396 TYR 0.021 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 626 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 464 time to evaluate : 5.646 Fit side-chains REVERT: A 24 LYS cc_start: 0.7632 (mtmt) cc_final: 0.7116 (ttpp) REVERT: A 498 GLU cc_start: 0.6838 (tp30) cc_final: 0.6580 (tp30) REVERT: B 24 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7260 (tmtt) REVERT: B 321 TYR cc_start: 0.4287 (t80) cc_final: 0.3987 (t80) REVERT: C 30 MET cc_start: 0.8383 (mmm) cc_final: 0.8048 (mmm) REVERT: C 467 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.7005 (t80) REVERT: D 1 MET cc_start: 0.3649 (ttt) cc_final: 0.3146 (mmm) REVERT: D 30 MET cc_start: 0.7483 (mmm) cc_final: 0.7151 (mmm) REVERT: D 88 ASN cc_start: 0.7779 (t0) cc_final: 0.7533 (t0) REVERT: D 137 MET cc_start: 0.6569 (mtt) cc_final: 0.6273 (mtt) REVERT: D 381 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5388 (tt0) REVERT: D 434 GLU cc_start: 0.5751 (pm20) cc_final: 0.5475 (pm20) REVERT: E 394 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7266 (t70) REVERT: E 481 LYS cc_start: 0.7654 (pttp) cc_final: 0.6572 (tptt) REVERT: F 69 LYS cc_start: 0.7974 (pttt) cc_final: 0.6858 (mmtp) REVERT: F 381 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5868 (tt0) REVERT: F 481 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.5502 (tptt) REVERT: G 1 MET cc_start: 0.5358 (ttt) cc_final: 0.4961 (tpt) REVERT: G 295 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.4468 (p90) REVERT: G 316 GLN cc_start: 0.6486 (tt0) cc_final: 0.6166 (tt0) REVERT: G 481 LYS cc_start: 0.7145 (pttp) cc_final: 0.6343 (tptt) REVERT: H 1 MET cc_start: 0.4300 (ttt) cc_final: 0.2545 (mmm) REVERT: H 228 ASN cc_start: 0.6199 (m-40) cc_final: 0.5907 (t0) REVERT: H 295 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5032 (p90) REVERT: H 316 GLN cc_start: 0.6417 (tt0) cc_final: 0.6060 (tt0) REVERT: H 461 TYR cc_start: 0.8654 (p90) cc_final: 0.8235 (p90) REVERT: I 481 LYS cc_start: 0.3922 (tptt) cc_final: 0.3555 (tptt) REVERT: I 490 LYS cc_start: 0.7246 (ptpp) cc_final: 0.6196 (mptt) REVERT: I 503 MET cc_start: 0.5332 (mmt) cc_final: 0.5069 (mmm) REVERT: J 1 MET cc_start: 0.3631 (ttt) cc_final: 0.0543 (tpt) REVERT: J 24 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7461 (tmtt) REVERT: J 203 ASN cc_start: 0.6879 (OUTLIER) cc_final: 0.6635 (p0) REVERT: K 295 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.5737 (p90) REVERT: L 148 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7960 (mp) REVERT: L 337 ASN cc_start: 0.6041 (m-40) cc_final: 0.5713 (m110) REVERT: M 1 MET cc_start: 0.2971 (ttt) cc_final: 0.2598 (ptm) REVERT: M 94 MET cc_start: 0.7057 (mtt) cc_final: 0.6821 (mtp) REVERT: M 295 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.4208 (p90) REVERT: M 450 ARG cc_start: 0.5908 (tmm-80) cc_final: 0.5364 (ttp-170) REVERT: M 481 LYS cc_start: 0.7227 (pttp) cc_final: 0.5850 (mmtt) outliers start: 162 outliers final: 116 residues processed: 596 average time/residue: 0.5918 time to fit residues: 603.1067 Evaluate side-chains 558 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 431 time to evaluate : 5.386 ------------------------------------------------------------------------------- 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 179 THR Chi-restraints excluded: chain A residue 295 PHE 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 100 LEU 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 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 98 ASP 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 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 80 SER 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 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 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 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 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 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 72 SER 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 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 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 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 I residue 433 LYS Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain J residue 12 SER 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 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 96 VAL Chi-restraints excluded: chain K residue 242 ASP 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 172 LEU Chi-restraints