Starting phenix.real_space_refine on Wed Nov 20 07:56:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/11_2024/8blf_16109.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/11_2024/8blf_16109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/11_2024/8blf_16109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/11_2024/8blf_16109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/11_2024/8blf_16109.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/11_2024/8blf_16109.cif" } resolution = 3.9 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= 0.004 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 87 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 31.49, per 1000 atoms: 0.58 Number of scatterers: 54376 At special positions: 0 Unit cell: (153.6, 151.68, 162.24, 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: 13.68 Conformation dependent library (CDL) restraints added in 7.3 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: 280 helices and 84 sheets defined 58.9% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 86 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 removed outlier: 3.572A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.505A pdb=" N ILE A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 4.469A pdb=" N VAL A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) 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: 4.149A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 409 removed outlier: 3.525A pdb=" N GLU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.591A 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: 3.873A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.606A 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: 3.521A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 242 removed outlier: 3.927A 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 removed outlier: 3.850A pdb=" N MET G 267 " --> pdb=" O VAL G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 removed outlier: 3.517A 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 425 Processing helix chain 'G' and resid 433 through 448 removed outlier: 3.807A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 459 Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 497 through 515 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.668A pdb=" N GLU B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 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 removed outlier: 3.588A pdb=" N ILE B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.505A pdb=" N ILE B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 4.464A pdb=" N VAL B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) 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: 4.067A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 409 removed outlier: 3.523A pdb=" N GLU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 425 Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.607A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 removed outlier: 3.862A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.573A 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: 3.535A 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: 3.520A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 removed outlier: 3.900A 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 removed outlier: 3.924A pdb=" N MET C 267 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 409 Processing helix chain 'C' and resid 416 through 425 Processing helix chain 'C' and resid 433 through 447 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.522A 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 515 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.703A pdb=" N GLU D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 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 removed outlier: 3.597A pdb=" N ILE D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.526A pdb=" N ILE D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 removed outlier: 4.460A pdb=" N VAL D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) 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: 4.110A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 409 removed outlier: 3.510A pdb=" N GLU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 425 Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.554A 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 59 Processing helix chain 'E' and resid 64 through 85 removed outlier: 3.851A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.546A 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 141 through 152 removed outlier: 3.550A pdb=" N ALA E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 removed outlier: 3.536A pdb=" N ILE E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 242 removed outlier: 3.813A 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 removed outlier: 3.765A pdb=" N MET E 267 " --> pdb=" O VAL E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.543A 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 425 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 515 Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.896A pdb=" N GLU