Starting phenix.real_space_refine on Sun Dec 29 01:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bld_16107/12_2024/8bld_16107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bld_16107/12_2024/8bld_16107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bld_16107/12_2024/8bld_16107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bld_16107/12_2024/8bld_16107.map" model { file = "/net/cci-nas-00/data/ceres_data/8bld_16107/12_2024/8bld_16107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bld_16107/12_2024/8bld_16107.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 280 5.16 5 C 33684 2.51 5 N 9394 2.21 5 O 10976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 54376 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.96, per 1000 atoms: 0.46 Number of scatterers: 54376 At special positions: 0 Unit cell: (153.6, 151.68, 163.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 280 16.00 P 42 15.00 O 10976 8.00 N 9394 7.00 C 33684 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: 10.79 Conformation dependent library (CDL) restraints added in 5.6 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13272 Finding SS restraints... Secondary structure from input PDB file: 278 helices and 91 sheets defined 58.8% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.837A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 281 through 297 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 375 removed outlier: 4.141A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 433 through 448 removed outlier: 3.734A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 4.000A pdb=" N ARG A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.679A pdb=" N VAL A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.803A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 52 through 59 Processing helix chain 'G' and resid 64 through 85 removed outlier: 3.976A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 141 through 152 removed outlier: 3.529A pdb=" N ALA G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.651A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 242 removed outlier: 3.950A pdb=" N MET G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 282 through 296 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 removed outlier: 3.578A pdb=" N GLY G 375 " --> pdb=" O LYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 426 Processing helix chain 'G' and resid 433 through 447 Processing helix chain 'G' and resid 448 through 458 Processing helix chain 'G' and resid 461 through 472 removed outlier: 3.619A pdb=" N VAL G 465 " --> pdb=" O GLU G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.924A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 52 through 59 removed outlier: 3.906A pdb=" N GLU B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 85 Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 255 through 269 Processing helix chain 'B' and resid 281 through 297 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 375 removed outlier: 4.118A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 removed outlier: 3.707A pdb=" N GLU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.913A pdb=" N ARG B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 472 removed outlier: 3.732A pdb=" N VAL B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.795A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.599A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 removed outlier: 3.881A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.526A pdb=" N ALA C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.684A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 242 removed outlier: 3.957A pdb=" N MET C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 259 through 267 Processing helix chain 'C' and resid 282 through 296 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 375 removed outlier: 3.596A pdb=" N GLY C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 433 through 447 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.968A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.861A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.531A pdb=" N ARG D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 removed outlier: 3.692A pdb=" N GLU D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 85 Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 281 through 297 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 375 removed outlier: 4.200A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 removed outlier: 3.884A pdb=" N GLU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 426 Processing helix chain 'D' and resid 433 through 448 removed outlier: 3.660A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.895A pdb=" N ARG D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 472 removed outlier: 3.728A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.668A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.584A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 85 removed outlier: 3.782A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 142 through 152 Processing helix chain 'E' and resid 155 through 169 Processing helix chain 'E' and resid 201 through 205 removed outlier: 3.661A pdb=" N ILE E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 242 removed outlier: 3.916A pdb=" N MET E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 267 Processing helix chain 'E' and resid 282 through 296 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.558A pdb=" N GLY E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 426 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 461 through 472 removed outlier: 3.942A pdb=" N VAL E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.749A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 52 through 59 removed outlier: 3.688A pdb=" N GLU F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 Processing helix chain 'F' and resid 88 through 108 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 281 through 297 Processing helix chain 'F' and resid 338 through 356 Processing helix chain 'F' and resid 358 through 375 removed outlier: 4.470A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 removed outlier: 3.852A pdb=" N GLU F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 426 Processing helix chain 'F' and resid 433 through 448 Processing helix chain 'F' and resid 448 through 459 removed outlier: 4.067A pdb=" N ARG F 452 " --> pdb=" O GLU F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 472 removed outlier: 3.641A pdb=" N VAL F 465 " --> pdb=" O GLU F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.752A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.520A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 85 removed outlier: 3.666A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 110 Processing helix chain 'H' and resid 112 through 135 removed outlier: 3.594A pdb=" N LEU H 116 " --> pdb=" O ASN H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 152 Processing helix chain 'H' and resid 155 through 169 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.684A pdb=" N ILE H 205 " --> pdb=" O PRO H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 242 removed outlier: 3.871A pdb=" N MET H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 259 through 267 Processing helix chain 'H' and resid 282 through 296 Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 375 Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 426 Processing helix chain 'H' and resid 433 through 447 Processing helix chain 'H' and resid 448 through 458 Processing helix chain 'H' and resid 461 through 472 removed outlier: 3.758A pdb=" N VAL H 465 " --> pdb=" O GLU H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 515 Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 52 through 59 removed outlier: 3.736A pdb=" N GLU I 59 " --> pdb=" O SER I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 