excluded: chain L residue 216 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 399 VAL 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 172 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 207 optimal weight: 4.9990 chunk 554 optimal weight: 50.0000 chunk 121 optimal weight: 0.6980 chunk 361 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 616 optimal weight: 6.9990 chunk 511 optimal weight: 7.9990 chunk 285 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 203 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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** D 155 GLN D 191 GLN D 398 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 426 ASN L 4 GLN M 298 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48750 Z= 0.184 Angle : 0.528 7.322 66378 Z= 0.287 Chirality : 0.044 0.185 7878 Planarity : 0.003 0.041 8567 Dihedral : 4.699 22.405 6669 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.86 % Allowed : 15.74 % Favored : 80.41 % 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: -0.52 (0.11), residues: 6110 helix: 1.54 (0.12), residues: 2002 sheet: 0.26 (0.18), residues: 936 loop : -1.89 (0.10), residues: 3172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 383 PHE 0.013 0.001 PHE B 234 TYR 0.019 0.001 TYR H 484 ARG 0.008 0.000 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 647 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 451 time to evaluate : 5.564 Fit side-chains REVERT: A 24 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7143 (ttpp) REVERT: B 24 LYS cc_start: 0.7564 (mtmt) cc_final: 0.7289 (tmtt) REVERT: B 71 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6744 (mt) REVERT: B 321 TYR cc_start: 0.4225 (t80) cc_final: 0.3813 (t80) REVERT: B 381 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6358 (tt0) REVERT: C 30 MET cc_start: 0.8398 (mmm) cc_final: 0.8053 (mmm) REVERT: C 467 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7111 (t80) REVERT: D 1 MET cc_start: 0.3839 (ttt) cc_final: 0.3249 (mmm) REVERT: D 30 MET cc_start: 0.7494 (mmm) cc_final: 0.6980 (mmm) REVERT: D 88 ASN cc_start: 0.7801 (t0) cc_final: 0.7559 (t0) REVERT: D 137 MET cc_start: 0.6545 (mtt) cc_final: 0.6341 (mtt) REVERT: D 242 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6889 (p0) REVERT: D 295 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.5941 (p90) REVERT: D 381 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5333 (tt0) REVERT: D 434 GLU cc_start: 0.5606 (pm20) cc_final: 0.5347 (pm20) REVERT: E 394 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7243 (t70) REVERT: E 481 LYS cc_start: 0.7628 (pttp) cc_final: 0.6563 (tptt) REVERT: F 189 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6894 (t70) REVERT: F 381 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5785 (tt0) REVERT: F 481 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.5454 (tptt) REVERT: G 110 PHE cc_start: 0.8153 (m-10) cc_final: 0.7878 (m-10) REVERT: G 295 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.4391 (p90) REVERT: G 321 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: G 481 LYS cc_start: 0.7108 (pttp) cc_final: 0.6321 (tptt) REVERT: H 1 MET cc_start: 0.4210 (ttt) cc_final: 0.2471 (mmm) REVERT: H 228 ASN cc_start: 0.6147 (m-40) cc_final: 0.5929 (t0) REVERT: H 295 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.5012 (p90) REVERT: H 461 TYR cc_start: 0.8644 (p90) cc_final: 0.8245 (p90) REVERT: I 118 MET cc_start: 0.7237 (mpp) cc_final: 0.6711 (mpp) REVERT: I 340 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: I 396 PHE cc_start: 0.8036 (m-10) cc_final: 0.7245 (t80) REVERT: I 481 LYS cc_start: 0.3811 (tptt) cc_final: 0.3452 (tptt) REVERT: I 490 LYS cc_start: 0.7231 (ptpp) cc_final: 0.6155 (mptt) REVERT: J 1 MET cc_start: 0.3584 (ttt) cc_final: 0.0540 (tpt) REVERT: J 24 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7459 (tmtt) REVERT: J 501 ASP cc_start: 0.6527 (p0) cc_final: 0.6240 (p0) REVERT: K 98 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.5876 (m-30) REVERT: K 114 VAL cc_start: 0.6646 (t) cc_final: 0.6390 (m) REVERT: K 295 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.5757 (p90) REVERT: L 148 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7923 (mp) REVERT: L 337 ASN cc_start: 0.6054 (m-40) cc_final: 0.5719 (m110) REVERT: M 1 MET cc_start: 0.2980 (ttt) cc_final: 0.2577 (ptm) REVERT: M 94 MET cc_start: 0.7035 (mtt) cc_final: 0.6789 (mtp) REVERT: M 295 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.4182 (p90) REVERT: M 302 GLU cc_start: 0.6632 (mt-10) cc_final: 0.5948 (mt-10) REVERT: M 370 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7405 (t) REVERT: M 450 ARG cc_start: 0.5927 (tmm-80) cc_final: 0.5395 (ttp-170) REVERT: M 481 LYS cc_start: 0.7470 (pttp) cc_final: 0.6050 (mmtt) outliers start: 196 outliers final: 149 residues processed: 612 average time/residue: 0.5580 time to fit residues: 584.2908 Evaluate side-chains 596 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 428 time to evaluate : 5.406 ------------------------------------------------------------------------------- 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 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 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 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 96 VAL Chi-restraints excluded: chain C residue 98 ASP 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 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 80 SER Chi-restraints excluded: chain D residue 98 ASP 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 96 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 MET 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 370 THR Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 98 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 189 ASP Chi-restraints excluded: chain F residue 295 PHE 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 98 ASP Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 321 TYR 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 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 321 TYR 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 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 428 THR Chi-restraints excluded: chain J residue 430 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 96 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 242 ASP 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 162 THR 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 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 172 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 594 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 351 optimal weight: 2.9990 chunk 450 optimal weight: 5.9990 chunk 348 optimal weight: 20.0000 chunk 518 optimal weight: 0.9980 chunk 344 optimal weight: 20.0000 chunk 613 optimal weight: 10.0000 chunk 384 optimal weight: 8.9990 chunk 374 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN K 33 ASN L 206 ASN M 298 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 48750 Z= 0.149 Angle : 0.501 6.898 66378 Z= 0.271 Chirality : 0.044 0.176 7878 Planarity : 0.003 0.039 8567 Dihedral : 4.461 21.605 6669 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.21 % Allowed : 16.76 % 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: -0.38 (0.11), residues: 6110 helix: 1.65 (0.12), residues: 2002 sheet: 0.55 (0.19), residues: 910 loop : -1.86 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 383 PHE 0.009 0.001 PHE J 295 TYR 0.018 0.001 TYR H 484 ARG 0.006 0.000 ARG A 450 *********************** 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 618 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 455 time to evaluate : 5.626 Fit side-chains REVERT: A 24 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7144 (ttpp) REVERT: B 24 LYS cc_start: 0.7619 (mtmt) cc_final: 0.7328 (tmtt) REVERT: B 71 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6644 (mt) REVERT: B 321 TYR cc_start: 0.4134 (t80) cc_final: 0.3701 (t80) REVERT: B 381 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6270 (tt0) REVERT: C 30 MET cc_start: 0.8334 (mmm) cc_final: 0.7989 (mmm) REVERT: C 467 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.7104 (t80) REVERT: D 1 MET cc_start: 0.4119 (ttt) cc_final: 0.2976 (mmm) REVERT: D 30 MET cc_start: 0.7541 (mmm) cc_final: 0.7064 (mmm) REVERT: D 88 ASN cc_start: 0.7777 (t0) cc_final: 0.7546 (t0) REVERT: D 242 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6908 (p0) REVERT: D 295 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6028 (p90) REVERT: D 381 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5283 (tt0) REVERT: D 434 GLU cc_start: 0.5645 (pm20) cc_final: 0.5359 (pm20) REVERT: E 394 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7246 (t70) REVERT: E 481 LYS cc_start: 0.7568 (pttp) cc_final: 0.6530 (tptt) REVERT: F 189 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6889 (t70) REVERT: F 381 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: F 481 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.5419 (tptt) REVERT: G 110 PHE cc_start: 0.8190 (m-10) cc_final: 0.7912 (m-10) REVERT: G 295 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.4343 (p90) REVERT: G 481 LYS cc_start: 0.7055 (pttp) cc_final: 0.6228 (tptp) REVERT: H 1 MET cc_start: 0.4157 (ttt) cc_final: 0.2081 (mmm) REVERT: H 295 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.4933 (p90) REVERT: I 118 MET cc_start: 0.7235 (mpp) cc_final: 0.6730 (mpp) REVERT: I 340 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: I 481 LYS cc_start: 0.4186 (tptt) cc_final: 0.3867 (tptt) REVERT: I 490 LYS cc_start: 0.7247 (ptpp) cc_final: 0.6192 (mptt) REVERT: J 1 MET cc_start: 0.3446 (ttt) cc_final: 0.0373 (tpt) REVERT: J 24 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7479 (tmtt) REVERT: K 114 VAL cc_start: 0.6425 (t) cc_final: 0.6166 (m) REVERT: K 295 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.5802 (p90) REVERT: L 148 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7838 (mp) REVERT: L 337 ASN cc_start: 0.6050 (m-40) cc_final: 0.5703 (m110) REVERT: M 1 MET cc_start: 0.3030 (ttt) cc_final: 0.2639 (ptm) REVERT: M 94 MET cc_start: 0.7014 (mtt) cc_final: 0.6775 (mtp) REVERT: M 137 MET cc_start: 0.4188 (mmp) cc_final: 0.3715 (mmp) REVERT: M 295 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.4239 (p90) REVERT: M 302 GLU cc_start: 0.6607 (mt-10) cc_final: 0.5905 (mt-10) REVERT: M 370 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7578 (t) REVERT: M 450 ARG cc_start: 0.5873 (tmm-80) cc_final: 0.5357 (ttp-170) REVERT: M 477 LEU cc_start: 0.8116 (mm) cc_final: 0.7852 (mm) REVERT: M 481 LYS cc_start: 0.7400 (pttp) cc_final: 0.5995 (mmtt) outliers start: 163 outliers final: 127 residues processed: 581 average time/residue: 0.5534 time to fit residues: 547.5177 Evaluate side-chains 576 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 432 time to evaluate : 5.503 ------------------------------------------------------------------------------- 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 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 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 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 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 96 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 148 ILE 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 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 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 96 VAL Chi-restraints excluded: chain E residue 118 MET 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 F residue 98 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 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 F residue 481 LYS Chi-restraints excluded: chain G residue 52 SER 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 397 LEU 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 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 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 GLN 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 467 PHE 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 42 ILE Chi-restraints excluded: chain J residue 115 LEU 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 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 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 172 LEU Chi-restraints excluded: chain L residue 192 ASP 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 M residue 96 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 225 VAL 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 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: 8.9990 chunk 366 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 390 optimal weight: 20.0000 chunk 418 optimal weight: 6.9990 chunk 303 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 chunk 482 optimal weight: 6.