F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 Processing helix chain 'F' and resid 88 through 109 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 removed outlier: 3.502A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.477A pdb=" N VAL F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) 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: 4.052A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 409 removed outlier: 3.522A pdb=" N GLU F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 425 Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.575A 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: 3.601A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 85 removed outlier: 3.800A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 78 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 141 through 152 removed outlier: 3.582A pdb=" N ALA H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 169 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.521A pdb=" N ILE H 205 " --> pdb=" O PRO H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 241 Processing helix chain 'H' and resid 259 through 267 removed outlier: 3.847A pdb=" N MET H 267 " --> pdb=" O VAL H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 297 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 375 removed outlier: 3.505A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 409 Processing helix chain 'H' and resid 416 through 425 Processing helix chain 'H' and resid 433 through 447 Processing helix chain 'H' and resid 448 through 459 Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 488 through 492 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 60 removed outlier: 3.666A pdb=" N GLU I 59 " --> pdb=" O SER I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 removed outlier: 3.523A pdb=" N ILE I 144 " --> pdb=" O ASP I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.510A pdb=" N ILE I 205 " --> pdb=" O PRO I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 244 removed outlier: 4.469A pdb=" N VAL I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) 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 375 removed outlier: 4.093A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 409 removed outlier: 3.533A pdb=" N GLU I 409 " --> pdb=" O ALA I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 425 Processing helix chain 'I' and resid 433 through 447 Processing helix chain 'I' and resid 448 through 459 Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 488 through 492 Processing helix chain 'I' and resid 497 through 516 removed outlier: 3.639A 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 60 removed outlier: 3.595A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 85 removed outlier: 3.911A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (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 removed outlier: 3.566A pdb=" N ALA J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.503A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.510A pdb=" N ILE J 205 " --> pdb=" O PRO J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 241 removed outlier: 3.940A 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 removed outlier: 3.755A pdb=" N MET J 267 " --> pdb=" O VAL J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 297 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: 3.580A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 409 Processing helix chain 'J' and resid 416 through 425 Processing helix chain 'J' and resid 433 through 447 Processing helix chain 'J' and resid 448 through 459 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 497 through 515 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 52 through 60 Processing helix chain 'K' and resid 64 through 86 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 removed outlier: 3.568A pdb=" N ILE K 144 " --> pdb=" O ASP K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.536A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 244 removed outlier: 4.462A pdb=" N VAL K 236 " --> pdb=" O GLU K 232 " (cutoff:3.500A) 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: 4.071A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 409 Processing helix chain 'K' and resid 416 through 425 Processing helix chain 'K' and resid 433 through 447 Processing helix chain 'K' and resid 448 through 459 Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.552A 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 59 Processing helix chain 'L' and resid 64 through 85 removed outlier: 3.916A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.557A 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 141 through 152 removed outlier: 3.562A pdb=" N ALA L 145 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 169 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.502A pdb=" N ILE L 205 " --> pdb=" O PRO L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 241 removed outlier: 4.375A 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 removed outlier: 3.597A pdb=" N MET L 267 " --> pdb=" O VAL L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 308 through 312 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 