85 Processing helix chain 'I' and resid 88 through 108 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.501A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 255 through 269 Processing helix chain 'I' and resid 281 through 297 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 374 Processing helix chain 'I' and resid 385 through 409 removed outlier: 3.745A pdb=" N GLU I 409 " --> pdb=" O ALA I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 426 Processing helix chain 'I' and resid 433 through 448 removed outlier: 3.781A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 459 removed outlier: 3.931A pdb=" N ARG I 452 " --> pdb=" O GLU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 472 removed outlier: 3.985A pdb=" N VAL I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 516 removed outlier: 3.661A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 52 through 59 Processing helix chain 'J' and resid 64 through 85 removed outlier: 3.796A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 141 through 152 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.665A pdb=" N ILE J 205 " --> pdb=" O PRO J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 242 removed outlier: 3.913A pdb=" N MET J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 259 through 267 Processing helix chain 'J' and resid 282 through 296 Processing helix chain 'J' and resid 308 through 312 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 375 removed outlier: 3.573A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 426 Processing helix chain 'J' and resid 433 through 448 removed outlier: 3.835A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 458 removed outlier: 3.507A pdb=" N ARG J 452 " --> pdb=" O GLU J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 472 removed outlier: 3.736A pdb=" N VAL J 465 " --> pdb=" O GLU J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 497 through 516 removed outlier: 3.775A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.525A pdb=" N ARG K 13 " --> pdb=" O GLY K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 4.001A pdb=" N GLU K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 85 Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 255 through 269 Processing helix chain 'K' and resid 281 through 297 Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 375 removed outlier: 4.106A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 removed outlier: 3.905A pdb=" N GLU K 409 " --> pdb=" O ALA K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 448 removed outlier: 4.035A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 459 removed outlier: 3.637A pdb=" N ARG K 452 " --> pdb=" O GLU K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 472 removed outlier: 3.642A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.688A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 29 Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.589A pdb=" N ILE L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 85 removed outlier: 3.967A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 142 through 152 Processing helix chain 'L' and resid 155 through 169 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.646A pdb=" N ILE L 205 " --> pdb=" O PRO L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 242 removed outlier: 3.810A pdb=" N MET L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 259 through 267 Processing helix chain 'L' and resid 282 through 296 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 375 removed outlier: 3.541A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 426 Processing helix chain 'L' and resid 433 through 448 removed outlier: 3.706A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 458 Processing helix chain 'L' and resid 461 through 472 removed outlier: 3.719A pdb=" N VAL L 465 " --> pdb=" O GLU L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 515 Processing helix chain 'M' and resid 9 through 29 Processing helix chain 'M' and resid 52 through 59 removed outlier: 4.174A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 255 through 269 Processing helix chain 'M' and resid 281 through 297 Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 358 through 374 Processing helix chain 'M' and resid 385 through 410 removed outlier: 3.521A pdb=" N GLU M 409 " --> pdb=" O ALA M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 426 Processing helix chain 'M' and resid 433 through 447 Processing helix chain 'M' and resid 448 through 459 removed outlier: 3.946A pdb=" N ARG M 452 " --> pdb=" O GLU M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 472 removed outlier: 3.671A pdb=" N VAL M 465 " --> pdb=" O GLU M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 516 removed outlier: 3.727A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 29 Processing helix chain 'N' and resid 52 through 60 removed outlier: 3.509A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 85 removed outlier: 4.135A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 110 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 141 through 152 removed outlier: 3.523A pdb=" N ALA N 145 " --> pdb=" O SER N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 169 Processing helix chain 'N' and resid 201 through 205 removed outlier: 3.620A pdb=" N ILE N 205 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 242 removed outlier: 3.851A pdb=" N MET N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 259 through 267 Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 308 through 312 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 375 removed outlier: 3.619A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 426 Processing helix chain 'N' and resid 433 through 447 Processing helix chain 'N' and resid 448 through 458 Processing helix chain 'N' and resid 461 through 472 removed outlier: 3.979A pdb=" N VAL N 465 " --> pdb=" O GLU N 461 " (cutoff:3.500A) Processing helix chain 'N' and resid 488 through 492 Processing helix chain 'N' and resid 497 through 515 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 4.351A pdb=" N THR A 517 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL B 39 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N CYS A 519 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 7.423A pdb=" N ASN A 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N VAL M 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N ASP M 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 180 removed outlier: 6.568A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.419A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 9.255A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.265A pdb=" N CYS G 519 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 48 through 50 Processing sheet with id=AB1, first strand: chain 'G' and resid 174 through 179 Processing sheet with id=AB2, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.881A pdb=" N THR G 330 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE G 325 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE G 332 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL G 323 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP G 334 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 213 through 216 removed outlier: 3.611A pdb=" N VAL G 323 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 8 removed outlier: 4.269A pdb=" N THR B 517 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL D 39 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS B 519 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.719A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.389A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 213 through 216 removed outlier: 9.354A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AC2, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 50 Processing sheet with