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 191 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 361 GLN I 398 ASN J 203 ASN K 33 ASN M 298 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 48750 Z= 0.278 Angle : 0.593 6.467 66378 Z= 0.324 Chirality : 0.046 0.187 7878 Planarity : 0.004 0.042 8567 Dihedral : 4.985 23.608 6669 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.64 % Allowed : 16.49 % Favored : 79.87 % 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: -0.62 (0.11), residues: 6110 helix: 1.44 (0.12), residues: 1989 sheet: 0.20 (0.19), residues: 910 loop : -1.90 (0.10), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 383 PHE 0.022 0.002 PHE B 234 TYR 0.016 0.002 TYR J 378 ARG 0.007 0.001 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 613 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 428 time to evaluate : 5.461 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7614 (mtmt) cc_final: 0.7136 (ttpp) REVERT: A 498 GLU cc_start: 0.6778 (tp30) cc_final: 0.6536 (tp30) REVERT: B 24 LYS cc_start: 0.7559 (mtmt) cc_final: 0.7309 (tmtt) REVERT: B 321 TYR cc_start: 0.4486 (t80) cc_final: 0.3688 (t80) REVERT: B 381 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6413 (tt0) REVERT: C 30 MET cc_start: 0.8404 (mmm) cc_final: 0.8029 (mmm) REVERT: C 467 PHE cc_start: 0.7579 (m-80) cc_final: 0.7129 (t80) REVERT: D 30 MET cc_start: 0.7530 (mmm) cc_final: 0.6865 (mmm) REVERT: D 88 ASN cc_start: 0.7802 (t0) cc_final: 0.7553 (t0) REVERT: D 98 ASP cc_start: 0.5539 (OUTLIER) cc_final: 0.5333 (m-30) REVERT: D 295 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.5833 (p90) REVERT: D 321 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.7325 (t80) REVERT: D 381 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5331 (tt0) REVERT: E 394 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7336 (t70) REVERT: E 481 LYS cc_start: 0.7747 (pttp) cc_final: 0.6616 (tptt) REVERT: F 98 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.5306 (m-30) REVERT: F 189 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6994 (t70) REVERT: G 110 PHE cc_start: 0.8187 (m-10) cc_final: 0.7880 (m-10) REVERT: G 295 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.4795 (p90) REVERT: G 481 LYS cc_start: 0.7281 (pttp) cc_final: 0.6293 (tptp) REVERT: H 1 MET cc_start: 0.4154 (OUTLIER) cc_final: 0.2117 (mmm) REVERT: H 295 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.5193 (p90) REVERT: H 461 TYR cc_start: 0.8681 (p90) cc_final: 0.8273 (p90) REVERT: I 118 MET cc_start: 0.7101 (mpp) cc_final: 0.6665 (mpp) REVERT: I 340 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: I 396 PHE cc_start: 0.8081 (m-10) cc_final: 0.7212 (t80) REVERT: I 413 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8746 (tt) REVERT: I 490 LYS cc_start: 0.7069 (ptpp) cc_final: 0.6005 (mptt) REVERT: J 1 MET cc_start: 0.3547 (ttt) cc_final: 0.0507 (tpt) REVERT: K 295 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.5829 (p90) REVERT: L 148 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7890 (mp) REVERT: L 337 ASN cc_start: 0.6213 (m-40) cc_final: 0.5847 (m110) REVERT: M 1 MET cc_start: 0.3299 (ttt) cc_final: 0.2619 (ptm) REVERT: M 94 MET cc_start: 0.7046 (mtt) cc_final: 0.6816 (mtp) REVERT: M 137 MET cc_start: 0.4222 (mmp) cc_final: 0.3765 (mmp) REVERT: M 295 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.4236 (p90) REVERT: M 302 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6027 (mt-10) REVERT: M 370 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7639 (t) REVERT: M 450 ARG cc_start: 0.6025 (tmm-80) cc_final: 0.5467 (ttp-170) REVERT: M 481 LYS cc_start: 0.7384 (pttp) cc_final: 0.6010 (mmtt) outliers start: 185 outliers final: 152 residues processed: 582 average time/residue: 0.5534 time to fit residues: 551.0773 Evaluate side-chains 577 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 408 time to evaluate : 5.480 ------------------------------------------------------------------------------- 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 98 ASP 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 100 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 148 ILE 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 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 114 VAL Chi-restraints excluded: chain C residue 148 ILE 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 80 SER Chi-restraints excluded: chain D residue 98 ASP 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 96 VAL Chi-restraints excluded: chain E residue 118 MET 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 98 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 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 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 397 LEU 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 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 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 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 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 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 