375 Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 425 Processing helix chain 'L' and resid 433 through 447 Processing helix chain 'L' and resid 448 through 459 Processing helix chain 'L' and resid 461 through 472 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 60 removed outlier: 3.622A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE M 60 " --> pdb=" O VAL M 56 " (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 removed outlier: 3.545A pdb=" N ILE M 144 " --> pdb=" O ASP M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.521A pdb=" N GLY M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 removed outlier: 3.521A pdb=" N ILE M 205 " --> pdb=" O PRO M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 244 removed outlier: 4.475A pdb=" N VAL M 236 " --> pdb=" O GLU M 232 " (cutoff:3.500A) 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 375 removed outlier: 4.166A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 409 removed outlier: 3.540A pdb=" N GLU M 409 " --> pdb=" O ALA M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 425 Processing helix chain 'M' and resid 433 through 447 Processing helix chain 'M' and resid 448 through 459 Processing helix chain 'M' and resid 461 through 472 Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'M' and resid 497 through 516 removed outlier: 3.593A 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: 3.518A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 85 removed outlier: 3.896A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 141 through 152 removed outlier: 3.676A 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: 3.506A pdb=" N ILE N 205 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 242 removed outlier: 4.119A 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 removed outlier: 3.778A pdb=" N MET N 267 " --> pdb=" O VAL N 263 " (cutoff:3.500A) 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: 3.528A 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 448 removed outlier: 3.882A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 459 Processing helix chain 'N' and resid 461 through 472 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: 7.048A pdb=" N VAL B 39 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET A 520 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.273A pdb=" N ASN A 37 " --> pdb=" O THR M 517 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS M 519 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.601A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.273A 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: 6.367A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 9.536A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.470A 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: 6.330A pdb=" N ASN N 37 " --> pdb=" O THR G 517 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS G 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 48 through 50 removed outlier: 7.037A pdb=" N ASN G 37 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N VAL C 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL G 39 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASP C 523 " --> pdb=" O VAL G 39 " (cutoff:3.500A) 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: 6.748A pdb=" N THR G 330 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE G 325 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE G 332 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL G 323 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP G 334 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.668A 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: 3.518A pdb=" N VAL G 323 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.808A 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: 7.142A pdb=" N VAL D 39 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET B 520 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.519A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.887A 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: 6.383A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.418A 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: 9.550A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.495A 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 removed outlier: 6.353A pdb=" N ASN C 37 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS E 519 " --> pdb=" O ASN C 37 " (cutoff:3.500A) 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: 6.752A pdb=" N THR C 330 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE C 325 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE C 332 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 323 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP C 334 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 213 through 216 removed outlier: 9.668A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC8, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC9, first strand: chain 'D' and resid 4 through 8 removed outlier: 4.139A pdb=" N THR D 517 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL F 39 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS D 519 