id=AC4, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AC5, first strand: chain 'C' and resid 193 through 195 removed outlier: 3.579A pdb=" N VAL C 323 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 273 through 277 removed outlier: 5.956A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 273 through 277 removed outlier: 5.956A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC9, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 8 removed outlier: 4.367A pdb=" N THR D 517 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL F 39 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS D 519 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 174 through 180 removed outlier: 6.560A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.401A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 213 through 216 removed outlier: 9.333A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD6, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AD7, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AD8, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AD9, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.539A pdb=" N VAL E 323 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 273 through 277 removed outlier: 5.842A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 273 through 277 removed outlier: 5.842A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AE4, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AE5, first strand: chain 'F' and resid 4 through 8 removed outlier: 4.195A pdb=" N THR F 517 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL I 39 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N CYS F 519 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.613A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.396A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 213 through 216 removed outlier: 9.358A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AF1, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AF2, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AF3, first strand: chain 'H' and resid 48 through 50 Processing sheet with id=AF4, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AF5, first strand: chain 'H' and resid 193 through 195 removed outlier: 3.501A pdb=" N VAL H 323 " --> pdb=" O LEU H 215 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.330A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.330A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF9, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AG1, first strand: chain 'I' and resid 4 through 8 removed outlier: 4.195A pdb=" N THR I 517 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL K 39 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS I 519 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 174 through 179 Processing sheet with id=AG3, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.363A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 213 through 216 removed outlier: 9.323A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG6, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AG7, first strand: chain 'J' and resid 48 through 50 Processing sheet with id=AG8, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AG9, first strand: chain 'J' and resid 193 through 195 Processing sheet with id=AH1, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.018A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.018A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AH4, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AH5, first strand: chain 'K' and resid 4 through 8 removed outlier: 7.299A pdb=" N VAL M 39 " --> pdb=" O GLU K 518 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET K 520 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 174 through 179 removed outlier: 6.546A pdb=" N VAL K 174 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE K 379 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.629A pdb=" N THR K 329 " --> pdb=" O ASN K 326 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 213 through 216 removed outlier: 9.346A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AI1, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AI2, first strand: chain 'L' and resid 48 through 50 Processing sheet with id=AI3, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AI4, first strand: chain 'L' and resid 193 through 195 Processing sheet with id=AI5, first strand: chain 'L' and resid 273 through 277 removed outlier: 5.988A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 273 through 277 removed outlier: 5.988A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AI8, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AI9, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.529A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.391A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'M' and resid 213 through 216 removed outlier: 9.339A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AJ4, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AJ5, first strand: chain 'N' and resid 174 through 179 Processing sheet with id=AJ6, first strand: chain 'N' and resid 193 through 195 Processing sheet with id=AJ7, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.288A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.288A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AK1, first strand: chain 'N' and resid 476 through 479 3688 hydrogen bonds defined for protein. 10605 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: 23.29 Time building geometry restraints manager: 12.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18624 1.34 - 1.46: 6685 1.46 - 1.58: 28907 1.58 - 1.70: 55 1.70 - 1.82: 518 Bond restraints: 54789 Sorted by residual: bond pdb=" CG1 ILE H 60 " pdb=" CD1 ILE H 60 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.71e+00 bond pdb=" CA ASP K 328 " pdb=" CB ASP K 328 " ideal model delta sigma weight residual 1.526 1.562 -0.036 1.68e-02 3.54e+03 4.57e+00 bond pdb=" CG1 ILE N 60 " pdb=" CD1 ILE N 60 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 3.95e+00 bond pdb=" CB PRO M 525 " pdb=" CG PRO M 525 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.81e+00 bond pdb=" CG ARG K 404 " pdb=" CD ARG K 404 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.30e+00 ... (remaining 54784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 73481 3.23 - 6.46: 519 6.46 - 9.68: 63 9.68 - 12.91: 10 12.91 - 16.14: 1 Bond angle restraints: 74074 Sorted by residual: angle pdb=" CB MET M 16 " pdb=" CG MET M 16 " pdb=" SD MET M 16 " ideal model delta sigma weight residual 112.70 128.84 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" C ARG H 58 " pdb=" N GLU H 59 " pdb=" CA GLU H 59 " ideal model delta sigma weight residual 121.14 113.00 8.14 1.75e+00 3.27e-01 2.16e+01 angle pdb=" CA PRO M 525 " pdb=" N PRO M 525 " pdb=" CD PRO M 525 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" CA MET M 16 " pdb=" CB MET M 16 " pdb=" CG MET M 16 " ideal model delta sigma weight residual 114.10 123.36 -9.26 2.00e+00 2.50e-01 2.14e+01 angle pdb=" N MET M 16 " pdb=" CA MET M 16 " pdb=" CB MET M 16 " ideal model delta sigma weight residual 110.39 118.02 -7.63 1.66e+00 3.63e-01 2.11e+01 ... (remaining 74069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 30789 16.37 - 32.73: 2580 32.73 - 49.10: 701 49.10 - 65.46: 98 65.46 - 81.83: 48 Dihedral angle restraints: 34216 sinusoidal: 13524 harmonic: 20692 Sorted by residual: dihedral pdb=" CA ASP B 41 " pdb=" C ASP B 41 " pdb=" N LYS B 42 " pdb=" CA LYS B 42 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASP D 41 " pdb=" C ASP D 41 " pdb=" N LYS D 42 " pdb=" CA LYS D 42 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU H 40 " pdb=" C LEU H 40 " pdb=" N ASP H 41 " pdb=" CA ASP H 41 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 34213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 7754 0.069 - 0.137: 1166 0.137 - 0.206: 58 0.206 - 0.275: 8 0.275 - 0.343: 2 Chirality