96 VAL Chi-restraints excluded: chain K residue 160 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 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP 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 428 THR 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 172 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL 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 334 THR 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: 0.9990 chunk 249 optimal weight: 0.0980 chunk 449 optimal weight: 20.0000 chunk 175 optimal weight: 50.0000 chunk 517 optimal weight: 20.0000 chunk 541 optimal weight: 30.0000 chunk 570 optimal weight: 9.9990 overall best weight: 10.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN C 285 ASN D 191 GLN E 255 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN H 298 GLN H 361 GLN K 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4348 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= 0.342 Angle : 0.641 10.247 66378 Z= 0.350 Chirality : 0.048 0.211 7878 Planarity : 0.004 0.043 8567 Dihedral : 5.316 24.325 6669 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.58 % Allowed : 16.90 % Favored : 79.52 % 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: -0.86 (0.11), residues: 6110 helix: 1.19 (0.11), residues: 1989 sheet: 0.01 (0.19), residues: 910 loop : -1.99 (0.10), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 480 PHE 0.024 0.002 PHE B 234 TYR 0.019 0.002 TYR G 442 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 601 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 419 time to evaluate : 5.481 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7628 (mtmt) cc_final: 0.7145 (ttpp) REVERT: A 498 GLU cc_start: 0.6937 (tp30) cc_final: 0.6682 (tp30) REVERT: B 24 LYS cc_start: 0.7534 (mtmt) cc_final: 0.7304 (tmtt) REVERT: B 118 MET cc_start: 0.7456 (mtp) cc_final: 0.6981 (mtp) REVERT: B 321 TYR cc_start: 0.4533 (t80) cc_final: 0.3667 (t80) REVERT: B 381 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: B 489 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7964 (t) REVERT: C 30 MET cc_start: 0.8345 (mmm) cc_final: 0.7988 (mmm) REVERT: C 467 PHE cc_start: 0.7597 (m-80) cc_final: 0.7161 (t80) REVERT: D 30 MET cc_start: 0.7513 (mmm) cc_final: 0.6841 (mmm) REVERT: D 88 ASN cc_start: 0.7813 (t0) cc_final: 0.7562 (t0) REVERT: D 295 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.5710 (p90) REVERT: D 321 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7174 (t80) REVERT: D 381 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5393 (tt0) REVERT: E 394 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7297 (t70) REVERT: E 481 LYS cc_start: 0.7764 (pttp) cc_final: 0.6637 (tptt) REVERT: F 98 ASP cc_start: 0.6105 (OUTLIER) cc_final: 0.5494 (m-30) REVERT: F 189 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7012 (t70) REVERT: G 295 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.4943 (p90) REVERT: G 481 LYS cc_start: 0.7314 (pttp) cc_final: 0.6267 (tptp) REVERT: H 1 MET cc_start: 0.4117 (OUTLIER) cc_final: 0.2102 (mmm) REVERT: H 295 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5126 (p90) REVERT: H 461 TYR cc_start: 0.8731 (p90) cc_final: 0.8270 (p90) REVERT: I 118 MET cc_start: 0.7109 (mpp) cc_final: 0.6675 (mpp) REVERT: I 340 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: I 396 PHE cc_start: 0.8073 (m-10) cc_final: 0.7197 (t80) REVERT: I 413 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8772 (tt) REVERT: I 490 LYS cc_start: 0.7105 (ptpp) cc_final: 0.6006 (mptt) REVERT: J 1 MET cc_start: 0.3566 (ttt) cc_final: 0.0569 (tpt) REVERT: J 311 GLU cc_start: 0.3685 (mt-10) cc_final: 0.3065 (tt0) REVERT: K 295 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.5598 (p90) REVERT: L 148 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7848 (mp) REVERT: L 337 ASN cc_start: 0.6228 (m-40) cc_final: 0.5945 (m110) REVERT: M 1 MET cc_start: 0.3414 (ttt) cc_final: 0.2693 (ptm) REVERT: M 94 MET cc_start: 0.7058 (mtt) cc_final: 0.6792 (mtp) REVERT: M 137 MET cc_start: 0.4374 (mmp) cc_final: 0.3909 (mmp) REVERT: M 295 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.4351 (p90) REVERT: M 302 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6168 (mt-10) REVERT: M 341 LYS cc_start: 0.4466 (mmtt) cc_final: 0.4229 (mptt) REVERT: M 370 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7622 (t) REVERT: M 450 ARG cc_start: 0.6006 (tmm-80) cc_final: 0.5456 (ttp-170) REVERT: M 481 LYS cc_start: 