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.533A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.383A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 213 through 216 removed outlier: 9.539A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD5, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AD6, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.842A pdb=" N ASN E 37 " --> pdb=" O CYS H 519 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL H 521 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL E 39 " --> pdb=" O VAL H 521 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ASP H 523 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AD8, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.754A pdb=" N THR E 330 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE E 325 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE E 332 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL E 323 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP E 334 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 213 through 216 removed outlier: 9.671A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AE2, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AE3, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.271A pdb=" N ASN I 37 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS F 519 " --> pdb=" O ASN I 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.538A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.360A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 213 through 216 removed outlier: 9.538A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE8, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AE9, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.027A pdb=" N ASN H 37 " --> pdb=" O CYS J 519 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL J 521 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL H 39 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ASP J 523 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AF2, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.759A pdb=" N THR H 330 " --> pdb=" O ILE H 325 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE H 325 " --> pdb=" O THR H 330 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE H 332 " --> pdb=" O VAL H 323 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL H 323 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP H 334 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 213 through 216 removed outlier: 9.673A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF5, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.924A pdb=" N VAL K 39 " --> pdb=" O GLU I 518 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N MET I 520 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.488A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.379A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 213 through 216 removed outlier: 9.553A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG2, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AG3, first strand: chain 'J' and resid 48 through 50 removed outlier: 7.969A pdb=" N ASN J 37 " --> pdb=" O GLU L 518 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET L 520 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL J 39 " --> pdb=" O MET L 520 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N THR L 522 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AG5, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.738A pdb=" N THR J 330 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE J 325 " --> pdb=" O THR J 330 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE J 332 " --> pdb=" O VAL J 323 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL J 323 " --> pdb=" O ILE J 332 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP J 334 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL J 323 " --> pdb=" O LEU J 215 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.738A pdb=" N THR J 330 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE J 325 " --> pdb=" O THR J 330 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE J 332 " --> pdb=" O VAL J 323 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL J 323 " --> pdb=" O ILE J 332 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP J 334 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG8, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AG9, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.258A pdb=" N ASN M 37 " --> pdb=" O THR K 517 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS K 519 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 174 through 179 removed outlier: 6.524A pdb=" N VAL K 174 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE K 379 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.363A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 213 through 216 removed outlier: 9.540A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH5, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AH6, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.266A pdb=" N ASN L 37 " --> pdb=" O THR N 517 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS N 519 " --> pdb=" O ASN L 37 