restraints: 8988 Sorted by residual: chirality pdb=" CG LEU E 40 " pdb=" CB LEU E 40 " pdb=" CD1 LEU E 40 " pdb=" CD2 LEU E 40 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE I 379 " pdb=" CA ILE I 379 " pdb=" CG1 ILE I 379 " pdb=" CG2 ILE I 379 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE A 379 " pdb=" CA ILE A 379 " pdb=" CG1 ILE A 379 " pdb=" CG2 ILE A 379 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 8985 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 524 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO M 525 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO M 525 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO M 525 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP K 328 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASP K 328 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP K 328 " 0.016 2.00e-02 2.50e+03 pdb=" N THR K 329 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 96 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C ALA N 96 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA N 96 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN N 97 " 0.014 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2868 2.72 - 3.26: 59119 3.26 - 3.81: 97193 3.81 - 4.35: 113886 4.35 - 4.90: 190600 Nonbonded interactions: 463666 Sorted by model distance: nonbonded pdb=" ND2 ASN G 112 " pdb=" OD1 ASP G 115 " model vdw 2.174 3.120 nonbonded pdb=" ND2 ASN E 112 " pdb=" OD2 ASP E 115 " model vdw 2.175 3.120 nonbonded pdb=" OG1 THR J 90 " pdb=" O1G ATP J 601 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR N 90 " pdb=" O1G ATP N 601 " model vdw 2.201 3.040 nonbonded pdb=" O ARG F 421 " pdb=" OG SER F 424 " model vdw 2.209 3.040 ... (remaining 463661 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' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'B' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'C' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'D' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'E' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'F' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'G' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'H' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'I' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'J' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'K' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'L' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'M' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'N' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.070 Extract box with map and model: 1.550 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 101.370 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.250 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 0.098 54789 Z= 0.292 Angle : 0.765 16.140 74074 Z= 0.418 Chirality : 0.047 0.343 8988 Planarity : 0.005 0.117 9618 Dihedral : 13.605 81.827 20944 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.34 (0.09), residues: 7308 helix: 0.89 (0.08), residues: 4025 sheet: -0.26 (0.15), residues: 1064 loop : -0.57 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 401 PHE 0.029 0.002 PHE A 44 TYR 0.012 0.001 TYR L 478 ARG 0.020 0.001 ARG I 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 4.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8797 (pmm) cc_final: 0.7813 (pmm) REVERT: A 100 ILE cc_start: 0.9133 (tp) cc_final: 0.8908 (tp) REVERT: G 49 ILE cc_start: 0.9038 (mt) cc_final: 0.8827 (mt) REVERT: G 69 MET cc_start: 0.7795 (mtt) cc_final: 0.7505 (mtt) REVERT: G 419 LEU cc_start: 0.8776 (tp) cc_final: 0.8528 (tt) REVERT: B 69 MET cc_start: 0.7599 (mtm) cc_final: 0.7375 (mtt) REVERT: B 120 ILE cc_start: 0.9383 (mt) cc_final: 0.9155 (tp) REVERT: B 447 MET cc_start: 0.8035 (ptm) cc_final: 0.7813 (ptm) REVERT: B 520 MET cc_start: 0.7713 (tpp) cc_final: 0.7398 (tpp) REVERT: C 390 LYS cc_start: 0.8661 (pttp) cc_final: 0.7475 (pttm) REVERT: C 478 TYR cc_start: 0.7718 (t80) cc_final: 0.7430 (t80) REVERT: D 100 ILE cc_start: 0.9081 (tp) cc_final: 0.8842 (tp) REVERT: D 513 LEU cc_start: 0.8631 (mm) cc_final: 0.7884 (tp) REVERT: E 162 ILE cc_start: 0.9488 (mm) cc_final: 0.9178 (tt) REVERT: I 111 MET cc_start: 0.7100 (ptp) cc_final: 0.6813 (mpp) REVERT: I 307 MET cc_start: 0.5589 (tmm) cc_final: 0.4870 (tpp) REVERT: I 524 LEU cc_start: 0.8499 (tp) cc_final: 0.8187 (tp) REVERT: J 162 ILE cc_start: 0.9202 (mm) cc_final: 0.8912 (tt) REVERT: J 389 MET cc_start: 0.7066 (mmt) cc_final: 0.6623 (mmm) REVERT: K 16 MET cc_start: 0.8513 (ptp) cc_final: 0.7850 (ptp) REVERT: K 100 ILE cc_start: 0.9224 (tp) cc_final: 0.8981 (tp) REVERT: K 267 MET cc_start: 0.1188 (ptt) cc_final: 0.0913 (ppp) REVERT: K 520 MET cc_start: 0.7873 (ttt) cc_final: 0.7286 (ttt) REVERT: L 49 ILE cc_start: 0.8791 (mt) cc_final: 0.8450 (mt) REVERT: L 97 GLN cc_start: 0.8858 (tt0) cc_final: 0.8528 (tt0) REVERT: L 389 MET cc_start: 0.6886 (mmm) cc_final: 0.6119 (mmm) REVERT: L 390 LYS cc_start: 0.7775 (pttp) cc_final: 0.7567 (mmtt) REVERT: M 69 MET cc_start: 0.8123 (ttp) cc_final: 0.7868 (ttp) REVERT: M 100 ILE cc_start: 0.9211 (tp) cc_final: 0.8874 (tp) REVERT: M 401 HIS cc_start: 0.8808 (t-90) cc_final: 0.8421 (t70) REVERT: N 111 MET cc_start: 0.7799 (tpt) cc_final: 0.7124 (tpt) REVERT: N 193 MET cc_start: 0.5989 (mmp) cc_final: 0.5464 (mmm) REVERT: N 390 LYS cc_start: 0.8160 (pttm) cc_final: 0.7664 (pttm) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.4799 time to fit residues: 463.1243 Evaluate side-chains 450 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 4.9990 chunk 551 optimal weight: 50.0000 chunk 306 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 372 optimal weight: 0.9980 chunk 294 optimal weight: 30.0000 chunk 570 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 346 optimal weight: 30.0000 chunk 424 optimal weight: 0.8980 chunk 661 optimal weight: 40.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN A 319 GLN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 146 GLN B 319 GLN ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN D 146 GLN D 319 GLN D 457 ASN E 290 GLN F 146 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN ** I 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 319 GLN ** I 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN J 290 GLN K 319 GLN ** K 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 GLN M 319 GLN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 54789 Z= 0.244 Angle : 0.577 11.405 74074 Z= 0.312 Chirality : 0.042 0.155 8988 Planarity : 0.004 0.058 9618 Dihedral : 8.429 85.431 8204 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.21 % Allowed : 4.75 % Favored : 95.04 % 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: 0.56 (0.09), residues: 7308 helix: 1.11 (0.08), residues: 4151 sheet: -0.07 (0.16), residues: 1036 loop : -0.72 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 401 PHE 0.010 0.001 PHE D 66 TYR 0.009 0.001 TYR L 478 ARG 0.007 0.000 ARG F 445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 541 time to evaluate : 4.