0.7199 (pttp) cc_final: 0.5794 (mmtt) outliers start: 182 outliers final: 151 residues processed: 574 average time/residue: 0.5605 time to fit residues: 552.7913 Evaluate side-chains 576 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 408 time to evaluate : 5.675 ------------------------------------------------------------------------------- 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 319 MET 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 127 THR Chi-restraints excluded: chain B residue 148 ILE 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 446 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 25 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 148 ILE 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 80 SER 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 96 VAL Chi-restraints excluded: chain E residue 118 MET 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 98 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 172 LEU 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 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 397 LEU 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 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 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 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 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 160 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 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP 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 465 ILE 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 172 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL 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 334 THR 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 375 optimal weight: 0.0980 chunk 605 optimal weight: 30.0000 chunk 369 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 420 optimal weight: 9.9990 chunk 634 optimal weight: 9.9990 chunk 584 optimal weight: 40.0000 chunk 505 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 390 optimal weight: 0.9980 chunk 309 optimal weight: 20.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- 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 191 GLN E 99 ASN I 398 ASN J 203 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4361 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= 0.218 Angle : 0.563 8.324 66378 Z= 0.306 Chirality : 0.045 0.199 7878 Planarity : 0.003 0.043 8567 Dihedral : 4.997 22.963 6669 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.40 % Allowed : 17.27 % Favored : 79.32 % 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: -0.66 (0.11), residues: 6110 helix: 1.42 (0.12), residues: 1976 sheet: 0.19 (0.17), residues: 1040 loop : -2.01 (0.10), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 383 PHE 0.014 0.001 PHE B 234 TYR 0.012 0.001 TYR I 67 ARG 0.009 0.001 ARG B 451 ********************** 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 600 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 427 time to evaluate : 5.630 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7120 (ttpp) REVERT: A 498 GLU cc_start: 0.6768 (tp30) cc_final: 0.6530 (tp30) REVERT: B 321 TYR cc_start: 0.4493 (t80) cc_final: 0.3828 (t80) REVERT: B 381 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: B 489 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.7934 (t) REVERT: C 30 MET cc_start: 0.8328 (mmm) cc_final: 0.8006 (mmm) REVERT: C 467 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7165 (t80) REVERT: D 30 MET cc_start: 0.7500 (mmm) cc_final: 0.6872 (mmm) REVERT: D 88 ASN cc_start: 0.7774 (t0) cc_final: 0.7542 (t0) REVERT: D 242 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6890 (p0) REVERT: D 295 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.5598 (p90) REVERT: D 321 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7250 (t80) REVERT: D 381 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5344 (tt0) REVERT: E 394 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7277 (t70) REVERT: E 481 LYS cc_start: 0.7731 (pttp) cc_final: 0.6619 (tptt) REVERT: F 98 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5429 (m-30) REVERT: F 189 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6971 (t70) REVERT: G 295 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.4597 (p90) REVERT: G 319 MET cc_start: 0.7930 (tpp) cc_final: 0.7726 (tpt) REVERT: G 481 LYS cc_start: 0.7279 (pttp) cc_final: 0.6228 (tptp) REVERT: H 1 MET