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AH8, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.713A pdb=" N THR L 330 " --> pdb=" O ILE L 325 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE L 325 " --> pdb=" O THR L 330 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE L 332 " --> pdb=" O VAL L 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL L 323 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP L 334 " --> pdb=" O LYS L 321 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.713A pdb=" N THR L 330 " --> pdb=" O ILE L 325 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE L 325 " --> pdb=" O THR L 330 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE L 332 " --> pdb=" O VAL L 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL L 323 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP L 334 " --> pdb=" O LYS L 321 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AI2, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AI3, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.510A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.385A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 213 through 216 removed outlier: 9.546A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AI7, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AI8, first strand: chain 'N' and resid 174 through 179 Processing sheet with id=AI9, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.749A pdb=" N THR N 330 " --> pdb=" O ILE N 325 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE N 325 " --> pdb=" O THR N 330 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE N 332 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL N 323 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP N 334 " --> pdb=" O LYS N 321 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 213 through 216 removed outlier: 9.693A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'N' and resid 476 through 479 3695 hydrogen bonds defined for protein. 10662 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: 26.96 Time building geometry restraints manager: 15.54 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: 18739 1.34 - 1.46: 8159 1.46 - 1.58: 27345 1.58 - 1.70: 28 1.70 - 1.82: 518 Bond restraints: 54789 Sorted by residual: bond pdb=" CG1 ILE M 100 " pdb=" CD1 ILE M 100 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 4.95e+00 bond pdb=" CB MET M 16 " pdb=" CG MET M 16 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.37e+00 bond pdb=" CB MET B 16 " pdb=" CG MET B 16 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.34e+00 bond pdb=" CB MET D 16 " pdb=" CG MET D 16 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.10e+00 bond pdb=" CB MET A 16 " pdb=" CG MET A 16 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 2.97e+00 ... (remaining 54784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 73720 3.32 - 6.64: 316 6.64 - 9.96: 30 9.96 - 13.28: 3 13.28 - 16.59: 5 Bond angle restraints: 74074 Sorted by residual: angle pdb=" CB MET B 16 " pdb=" CG MET B 16 " pdb=" SD MET B 16 " ideal model delta sigma weight residual 112.70 96.11 16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" CB MET M 16 " pdb=" CG MET M 16 " pdb=" SD MET M 16 " ideal model delta sigma weight residual 112.70 97.88 14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CB MET K 16 " pdb=" CG MET K 16 " pdb=" SD MET K 16 " ideal model delta sigma weight residual 112.70 98.32 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" CB MET D 16 " pdb=" CG MET D 16 " pdb=" SD MET D 16 " ideal model delta sigma weight residual 112.70 98.97 13.73 3.00e+00 1.11e-01 2.10e+01 angle pdb=" CB MET A 16 " pdb=" CG MET A 16 " pdb=" SD MET A 16 " ideal model delta sigma weight residual 112.70 99.27 13.43 3.00e+00 1.11e-01 2.01e+01 ... (remaining 74069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 31148 17.95 - 35.91: 2422 35.91 - 53.86: 503 53.86 - 71.82: 103 71.82 - 89.77: 40 Dihedral angle restraints: 34216 sinusoidal: 13524 harmonic: 20692 Sorted by residual: dihedral pdb=" CA GLU H 61 " pdb=" C GLU H 61 " pdb=" N LEU H 62 " pdb=" CA LEU H 62 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLU N 61 " pdb=" C GLU N 61 " pdb=" N LEU N 62 " pdb=" CA LEU N 62 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ALA G 260 " pdb=" CA ALA G 260 " ideal model delta harmonic sigma weight residual -180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 34213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 6917 0.050 - 0.100: 1685 0.100 - 0.151: 373 0.151 - 0.201: 7 0.201 - 0.251: 6 Chirality restraints: 8988 Sorted by residual: chirality pdb=" CB ILE D 49 " pdb=" CA ILE D 49 " pdb=" CG1 ILE D 49 " pdb=" CG2 ILE D 49 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE F 49 " pdb=" CA ILE F 49 " pdb=" CG1 ILE F 49 " pdb=" CG2 ILE F 49 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE I 49 " pdb=" CA ILE I 49 " pdb=" CG1 ILE I 49 " pdb=" CG2 ILE I 49 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 8985 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 59 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" CD GLU B 59 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B 59 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 59 