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8838 (pmm) cc_final: 0.8313 (pmm) REVERT: G 389 MET cc_start: 0.7812 (mmp) cc_final: 0.7581 (mmp) REVERT: B 17 LEU cc_start: 0.9271 (tp) cc_final: 0.9057 (tp) REVERT: B 69 MET cc_start: 0.7564 (mtm) cc_final: 0.7298 (mtt) REVERT: C 111 MET cc_start: 0.7444 (tpt) cc_final: 0.7056 (tpp) REVERT: C 513 LEU cc_start: 0.8862 (tp) cc_final: 0.8631 (tp) REVERT: D 100 ILE cc_start: 0.8969 (tp) cc_final: 0.8685 (tp) REVERT: D 447 MET cc_start: 0.8395 (ptm) cc_final: 0.8092 (ptp) REVERT: D 513 LEU cc_start: 0.8776 (mm) cc_final: 0.7960 (tp) REVERT: E 162 ILE cc_start: 0.9401 (mm) cc_final: 0.9192 (tt) REVERT: E 355 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8031 (pp20) REVERT: F 166 MET cc_start: 0.9475 (tpt) cc_final: 0.9223 (tpt) REVERT: H 390 LYS cc_start: 0.8397 (pttt) cc_final: 0.8102 (pttp) REVERT: I 73 MET cc_start: 0.7431 (mtm) cc_final: 0.7202 (mtm) REVERT: I 307 MET cc_start: 0.5483 (tmm) cc_final: 0.4795 (tpp) REVERT: J 73 MET cc_start: 0.7624 (mtp) cc_final: 0.7368 (mtt) REVERT: J 115 ASP cc_start: 0.7581 (m-30) cc_final: 0.6580 (m-30) REVERT: J 162 ILE cc_start: 0.9224 (mm) cc_final: 0.8904 (tt) REVERT: J 389 MET cc_start: 0.7113 (mmt) cc_final: 0.6882 (mmm) REVERT: K 16 MET cc_start: 0.8542 (ptp) cc_final: 0.7826 (ptp) REVERT: K 100 ILE cc_start: 0.9208 (tp) cc_final: 0.8971 (tp) REVERT: K 520 MET cc_start: 0.7493 (ttt) cc_final: 0.7240 (ttt) REVERT: L 97 GLN cc_start: 0.8941 (tt0) cc_final: 0.8602 (tt0) REVERT: L 389 MET cc_start: 0.7058 (mmm) cc_final: 0.5939 (mmm) REVERT: L 390 LYS cc_start: 0.7775 (pttp) cc_final: 0.7497 (mmtt) REVERT: M 61 GLU cc_start: 0.7425 (pt0) cc_final: 0.7149 (pt0) REVERT: M 100 ILE cc_start: 0.9252 (tp) cc_final: 0.8968 (tp) REVERT: M 401 HIS cc_start: 0.8888 (t-90) cc_final: 0.8564 (t-170) REVERT: M 447 MET cc_start: 0.8398 (ptm) cc_final: 0.8161 (ptm) REVERT: N 111 MET cc_start: 0.7751 (tpt) cc_final: 0.7394 (tpp) REVERT: N 193 MET cc_start: 0.5925 (mmp) cc_final: 0.5403 (mmm) REVERT: N 447 MET cc_start: 0.7865 (ptp) cc_final: 0.7456 (mtm) outliers start: 12 outliers final: 0 residues processed: 552 average time/residue: 0.4746 time to fit residues: 460.7567 Evaluate side-chains 451 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 4.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.7980 chunk 205 optimal weight: 20.0000 chunk 550 optimal weight: 0.8980 chunk 450 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 662 optimal weight: 0.9980 chunk 715 optimal weight: 5.9990 chunk 589 optimal weight: 7.9990 chunk 656 optimal weight: 9.9990 chunk 225 optimal weight: 0.0980 chunk 531 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 GLN ** I 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 GLN M 37 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54789 Z= 0.174 Angle : 0.547 9.226 74074 Z= 0.292 Chirality : 0.042 0.182 8988 Planarity : 0.003 0.058 9618 Dihedral : 8.114 87.293 8204 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.12 % Allowed : 3.49 % Favored : 96.38 % 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: 0.71 (0.10), residues: 7308 helix: 1.22 (0.08), residues: 4116 sheet: -0.02 (0.16), residues: 1050 loop : -0.61 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 401 PHE 0.011 0.001 PHE C 195 TYR 0.008 0.001 TYR L 478 ARG 0.007 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 564 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8777 (pmm) cc_final: 0.8232 (pmm) REVERT: G 69 MET cc_start: 0.8023 (mtt) cc_final: 0.7657 (mtt) REVERT: G 111 MET cc_start: 0.7613 (tpt) cc_final: 0.7237 (tpp) REVERT: G 115 ASP cc_start: 0.7563 (m-30) cc_final: 0.7145 (m-30) REVERT: G 389 MET cc_start: 0.7910 (mmp) cc_final: 0.7618 (mmp) REVERT: B 16 MET cc_start: 0.8582 (ppp) cc_final: 0.8288 (ppp) REVERT: B 17 LEU cc_start: 0.9247 (tp) cc_final: 0.8921 (tp) REVERT: C 111 MET cc_start: 0.7303 (tpt) cc_final: 0.6759 (tpp) REVERT: C 162 ILE cc_start: 0.9470 (mt) cc_final: 0.9247 (tt) REVERT: C 478 TYR cc_start: 0.7679 (t80) cc_final: 0.7302 (t80) REVERT: D 17 LEU cc_start: 0.9331 (tp) cc_final: 0.8999 (tp) REVERT: D 100 ILE cc_start: 0.8969 (tp) cc_final: 0.8707 (tt) REVERT: D 447 MET cc_start: 0.8301 (ptm) cc_final: 0.7815 (ptp) REVERT: E 111 MET cc_start: 0.7685 (tpp) cc_final: 0.7439 (tpp) REVERT: E 166 MET cc_start: 0.9106 (tmm) cc_final: 0.8876 (tmm) REVERT: E 168 LYS cc_start: 0.9535 (mmtm) cc_final: 0.9219 (tptp) REVERT: F 61 GLU cc_start: 0.7835 (pm20) cc_final: 0.7495 (pm20) REVERT: F 67 GLU cc_start: 0.8398 (mp0) cc_final: 0.8085 (mp0) REVERT: F 166 MET cc_start: 0.9456 (tpt) cc_final: 0.9200 (tpt) REVERT: H 390 LYS cc_start: 0.8408 (pttt) cc_final: 0.8202 (pttp) REVERT: I 307 MET cc_start: 0.5383 (tmm) cc_final: 0.4718 (tpp) REVERT: J 115 ASP cc_start: 0.7263 (m-30) cc_final: 0.6525 (m-30) REVERT: J 162 ILE cc_start: 0.9218 (mm) cc_final: 0.8886 (tt) REVERT: K 16 MET cc_start: 0.8499 (ptp) cc_final: 0.7008 (ptp) REVERT: K 100 ILE cc_start: 0.9201 (tp) cc_final: 0.8944 (tp) REVERT: L 97 GLN cc_start: 0.8856 (tt0) cc_final: 0.8556 (tt0) REVERT: L 115 ASP cc_start: 0.7303 (m-30) cc_final: 0.6406 (m-30) REVERT: L 193 MET cc_start: 0.6258 (tpt) cc_final: 0.5583 (mmm) REVERT: L 389 MET cc_start: 0.7075 (mmm) cc_final: 0.6058 (mmm) REVERT: L 390 LYS cc_start: 0.7797 (pttp) cc_final: 0.7508 (mmtt) REVERT: M 100 ILE cc_start: 0.9202 (tp) cc_final: 0.8798 (tp) REVERT: M 401 HIS cc_start: 0.8876 (t-90) cc_final: 0.8540 (t-170) REVERT: M 447 MET cc_start: 0.8203 (ptm) cc_final: 0.7174 (ttp) REVERT: M 491 MET cc_start: 0.8584 (ptp) cc_final: 0.8366 (ptp) REVERT: N 115 ASP cc_start: 0.7541 (m-30) cc_final: 0.7220 (m-30) REVERT: N 193 MET cc_start: 0.5765 (mmp) cc_final: 0.5315 (mmm) REVERT: N 389 MET cc_start: 0.7260 (mmm) cc_final: 0.6883 (mmm) REVERT: N 390 LYS cc_start: 0.8167 (pttm) cc_final: 0.7430 (pttp) REVERT: N 488 MET cc_start: 0.7851 (mmp) cc_final: 0.7635 (mmm) outliers start: 7 outliers final: 0 residues processed: 569 average time/residue: 0.5110 time to fit residues: 510.6616 Evaluate side-chains 464 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 4.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 0.0060 chunk 497 optimal weight: 7.9990 chunk 343 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 316 optimal weight: 3.9990 chunk 444 optimal weight: 5.9990 chunk 664 optimal weight: 9.9990 chunk 703 optimal weight: 20.0000 chunk 347 optimal weight: 30.0000 chunk 629 optimal weight: 5.9990 chunk 189 optimal weight: 50.0000 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN G 112 ASN B 319 GLN ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN F 457 ASN I 457 ASN K 457 ASN L 112 ASN L 290 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 319 GLN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 54789 Z= 0.273 Angle : 0.584 10.781 74074 Z= 0.314 Chirality : 0.043 0.230 8988 Planarity : 0.003 0.044 9618 Dihedral : 7.821 87.215 8204 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % 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: 0.76 (0.10), residues: 7308 helix: 1.31 (0.08), residues: 4116 sheet: -0.02 (0.15), residues: 1106 loop : -0.69 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 401 PHE 0.009 0.001 PHE D 66 TYR 0.009 0.001 TYR D 506 ARG 0.008 0.000 ARG D 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 530 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7325 (mtm180) REVERT: G 115 ASP cc_start: 0.7717 (m-30) cc_final: 0.7432 (m-30) REVERT: G 389 MET cc_start: 0.7861 (mmp) cc_final: 0.7471 (mmp) REVERT: G 390 LYS cc_start: 0.8581 (pttp) cc_final: 0.8244 (pttm) REVERT: B 111 MET cc_start: 0.7449 (mpp) cc_final: 0.7236 (mpp) REVERT: C 69 MET cc_start: 0.8051 (mtp) cc_final: 0.7753 (mtt) REVERT: C 111 MET cc_start: 0.7360 (tpt) cc_final: 0.6936 (tpp) REVERT: D 447 MET cc_start: 0.8506 (ptm) cc_final: 0.7943 (ptp) REVERT: D 513 LEU cc_start: 0.8846 (mm) cc_final: 0.8108 (tp) REVERT: D 514 MET cc_start: 0.8787 (ttm) cc_final: 0.8471 (ttp) REVERT: F 16 MET cc_start: 0.8409 (ppp) cc_final: 0.7820 (ppp) REVERT: F 61 GLU cc_start: 0.7870 (pm20) cc_final: 0.7628 (pm20) REVERT: F 67 GLU cc_start: 0.8480 (mp0) cc_final: 0.8006 (mp0) REVERT: F 166 MET cc_start: 0.9472 (tpt) cc_final: 0.9150 (tmm) REVERT: H 390 LYS cc_start: 0.8327 (pttt) cc_final: 0.8102 (pttp) REVERT: H 488 MET cc_start: 0.7556 (mmt) cc_final: 0.7332 (mmt) REVERT: I 288 MET cc_start: 0.9067 (ppp) cc_final: 0.8825 (ppp) REVERT: I 307 MET cc_start: 0.5468 (tmm) cc_final: 0.4808 (tpp) REVERT: J 97 GLN cc_start: 0.9000 (tt0) cc_final: 0.8772 (tt0) REVERT: J 115 ASP cc_start: 0.7237 (m-30) cc_final: 0.6572 (m-30) REVERT: J 162 ILE cc_start: 0.9272 (mm) cc_final: 0.8903 (tt) REVERT: K 16 MET cc_start: 0.8245 (ptp) cc_final: 0.7357 (ptp) REVERT: K 17 LEU cc_start: 0.9432 (tp) cc_final: 0.9182 (tp) REVERT: K 100 ILE cc_start: 0.9146 (tp) cc_final: 0.8755 (tp) REVERT: K 520 MET cc_start: 0.7747 (ttt) cc_final: 0.7121 (ttt) REVERT: L 111 MET cc_start: 0.7464 (tpt) cc_final: 0.7235 (tpp) REVERT: L 115 ASP cc_start: 0.7411 (m-30) cc_final: 0.6437 (m-30) REVERT: L 385 THR cc_start: 0.7960 (p) cc_final: 0.7714 (p) REVERT: L 389 MET cc_start: 0.7120 (mmm) cc_final: 0.6143 (mmm) REVERT: M 401 HIS cc_start: 0.8936 (t-90) cc_final: 0.8561 (t-170) REVERT: N 111 MET cc_start: 0.7674 (tpt) cc_final: 0.7337 (tpp) REVERT: N 114 MET cc_start: 0.8519 (pmm) cc_final: 0.8231 (pmm) REVERT: N 115 ASP cc_start: 0.7543 (m-30) cc_final: 0.7141 (m-30) REVERT: N 193 MET cc_start: 0.5996 (mmp) cc_final: 0.5494 (mmm) REVERT: N 390 LYS cc_start: 0.8221 (pttm) cc_final: 0.7582 (pttp) REVERT: N 523 ASP cc_start: 0.6947 (m-30) cc_final: 0.6614 (t70) outliers start: 3 outliers final: 1 residues processed: 533 average time/residue: 0.4793 time to fit residues: 447.8348 Evaluate side-chains 456 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 10.0000 chunk 399 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 523 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 600 optimal weight: 6.9990 chunk 486 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 359 optimal weight: 9.9990 chunk 631 optimal weight: 5.9990 chunk 177 optimal weight: 50.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 ASN F 194 GLN K 319 GLN M 457 ASN N 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 54789 Z= 0.343 Angle : 0.633 12.050 74074 Z= 0.339 Chirality : 0.044 0.211 8988 Planarity : 0.004 0.054 9618 Dihedral : 7.794 85.256 8204 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.07 % Allowed : 2.94 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 7308 helix: 1.26 (0.08), residues: 4088 sheet: -0.10 (0.15), residues: 1176 loop : -0.67 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 401 PHE 0.013 0.001 PHE D 66 TYR 0.013 0.001 TYR D 506 ARG 0.014 0.001 ARG M 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 522 time to evaluate : 4.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8456 (mp0) cc_final: 0.8089 (mp0) REVERT: G 111 MET cc_start: 0.7880 (tpt) cc_final: 0.7444 (tpp) REVERT: G 114 MET cc_start: 0.8290 (ptp) cc_final: 0.8049 (tpp) REVERT: G 389 MET cc_start: 0.7951 (mmp) cc_final: 0.7475 (mmp) REVERT: G 513 LEU cc_start: 0.8893 (tp) cc_final: 0.8657 (tp) REVERT: B 447 MET cc_start: 0.8458 (ptm) cc_final: 0.7989 (ptt) REVERT: B 524 LEU cc_start: 0.8102 (tp) cc_final: 0.7875 (tp) REVERT: C 69 MET cc_start: 0.8210 (mtp) cc_final: 0.7962 (mtt) REVERT: C 390 LYS cc_start: 0.8713 (pttp) cc_final: 0.7669 (pttm) REVERT: C 513 LEU cc_start: 0.8869 (tp) cc_final: 0.8667 (tp) REVERT: D 447 MET cc_start: 0.8560 (ptm) cc_final: 0.8328 (ptp) REVERT: D 513 LEU cc_start: 0.8961 (mm) cc_final: 0.8140 (tp) REVERT: E 16 MET cc_start: 0.7930 (mmt) cc_final: 0.7474 (mmt) REVERT: E 355 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: F 61 GLU cc_start: 0.7809 (pm20) cc_final: 0.7591 (pm20) REVERT: F 67 GLU cc_start: 0.8450 (mp0) cc_final: 0.8029 (mp0) REVERT: F 166 MET cc_start: 0.9471 (tpt) cc_final: 0.9215 (tmm) REVERT: H 389 MET cc_start: 0.7847 (mmm) cc_final: 0.7571 (mmm) REVERT: H 390 LYS cc_start: 0.8446 (pttt) cc_final: 0.8096 (pttp) REVERT: I 307 MET cc_start: 0.5395 (tmm) cc_final: 0.4743 (tpp) REVERT: J 97 GLN cc_start: 0.9075 (tt0) cc_final: 0.8822 (tt0) REVERT: J 115 ASP cc_start: 0.7478 (m-30) cc_final: 0.6571 (m-30) REVERT: J 162 ILE cc_start: 0.9437 (mm) cc_final: 0.9097 (tt) REVERT: K 16 MET cc_start: 0.8342 (ptp) cc_final: 0.7522 (ptp) REVERT: K 100 ILE cc_start: 0.9208 (tp) cc_final: 0.8819 (tp) REVERT: K 520 MET cc_start: 0.7924 (ttt) cc_final: 0.7412 (ttt) REVERT: L 16 MET cc_start: 0.8444 (ttp) cc_final: 0.8148 (ttm) REVERT: L 193 MET cc_start: 0.6805 (tpt) cc_final: 0.6166 (mmm) REVERT: L 389 MET cc_start: 0.7155 (mmm) cc_final: 0.6897 (mmm) REVERT: M 61 GLU cc_start: 0.7402 (pt0) cc_final: 0.7104 (pt0) REVERT: M 67 GLU cc_start: 0.8495 (mp0) cc_final: 0.8157 (mp0) REVERT: M 401 HIS cc_start: 0.9010 (t-90) cc_final: 0.8612 (t-170) REVERT: N 193 MET cc_start: 0.6399 (mmp) cc_final: 0.5873 (mmm) REVERT: N 390 LYS cc_start: 0.8298 (pttm) cc_final: 0.7610 (pttp) REVERT: N 488 MET cc_start: 0.8396 (mmt) cc_final: 0.7997 (mmt) REVERT: N 523 ASP cc_start: 0.7033 (m-30) cc_final: 0.6636 (t70) outliers start: 4 outliers final: 1 residues processed: 526 average time/residue: 0.4741 time to fit residues: 438.3905 Evaluate side-chains 444 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 442 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 4.9990 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 413 optimal weight: 4.9990 chunk 173 optimal weight: 30.0000 chunk 704 optimal weight: 7.9990 chunk 584 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 369 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 54789 Z= 0.268 Angle : 0.598 11.153 74074 Z= 0.320 Chirality : 0.043 0.186 8988 Planarity : 0.004 0.060 9618 Dihedral : 7.703 85.646 8204 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.93 % 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: 0.74 (0.10), residues: 7308 helix: 1.29 (0.08), residues: 4095 sheet: -0.09 (0.15), residues: 1176 loop : -0.66 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 401 PHE 0.011 0.001 PHE D 66 TYR 0.010 0.001 TYR D 506 ARG 0.011 0.001 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 534 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8592 (mp0) cc_final: 0.8041 (mp0) REVERT: A 100 ILE cc_start: 0.9133 (tp) cc_final: 0.8887 (tp) REVERT: G 73 MET cc_start: 0.7860 (mtm) cc_final: 0.7646 (mtm) REVERT: G 111 MET cc_start: 0.7646 (tpt) cc_final: 0.7381 (tpp) REVERT: G 513 LEU cc_start: 0.8818 (tp) cc_final: 0.8508 (tp) REVERT: B 524 LEU cc_start: 0.8123 (tp) cc_final: 0.7861 (tp) REVERT: C 111 MET cc_start: 0.7503 (tpt) cc_final: 0.7173 (tpp) REVERT: C 390 LYS cc_start: 0.8715 (pttp) cc_final: 0.7694 (pttm) REVERT: C 513 LEU cc_start: 0.8837 (tp) cc_final: 0.8630 (tp) REVERT: D 513 LEU cc_start: 0.8935 (mm) cc_final: 0.8119 (tp) REVERT: F 61 GLU cc_start: 0.7847 (pm20) cc_final: 0.7595 (pm20) REVERT: F 67 GLU cc_start: 0.8482 (mp0) cc_final: 0.8134 (mp0) REVERT: F 166 MET cc_start: 0.9464 (tpt) cc_final: 0.9223 (tmm) REVERT: H 389 MET cc_start: 0.7876 (mmm) cc_final: 0.7606 (mmm) REVERT: H 390 LYS cc_start: 0.8501 (pttt) cc_final: 0.8226 (pttp) REVERT: H 488 MET cc_start: 0.7809 (mmt) cc_final: 0.7560 (mmt) REVERT: H 513 LEU cc_start: 0.9125 (tp) cc_final: 0.8727 (tp) REVERT: I 288 MET cc_start: 0.9095 (ppp) cc_final: 0.8885 (ppp) REVERT: I 307 MET cc_start: 0.5362 (tmm) cc_final: 0.4718 (tpp) REVERT: I 447 MET cc_start: 0.8828 (ptm) cc_final: 0.8406 (ptm) REVERT: J 97 GLN cc_start: 0.9032 (tt0) cc_final: 0.8791 (tt0) REVERT: J 115 ASP cc_start: 0.7503 (m-30) cc_final: 0.6482 (m-30) REVERT: K 16 MET cc_start: 0.8259 (ptp) cc_final: 0.7179 (ptp) REVERT: K 288 MET cc_start: 0.8992 (ppp) cc_final: 0.8784 (ppp) REVERT: L 111 MET cc_start: 0.7266 (tpp) cc_final: 0.7004 (tpp) REVERT: L 115 ASP cc_start: 0.7415 (m-30) cc_final: 0.6488 (m-30) REVERT: L 193 MET cc_start: 0.6778 (tpt) cc_final: 0.6228 (mmm) REVERT: L 389 MET cc_start: 0.7135 (mmm) cc_final: 0.6879 (mmm) REVERT: M 61 GLU cc_start: 0.7349 (pt0) cc_final: 0.7040 (pt0) REVERT: M 67 GLU cc_start: 0.8584 (mp0) cc_final: 0.8179 (mp0) REVERT: M 401 HIS cc_start: 0.8985 (t-90) cc_final: 0.8534 (t-170) REVERT: N 193 MET cc_start: 0.6452 (mmp) cc_final: 0.6176 (mmm) REVERT: N 194 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: N 390 LYS cc_start: 0.8250 (pttm) cc_final: 0.7685 (pttp) REVERT: N 523 ASP cc_start: 0.7056 (m-30) cc_final: 0.6730 (t70) outliers start: 1 outliers final: 0 residues processed: 534 average time/residue: 0.4861 time to fit residues: 453.6973 Evaluate side-chains 448 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 447 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 2.9990 chunk 79 optimal weight: 40.0000 chunk 401 optimal weight: 20.0000 