cc_start: 0.3984 (OUTLIER) cc_final: 0.2035 (mmm) REVERT: H 295 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5100 (p90) REVERT: H 461 TYR cc_start: 0.8700 (p90) cc_final: 0.8253 (p90) REVERT: I 118 MET cc_start: 0.7145 (mpp) cc_final: 0.6704 (mpp) REVERT: I 340 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: I 396 PHE cc_start: 0.8010 (m-10) cc_final: 0.7231 (t80) REVERT: I 413 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8740 (tt) REVERT: I 490 LYS cc_start: 0.7103 (ptpp) cc_final: 0.6019 (mptt) REVERT: J 1 MET cc_start: 0.3451 (ttt) cc_final: 0.0506 (tpt) REVERT: J 245 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7518 (mttm) REVERT: K 295 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.5818 (p90) REVERT: L 148 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7784 (mp) REVERT: L 337 ASN cc_start: 0.6210 (m-40) cc_final: 0.5845 (m110) REVERT: M 1 MET cc_start: 0.3375 (ttt) cc_final: 0.2666 (ptm) REVERT: M 94 MET cc_start: 0.7003 (mtt) cc_final: 0.6752 (mtp) REVERT: M 137 MET cc_start: 0.4487 (mmp) cc_final: 0.3962 (mmp) REVERT: M 295 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.4302 (p90) REVERT: M 302 GLU cc_start: 0.6657 (mt-10) cc_final: 0.5966 (mt-10) REVERT: M 341 LYS cc_start: 0.4377 (mmtt) cc_final: 0.4072 (mptt) REVERT: M 370 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7608 (t) REVERT: M 450 ARG cc_start: 0.6016 (tmm-80) cc_final: 0.5465 (ttp-170) REVERT: M 481 LYS cc_start: 0.7211 (pttp) cc_final: 0.5797 (mmtt) outliers start: 173 outliers final: 145 residues processed: 567 average time/residue: 0.5526 time to fit residues: 536.7975 Evaluate side-chains 573 residues out of total 5083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 409 time to evaluate : 5.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 119 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 148 ILE 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 446 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 114 VAL 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 80 SER Chi-restraints excluded: chain D residue 98 ASP 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 96 VAL Chi-restraints excluded: chain E residue 118 MET 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 F residue 98 ASP Chi-restraints excluded: chain F residue 116 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 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 397 LEU 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 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 H residue 467 PHE 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 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 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 411 MET 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 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 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 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 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 172 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL 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 334 THR 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: 6.9990 chunk 154 optimal weight: 10.0000 chunk 465 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 506 optimal weight: 40.0000 chunk 211 optimal weight: 20.0000 chunk 519 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- 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 191 GLN D 293 ASN F 57 GLN J 169 GLN J 203 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.108389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097540 restraints weight = 134371.000| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.53 r_work: 0.3409 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4441 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= 0.273 Angle : 0.597 8.986 66378 Z= 0.326 Chirality : 0.046 0.190 7878 Planarity : 0.004 0.043 8567 Dihedral : 5.134 23.546 6669 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.46 % Allowed : 17.19 % Favored : 79.34 % 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: -0.77 (0.11), residues: 6110 helix: 1.28 (0.12), residues: 1989 sheet: 0.12 (0.17), residues: 1040 loop : -2.06 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 383 PHE 0.020 0.002 PHE B 234 TYR 0.015 0.002 TYR I 67 ARG 0.009 0.001 ARG L 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12411.58 seconds wall clock time: 220 minutes 44.15 seconds (13244.15 seconds total)