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 387 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C VAL F 387 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL F 387 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU F 388 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 44 " 0.007 2.00e-02 2.50e+03 1.15e-02 2.31e+00 pdb=" CG PHE L 44 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE L 44 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE L 44 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE L 44 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 44 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 44 " -0.000 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6298 2.75 - 3.29: 56957 3.29 - 3.82: 95750 3.82 - 4.36: 111058 4.36 - 4.90: 192100 Nonbonded interactions: 462163 Sorted by model distance: nonbonded pdb=" OE2 GLU J 238 " pdb=" OG SER L 228 " model vdw 2.210 3.040 nonbonded pdb=" O LEU N 262 " pdb=" OG1 THR N 266 " model vdw 2.229 3.040 nonbonded pdb=" O LEU C 262 " pdb=" OG1 THR C 266 " model vdw 2.234 3.040 nonbonded pdb=" O LEU H 262 " pdb=" OG1 THR H 266 " model vdw 2.239 3.040 nonbonded pdb=" O LEU G 262 " pdb=" OG1 THR G 266 " model vdw 2.241 3.040 ... (remaining 462158 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: 2.670 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: 0.090 Extract box with map and model: 1.990 Check model and map are aligned: 0.390 Set scattering table: 0.500 Process input model: 121.480 Find NCS groups from input model: 3.360 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.087 54789 Z= 0.281 Angle : 0.680 16.594 74074 Z= 0.378 Chirality : 0.045 0.251 8988 Planarity : 0.004 0.033 9618 Dihedral : 13.764 89.772 20944 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % 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: 0.29 (0.09), residues: 7308 helix: 0.87 (0.08), residues: 4095 sheet: -0.39 (0.15), residues: 1015 loop : -0.63 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 401 PHE 0.026 0.002 PHE L 44 TYR 0.023 0.001 TYR F 485 ARG 0.007 0.000 ARG I 58 *********************** 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 364 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 6.477 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: A 267 MET cc_start: -0.0990 (mpp) cc_final: -0.1263 (mpp) REVERT: A 389 MET cc_start: 0.3096 (mmt) cc_final: 0.2864 (mmm) REVERT: F 327 LYS cc_start: 0.7731 (mmpt) cc_final: 0.7414 (mmmt) REVERT: H 389 MET cc_start: 0.7019 (tpp) cc_final: 0.6265 (ttm) REVERT: H 488 MET cc_start: 0.8134 (mmt) cc_final: 0.7384 (mmt) REVERT: J 233 MET cc_start: 0.5298 (ppp) cc_final: 0.4235 (ptt) REVERT: K 267 MET cc_start: -0.1583 (mpp) cc_final: -0.1815 (mpp) REVERT: K 327 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7384 (mmmt) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.6099 time to fit residues: 389.5158 Evaluate side-chains 299 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 6.128 ------------------------------------------------------------------------------- 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: 1.9990 chunk 551 optimal weight: 0.5980 chunk 306 optimal weight: 0.6980 chunk 188 optimal weight: 0.0060 chunk 372 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 570 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 424 optimal weight: 5.9990 chunk 661 optimal weight: 20.0000 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 453 GLN B 290 GLN B 319 GLN D 72 GLN D 319 GLN F 319 GLN F 453 GLN I 319 GLN K 194 GLN K 319 GLN M 37 ASN M 290 GLN M 319 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54789 Z= 0.170 Angle : 0.541 11.432 74074 Z= 0.291 Chirality : 0.042 0.153 8988 Planarity : 0.003 0.027 9618 Dihedral : 8.211 69.791 8204 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.43 % Allowed : 6.01 % Favored : 93.57 % 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: 1.26 (0.08), residues: 4186 sheet: -0.26 (0.15), residues: 1001 loop : -0.61 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 401 PHE 0.024 0.002 PHE M 195 TYR 0.021 0.001 TYR M 485 ARG 0.004 0.000 ARG I 58 *********************** 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 389 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 365 time to evaluate : 6.219 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 193 MET cc_start: 0.6369 (tpt) cc_final: 0.5824 (tpp) REVERT: G 267 MET cc_start: -0.2826 (OUTLIER) cc_final: -0.3111 (mpp) REVERT: B 193 MET cc_start: 0.6837 (tpt) cc_final: 0.6290 (tpp) REVERT: B 520 MET cc_start: 0.8350 (mtp) cc_final: 0.7928 (mtt) REVERT: C 387 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7519 (m) REVERT: D 69 MET cc_start: 0.5773 (mmt) cc_final: 0.5569 (mmt) REVERT: D 193 MET cc_start: 0.6905 (tpt) cc_final: 0.6079 (tpp) REVERT: E 288 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7355 (mmt) REVERT: H 267 MET cc_start: 0.0596 (ptt) cc_final: -0.0288 (mpp) REVERT: H 389 MET cc_start: 0.7037 (tpp) cc_final: 0.6340 (ttm) REVERT: I 193 MET cc_start: 0.6562 (tpt) cc_final: 0.6099 (tpp) REVERT: J 233 MET cc_start: 0.5210 (ppp) cc_final: 0.4349 (ptt) REVERT: J 288 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7058 (mmt) REVERT: K 267 MET cc_start: -0.1080 (mpp) cc_final: -0.1431 (mtm) REVERT: K 327 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7327 (mmmt) REVERT: L 288 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7233 (mmt) REVERT: L 491 MET cc_start: 0.7411 (ptp) cc_final: 0.7137 (ptp) REVERT: M 193 MET cc_start: 0.6810 (tpt) cc_final: 0.6187 (tpp) REVERT: N 288 MET cc_start: 0.7006 (ptp) cc_final: 0.6753 (ptp) outliers start: 24 outliers final: 3 residues processed: 378 average time/residue: 0.6137 time to fit residues: 406.5296 Evaluate side-chains 311 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 303 time to evaluate : 5.