chunk 514 optimal weight: 0.0030 chunk 398 optimal weight: 6.9990 chunk 592 optimal weight: 0.0040 chunk 393 optimal weight: 40.0000 chunk 701 optimal weight: 30.0000 chunk 439 optimal weight: 30.0000 chunk 427 optimal weight: 0.7980 chunk 323 optimal weight: 0.9990 overall best weight: 0.9606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 GLN L 194 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 54789 Z= 0.177 Angle : 0.567 10.840 74074 Z= 0.299 Chirality : 0.042 0.176 8988 Planarity : 0.003 0.060 9618 Dihedral : 7.486 88.797 8204 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.04 % Allowed : 1.44 % Favored : 98.53 % 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: 0.87 (0.10), residues: 7308 helix: 1.41 (0.08), residues: 4095 sheet: -0.03 (0.15), residues: 1176 loop : -0.62 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.010 0.001 PHE K 195 TYR 0.012 0.001 TYR N 203 ARG 0.008 0.000 ARG D 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 553 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8630 (mp0) cc_final: 0.8143 (mp0) REVERT: A 445 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7204 (mtm180) REVERT: A 447 MET cc_start: 0.8303 (ptt) cc_final: 0.8067 (ppp) REVERT: G 111 MET cc_start: 0.7788 (tpt) cc_final: 0.7498 (tpp) REVERT: G 513 LEU cc_start: 0.8679 (tp) cc_final: 0.8320 (tp) REVERT: B 447 MET cc_start: 0.8051 (ptm) cc_final: 0.7602 (ptt) REVERT: B 524 LEU cc_start: 0.7958 (tp) cc_final: 0.7740 (tp) REVERT: C 111 MET cc_start: 0.7441 (tpt) cc_final: 0.6822 (tpp) REVERT: D 100 ILE cc_start: 0.8846 (tp) cc_final: 0.8607 (tp) REVERT: D 513 LEU cc_start: 0.8848 (mm) cc_final: 0.8019 (tp) REVERT: D 514 MET cc_start: 0.8867 (ttm) cc_final: 0.8643 (ttp) REVERT: E 168 LYS cc_start: 0.9556 (mmtm) cc_final: 0.9297 (tptp) REVERT: F 16 MET cc_start: 0.7897 (ppp) cc_final: 0.7437 (ppp) REVERT: F 61 GLU cc_start: 0.7769 (pm20) cc_final: 0.7557 (pm20) REVERT: F 67 GLU cc_start: 0.8402 (mp0) cc_final: 0.7961 (mp0) REVERT: H 389 MET cc_start: 0.7860 (mmm) cc_final: 0.7555 (mmm) REVERT: H 390 LYS cc_start: 0.8452 (pttt) cc_final: 0.8216 (pttp) REVERT: H 488 MET cc_start: 0.7794 (mmt) cc_final: 0.7560 (mmt) REVERT: I 307 MET cc_start: 0.5505 (tmm) cc_final: 0.4785 (tpp) REVERT: I 447 MET cc_start: 0.8583 (ptm) cc_final: 0.8085 (ptm) REVERT: J 162 ILE cc_start: 0.9445 (mm) cc_final: 0.9083 (tt) REVERT: J 385 THR cc_start: 0.8719 (p) cc_final: 0.8234 (p) REVERT: J 389 MET cc_start: 0.7243 (mmm) cc_final: 0.6063 (mmm) REVERT: K 16 MET cc_start: 0.8200 (ptp) cc_final: 0.7228 (ptp) REVERT: L 59 GLU cc_start: 0.7233 (mp0) cc_final: 0.7000 (mm-30) REVERT: L 73 MET cc_start: 0.8065 (mtm) cc_final: 0.7630 (mtm) REVERT: L 111 MET cc_start: 0.7393 (tpp) cc_final: 0.7051 (tpp) REVERT: L 115 ASP cc_start: 0.7381 (m-30) cc_final: 0.6642 (m-30) REVERT: L 166 MET cc_start: 0.8828 (mmm) cc_final: 0.8447 (mmm) REVERT: L 193 MET cc_start: 0.6844 (tpt) cc_final: 0.6350 (mmm) REVERT: L 194 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: L 389 MET cc_start: 0.7146 (mmm) cc_final: 0.6897 (mmm) REVERT: M 61 GLU cc_start: 0.7322 (pt0) cc_final: 0.6941 (pt0) REVERT: M 67 GLU cc_start: 0.8561 (mp0) cc_final: 0.8274 (mp0) REVERT: M 401 HIS cc_start: 0.8987 (t-90) cc_final: 0.8516 (t-170) REVERT: N 111 MET cc_start: 0.7552 (tpt) cc_final: 0.7288 (tpp) REVERT: N 194 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: N 390 LYS cc_start: 0.8181 (pttm) cc_final: 0.7500 (pttp) REVERT: N 488 MET cc_start: 0.8337 (mmt) cc_final: 0.7862 (mmt) outliers start: 2 outliers final: 0 residues processed: 555 average time/residue: 0.4809 time to fit residues: 466.6367 Evaluate side-chains 454 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 452 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 0.8980 chunk 280 optimal weight: 0.1980 chunk 419 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 446 optimal weight: 20.0000 chunk 478 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 551 optimal weight: 20.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN L 194 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 54789 Z= 0.179 Angle : 0.577 15.853 74074 Z= 0.302 Chirality : 0.042 0.249 8988 Planarity : 0.003 0.058 9618 Dihedral : 7.295 88.879 8204 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.04 % Allowed : 1.17 % Favored : 98.79 % 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: 0.92 (0.10), residues: 7308 helix: 1.43 (0.08), residues: 4095 sheet: -0.02 (0.15), residues: 1106 loop : -0.56 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.010 0.001 PHE B 8 TYR 0.011 0.001 TYR J 203 ARG 0.023 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 529 time to evaluate : 4.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8587 (mp0) cc_final: 0.8122 (mp0) REVERT: A 100 ILE cc_start: 0.9072 (tp) cc_final: 0.8712 (tp) REVERT: A 447 MET cc_start: 0.8335 (ptt) cc_final: 0.8046 (ppp) REVERT: G 114 MET cc_start: 0.8311 (ptp) cc_final: 0.8061 (tpp) REVERT: G 387 VAL cc_start: 0.8610 (m) cc_final: 0.8330 (p) REVERT: G 513 LEU cc_start: 0.8550 (tp) cc_final: 0.8282 (tp) REVERT: B 524 LEU cc_start: 0.7983 (tp) cc_final: 0.7773 (tp) REVERT: C 111 MET cc_start: 0.7465 (tpt) cc_final: 0.7079 (tpp) REVERT: C 513 LEU cc_start: 0.8660 (tp) cc_final: 0.8426 (tp) REVERT: D 100 ILE cc_start: 0.8866 (tp) cc_final: 0.8608 (tp) REVERT: D 447 MET cc_start: 0.8247 (ptm) cc_final: 0.7228 (ttp) REVERT: D 513 LEU cc_start: 0.8835 (mm) cc_final: 0.8036 (tp) REVERT: E 168 LYS cc_start: 0.9550 (mmtm) cc_final: 0.9304 (tptp) REVERT: F 61 GLU cc_start: 0.7777 (pm20) cc_final: 0.7563 (pm20) REVERT: F 67 GLU cc_start: 0.8326 (mp0) cc_final: 0.7937 (mp0) REVERT: H 389 MET cc_start: 0.7867 (mmm) cc_final: 0.7529 (mmm) REVERT: H 390 LYS cc_start: 0.8433 (pttt) cc_final: 0.8227 (pttp) REVERT: I 307 MET cc_start: 0.5598 (tmm) cc_final: 0.4841 (tpp) REVERT: I 447 MET cc_start: 0.8504 (ptm) cc_final: 0.8005 (ptm) REVERT: J 162 ILE cc_start: 0.9450 (mm) cc_final: 0.9164 (tt) REVERT: J 385 THR cc_start: 0.8728 (p) cc_final: 0.8244 (p) REVERT: J 389 MET cc_start: 0.7284 (mmm) cc_final: 0.6209 (mmm) REVERT: K 16 MET cc_start: 0.8383 (ptp) cc_final: 0.7531 (ptp) REVERT: K 100 ILE cc_start: 0.9016 (tp) cc_final: 0.8799 (tt) REVERT: K 520 MET cc_start: 0.7898 (ttt) cc_final: 0.7239 (ttt) REVERT: L 59 GLU cc_start: 0.7367 (mp0) cc_final: 0.7116 (mm-30) REVERT: L 73 MET cc_start: 0.8127 (mtm) cc_final: 0.7771 (mtm) REVERT: L 111 MET cc_start: 0.7536 (tpp) cc_final: 0.7165 (tpp) REVERT: L 115 ASP cc_start: 0.7337 (m-30) cc_final: 0.6637 (m-30) REVERT: L 166 MET cc_start: 0.8815 (mmm) cc_final: 0.8434 (mmm) REVERT: L 193 MET cc_start: 0.6678 (tpt) cc_final: 0.6233 (mmm) REVERT: L 194 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: L 389 MET cc_start: 0.7248 (mmm) cc_final: 0.6966 (mmm) REVERT: M 61 GLU cc_start: 0.7298 (pt0) cc_final: 0.7026 (pt0) REVERT: M 401 HIS cc_start: 0.8994 (t-90) cc_final: 0.8561 (t-170) REVERT: N 193 MET cc_start: 0.6877 (mmm) cc_final: 0.6407 (mmm) REVERT: N 194 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: N 390 LYS cc_start: 0.8153 (pttm) cc_final: 0.7633 (pttp) outliers start: 2 outliers final: 0 residues processed: 531 average time/residue: 0.4825 time to fit residues: 446.9995 Evaluate side-chains 444 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 442 time to evaluate : 4.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 0.4980 chunk 672 optimal weight: 4.9990 chunk 613 optimal weight: 8.9990 chunk 653 optimal weight: 20.0000 chunk 393 optimal weight: 40.0000 chunk 284 optimal weight: 9.9990 chunk 513 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 590 optimal weight: 20.0000 chunk 618 optimal weight: 0.3980 chunk 651 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 ASN ** J 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 54789 Z= 0.235 Angle : 0.604 10.612 74074 Z= 0.322 Chirality : 0.043 0.248 8988 Planarity : 0.003 0.059 9618 Dihedral : 7.191 88.621 8204 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.10), residues: 7308 helix: 1.40 (0.08), residues: 4095 sheet: -0.02 (0.15), residues: 1176 loop : -0.58 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 401 PHE 0.010 0.001 PHE D 66 TYR 0.009 0.001 TYR D 506 ARG 0.018 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 517 time to evaluate : 4.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8587 (mp0) cc_final: 0.8009 (mp0) REVERT: A 100 ILE cc_start: 0.9099 (tp) cc_final: 0.8731 (tp) REVERT: G 111 MET cc_start: 0.7629 (tpt) cc_final: 0.7334 (tpp) REVERT: G 389 MET cc_start: 0.7515 (mmt) cc_final: 0.6955 (mmm) REVERT: G 513 LEU cc_start: 0.8607 (tp) cc_final: 0.8374 (tp) REVERT: B 67 GLU cc_start: 0.8325 (mp0) cc_final: 0.8052 (mp0) REVERT: B 447 MET cc_start: 0.7978 (ptm) cc_final: 0.7297 (ppp) REVERT: B 524 LEU cc_start: 0.8021 (tp) cc_final: 0.7788 (tp) REVERT: C 111 MET cc_start: 0.7415 (tpt) cc_final: 0.6989 (tpp) REVERT: D 69 MET cc_start: 0.7869 (mtp) cc_final: 0.7645 (mtp) REVERT: D 100 ILE cc_start: 0.9035 (tp) cc_final: 0.8723 (tp) REVERT: D 447 MET cc_start: 0.8391 (ptm) cc_final: 0.7330 (ttp) REVERT: D 513 LEU cc_start: 0.8874 (mm) cc_final: 0.8129 (tp) REVERT: E 168 LYS cc_start: 0.9555 (mmtm) cc_final: 0.9244 (tptp) REVERT: F 61 GLU cc_start: 0.7799 (pm20) cc_final: 0.7585 (pm20) REVERT: F 67 GLU cc_start: 0.8390 (mp0) cc_final: 0.7944 (mp0) REVERT: H 389 MET cc_start: 0.7782 (mmm) cc_final: 0.7417 (mmm) REVERT: H 390 LYS cc_start: 0.8498 (pttt) cc_final: 0.8223 (pttp) REVERT: I 307 MET cc_start: 0.5598 (tmm) cc_final: 0.4835 (tpp) REVERT: I 447 MET cc_start: 0.8545 (ptm) cc_final: 0.8069 (ptm) REVERT: J 162 ILE cc_start: 0.9465 (mm) cc_final: 0.9182 (tt) REVERT: J 491 MET cc_start: 0.8760 (pmm) cc_final: 0.8546 (pmm) REVERT: K 16 MET cc_start: 0.8363 (ptp) cc_final: 0.7506 (ptp) REVERT: K 100 ILE cc_start: 0.8946 (tp) cc_final: 0.8726 (tt) REVERT: K 520 MET cc_start: 0.7599 (ttt) cc_final: 0.7031 (ttt) REVERT: L 73 MET cc_start: 0.8162 (mtm) cc_final: 0.7809 (mtm) REVERT: L 115 ASP cc_start: 0.7283 (m-30) cc_final: 0.6476 (m-30) REVERT: L 166 MET cc_start: 0.8829 (mmm) cc_final: 0.8473 (mmm) REVERT: L 193 MET cc_start: 0.6733 (tpt) cc_final: 0.6328 (mmm) REVERT: L 194 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: L 389 MET cc_start: 0.7216 (mmm) cc_final: 0.6933 (mmm) REVERT: M 61 GLU cc_start: 0.7400 (pt0) cc_final: 0.7131 (pt0) REVERT: M 67 GLU cc_start: 0.8500 (mp0) cc_final: 0.8162 (mp0) REVERT: M 401 HIS cc_start: 0.9027 (t-90) cc_final: 0.8602 (t-170) REVERT: M 447 MET cc_start: 0.8304 (ptm) cc_final: 0.7702 (ttp) REVERT: N 69 MET cc_start: 0.8036 (mtm) cc_final: 0.7557 (mtm) REVERT: N 193 MET cc_start: 0.6875 (mmm) cc_final: 0.6317 (mmm) REVERT: N 390 LYS cc_start: 0.8292 (pttm) cc_final: 0.7660 (pttp) REVERT: N 447 MET cc_start: 0.7791 (ptp) cc_final: 0.7568 (mtm) outliers start: 1 outliers final: 0 residues processed: 518 average time/residue: 0.4890 time to fit residues: 445.1805 Evaluate side-chains 441 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.6980 chunk 691 optimal weight: 20.0000 chunk 422 optimal weight: 0.9980 chunk 328 optimal weight: 9.9990 chunk 480 optimal weight: 1.9990 chunk 725 optimal weight: 6.9990 chunk 667 optimal weight: 1.9990 chunk 577 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 446 optimal weight: 9.9990 chunk 354 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 54789 Z= 0.192 Angle : 0.591 11.670 74074 Z= 0.312 Chirality : 0.043 0.264 8988 Planarity : 0.003 0.058 9618 Dihedral : 7.124 89.274 8204 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.02 % Allowed : 0.21 % Favored : 99.77 % 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: 0.96 (0.10), residues: 7308 helix: 1.45 (0.08), residues: 4081 sheet: -0.00 (0.15), residues: 1190 loop : -0.50 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.009 0.001 PHE D 66 TYR 0.012 0.001 TYR L 203 ARG 0.017 0.000 ARG D 445 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 516 time to evaluate : 4.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8577 (mp0) cc_final: 0.8095 (mp0) REVERT: A 100 ILE cc_start: 0.9108 (tp) cc_final: 0.8756 (tp) REVERT: A 447 MET cc_start: 0.8380 (ptt) cc_final: 0.8028 (ppp) REVERT: G 69 MET cc_start: 0.8061 (mtt) cc_final: 0.7779 (mtt) REVERT: G 111 MET cc_start: 0.7666 (tpt) cc_final: 0.7318 (tpp) REVERT: G 389 MET cc_start: 0.7630 (mmt) cc_final: 0.7034 (mmm) REVERT: G 513 LEU cc_start: 0.8621 (tp) cc_final: 0.8382 (tp) REVERT: B 67 GLU cc_start: 0.8408 (mp0) cc_final: 0.8142 (mp0) REVERT: B 447 MET cc_start: 0.7988 (ptm) cc_final: 0.7012 (ppp) REVERT: B 524 LEU cc_start: 0.8001 (tp) cc_final: 0.7759 (tp) REVERT: C 111 MET cc_start: 0.7484 (tpt) cc_final: 0.7121 (tpp) REVERT: D 100 ILE cc_start: 0.8964 (tp) cc_final: 0.8705 (tp) REVERT: D 447 MET cc_start: 0.8332 (ptm) cc_final: 0.7176 (ttp) REVERT: D 513 LEU cc_start: 0.8761 (mm) cc_final: 0.7979 (tp) REVERT: E 69 MET cc_start: 0.8070 (mtt) cc_final: 0.7811 (mtt) REVERT: E 168 LYS cc_start: 0.9555 (mmtm) cc_final: 0.9227 (tptp) REVERT: E 522 THR cc_start: 0.8001 (m) cc_final: 0.7783 (p) REVERT: F 61 GLU cc_start: 0.7761 (pm20) cc_final: 0.7529 (pm20) REVERT: F 67 GLU cc_start: 0.8369 (mp0) cc_final: 0.7940 (mp0) REVERT: H 389 MET cc_start: 0.7774 (mmm) cc_final: 0.7415 (mmm) REVERT: H 390 LYS cc_start: 0.8473 (pttt) cc_final: 0.8239 (pttp) REVERT: I 307 MET cc_start: 0.5557 (tmm) cc_final: 0.4822 (tpp) REVERT: I 447 MET cc_start: 0.8470 (ptm) cc_final: 0.7995 (ptm) REVERT: J 162 ILE cc_start: 0.9463 (mm) cc_final: 0.9185 (tt) REVERT: J 491 MET cc_start: 0.8666 (pmm) cc_final: 0.8452 (pmm) REVERT: K 16 MET cc_start: 0.8432 (ptp) cc_final: 0.7579 (ptp) REVERT: K 100 ILE cc_start: 0.8999 (tp) cc_final: 0.8768 (tt) REVERT: K 520 MET cc_start: 0.7951 (ttt) cc_final: 0.7338 (ttt) REVERT: L 59 GLU cc_start: 0.7341 (mp0) cc_final: 0.6899 (mm-30) REVERT: L 111 MET cc_start: 0.7421 (tpt) cc_final: 0.7101 (tpp) REVERT: L 166 MET cc_start: 0.8811 (mmm) cc_final: 0.8458 (mmm) REVERT: L 194 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8453 (pm20) REVERT: L 389 MET cc_start: 0.7240 (mmm) cc_final: 0.6947 (mmm) REVERT: M 61 GLU cc_start: 0.7346 (pt0) cc_final: 0.7063 (pt0) REVERT: M 67 GLU cc_start: 0.8534 (mp0) cc_final: 0.8147 (mp0) REVERT: M 401 HIS cc_start: 0.9004 (t-90) cc_final: 0.8576 (t-170) REVERT: N 193 MET cc_start: 0.6825 (mmm) cc_final: 0.6329 (mmm) REVERT: N 390 LYS cc_start: 0.8226 (pttm) cc_final: 0.7844 (pttp) outliers start: 1 outliers final: 0 residues processed: 517 average time/residue: 0.4646 time to fit residues: 422.8995 Evaluate side-chains 443 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 4.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 4.9990 chunk 615 optimal weight: 1.9990 chunk 176 optimal weight: 0.3980 chunk 532 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 578 optimal weight: 0.6980 chunk 242 optimal weight: 9.9990 chunk 593 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.093526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.058330 restraints weight = 250824.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060254 restraints weight = 144020.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061514 restraints weight = 98019.466| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 54789 Z= 0.202 Angle : 0.593 12.037 74074 Z= 0.314 Chirality : 0.043 0.242 8988 Planarity : 0.003 0.065 9618 Dihedral : 6.985 89.873 8204 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.02 % Allowed : 0.27 % Favored : 99.72 % 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: 0.96 (0.10), residues: 7308 helix: 1.46 (0.08), residues: 4095 sheet: -0.01 (0.15), residues: 1190 loop : -0.51 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 401 PHE 0.010 0.001 PHE B 8 TYR 0.007 0.001 TYR L 203 ARG 0.014 0.000 ARG D 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8972.72 seconds wall clock time: 160 minutes 25.08 seconds (9625.08 seconds total)