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 550 optimal weight: 20.0000 chunk 450 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 662 optimal weight: 2.9990 chunk 715 optimal weight: 1.9990 chunk 589 optimal weight: 6.9990 chunk 656 optimal weight: 10.0000 chunk 225 optimal weight: 30.0000 chunk 531 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 37 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54789 Z= 0.208 Angle : 0.522 11.539 74074 Z= 0.279 Chirality : 0.041 0.141 8988 Planarity : 0.003 0.028 9618 Dihedral : 7.827 71.006 8204 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.64 % Allowed : 8.40 % Favored : 90.96 % 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: 1.44 (0.08), residues: 4144 sheet: -0.11 (0.15), residues: 1008 loop : -0.53 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 401 PHE 0.012 0.001 PHE K 195 TYR 0.017 0.001 TYR M 485 ARG 0.002 0.000 ARG K 368 *********************** 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 362 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 326 time to evaluate : 5.483 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: G 267 MET cc_start: -0.2778 (OUTLIER) cc_final: -0.3048 (mpp) REVERT: G 491 MET cc_start: 0.6661 (ptp) cc_final: 0.6410 (ptp) REVERT: D 100 ILE cc_start: 0.8791 (tt) cc_final: 0.8490 (tt) REVERT: F 83 ASP cc_start: 0.7232 (m-30) cc_final: 0.6846 (p0) REVERT: F 514 MET cc_start: 0.8531 (ttt) cc_final: 0.8318 (ttp) REVERT: H 267 MET cc_start: 0.0585 (ptt) cc_final: -0.0188 (mpp) REVERT: H 389 MET cc_start: 0.7042 (tpp) cc_final: 0.6282 (ttm) REVERT: J 233 MET cc_start: 0.5158 (ppp) cc_final: 0.4335 (ptt) REVERT: K 267 MET cc_start: -0.0374 (OUTLIER) cc_final: -0.0742 (mtm) REVERT: K 327 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7352 (mmmt) REVERT: L 288 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7517 (ptp) REVERT: M 69 MET cc_start: 0.6836 (tpp) cc_final: 0.6314 (tpp) REVERT: N 267 MET cc_start: -0.2613 (OUTLIER) cc_final: -0.2827 (mpp) outliers start: 36 outliers final: 9 residues processed: 352 average time/residue: 0.5423 time to fit residues: 337.0410 Evaluate side-chains 311 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 298 time to evaluate : 6.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain N residue 267 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 8.9990 chunk 497 optimal weight: 3.9990 chunk 343 optimal weight: 50.0000 chunk 73 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 444 optimal weight: 7.9990 chunk 664 optimal weight: 5.9990 chunk 703 optimal weight: 20.0000 chunk 347 optimal weight: 30.0000 chunk 629 optimal weight: 0.0370 chunk 189 optimal weight: 30.0000 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN B 72 GLN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN D 437 ASN F 37 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN K 437 ASN M 72 GLN M 437 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 54789 Z= 0.423 Angle : 0.624 13.218 74074 Z= 0.332 Chirality : 0.045 0.166 8988 Planarity : 0.004 0.035 9618 Dihedral : 7.960 72.838 8204 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.22 % Allowed : 9.75 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 7308 helix: 1.21 (0.08), residues: 4144 sheet: -0.19 (0.15), residues: 1008 loop : -0.64 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 401 PHE 0.015 0.002 PHE E 8 TYR 0.019 0.002 TYR C 485 ARG 0.004 0.001 ARG A 13 *********************** 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 368 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 299 time to evaluate : 5.810 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: G 267 MET cc_start: -0.2886 (OUTLIER) cc_final: -0.3166 (mpp) REVERT: B 267 MET cc_start: 0.0264 (OUTLIER) cc_final: -0.0272 (mtp) REVERT: B 519 CYS cc_start: 0.8419 (m) cc_final: 0.8176 (t) REVERT: C 59 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: F 488 MET cc_start: 0.9162 (mmm) cc_final: 0.8267 (mmm) REVERT: H 267 MET cc_start: 0.0911 (ptt) cc_final: 0.0090 (mpp) REVERT: H 389 MET cc_start: 0.7037 (tpp) cc_final: 0.6441 (ttp) REVERT: J 233 MET cc_start: 0.5069 (ppp) cc_final: 0.4217 (ptt) REVERT: K 267 MET cc_start: -0.0670 (OUTLIER) cc_final: -0.1057 (mtm) REVERT: K 363 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: K 514 MET cc_start: 0.8600 (ttt) cc_final: 0.8312 (ttp) REVERT: L 288 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7528 (ptp) REVERT: M 69 MET cc_start: 0.7279 (tpp) cc_final: 0.6658 (tpp) REVERT: M 327 LYS cc_start: 0.7747 (mmmt) cc_final: 0.7523 (mmmt) REVERT: N 267 MET cc_start: -0.2463 (mpp) cc_final: -0.2691 (mpp) outliers start: 69 outliers final: 38 residues processed: 347 average time/residue: 0.6038 time to fit residues: 371.2427 Evaluate side-chains 334 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 5.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 514 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 3.9990 chunk 399 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 523 optimal weight: 0.8980 chunk 290 optimal weight: 50.0000 chunk 600 optimal weight: 50.0000 chunk 486 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 359 optimal weight: 0.9980 chunk 631 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN I 194 GLN M 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 54789 Z= 0.236 Angle : 0.536 11.126 74074 Z= 0.285 Chirality : 0.042 0.148 8988 Planarity : 0.003 0.030 9618 Dihedral : 7.735 72.123 8204 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.13 % Allowed : 11.27 % Favored : 87.59 % 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: 0.82 (0.10), residues: 7308 helix: 1.37 (0.08), residues: 4151 sheet: -0.17 (0.15), residues: 1008 loop : -0.61 (0.12), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 401 PHE 0.009 0.001 PHE B 66 TYR 0.015 0.001 TYR M 485 ARG 0.002 0.000 ARG K 368 *********************** 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 384 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 320 time to evaluate : 5.935 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: G 267 MET cc_start: -0.2954 (OUTLIER) cc_final: -0.3248 (mpp) REVERT: B 267 MET cc_start: 0.0305 (OUTLIER) cc_final: -0.0241 (mtp) REVERT: C 59 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: F 488 MET cc_start: 0.9049 (mmm) cc_final: 0.8161 (mmm) REVERT: H 267 MET cc_start: 0.0923 (ptt) cc_final: 0.0100 (mpp) REVERT: H 288 MET cc_start: 0.7280 (ptp) cc_final: 0.6977 (ptp) REVERT: J 233 MET cc_start: 0.5086 (ppp) cc_final: 0.4233 (ptt) REVERT: K 267 MET cc_start: -0.0412 (OUTLIER) cc_final: -0.0906 (mtp) REVERT: K 327 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7414 (mmmt) REVERT: K 363 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: K 514 MET cc_start: 0.8528 (ttt) cc_final: 0.8281 (ttp) REVERT: L 288 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7561 (ptp) REVERT: M 69 MET cc_start: 0.7037 (tpp) cc_final: 0.6494 (tpp) REVERT: M 327 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7525 (mmmt) REVERT: N 267 MET cc_start: -0.2467 (OUTLIER) cc_final: -0.2708 (mpp) outliers start: 64 outliers final: 29 residues processed: 367 average time/residue: 0.6009 time to fit residues: 390.3241 Evaluate side-chains 340 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 5.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain N residue 267 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 8.9990 chunk 633 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 413 optimal weight: 0.0050 chunk 173 optimal weight: 20.0000 chunk 704 optimal weight: 9.9990 chunk 584 optimal weight: 1.9990 chunk 326 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 232 optimal weight: 30.0000 chunk 369 optimal weight: 0.6980 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54789 Z= 0.222 Angle : 0.538 11.719 74074 Z= 0.284 Chirality : 0.041 0.155 8988 Planarity : 0.003 0.030 9618 Dihedral : 7.572 71.615 8204 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.36 % Allowed : 11.73 % Favored : 86.90 % 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: 1.43 (0.08), residues: 4158 sheet: -0.16 (0.15), residues: 1008 loop : -0.59 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 401 PHE 0.013 0.001 PHE E 8 TYR 0.015 0.001 TYR N 485 ARG 0.002 0.000 ARG K 368 *********************** 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 399 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 322 time to evaluate : 6.065 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 519 CYS cc_start: 0.8033 (m) cc_final: 0.7766 (t) REVERT: G 267 MET cc_start: -0.2953 (OUTLIER) cc_final: -0.3211 (mpp) REVERT: B 267 MET cc_start: 0.0298 (OUTLIER) cc_final: -0.0226 (mtp) REVERT: C 59 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: F 488 MET cc_start: 0.9009 (mmm) cc_final: 0.8122 (mmm) REVERT: H 267 MET cc_start: 0.0942 (ptt) cc_final: 0.0150 (mpp) REVERT: H 288 MET cc_start: 0.7375 (ptp) cc_final: 0.7129 (ptp) REVERT: H 389 MET cc_start: 0.7149 (tpp) cc_final: 0.6094 (ttp) REVERT: I 69 MET cc_start: 0.6151 (tpp) cc_final: 0.5889 (tpp) REVERT: J 233 MET cc_start: 0.4608 (ppp) cc_final: 0.3861 (ptt) REVERT: K 267 MET cc_start: -0.0426 (OUTLIER) cc_final: -0.0920 (mtp) REVERT: K 327 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7362 (mmmt) REVERT: K 363 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: L 134 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8833 (mp) REVERT: L 288 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7574 (ptp) REVERT: L 491 MET cc_start: 0.6920 (ptp) cc_final: 0.6719 (ptp) REVERT: L 520 MET cc_start: 0.7726 (mtt) cc_final: 0.7509 (mtt) REVERT: M 69 MET cc_start: 0.6804 (tpp) cc_final: 0.6510 (tpp) REVERT: M 514 MET cc_start: 0.8661 (ttm) cc_final: 0.8456 (ttp) REVERT: N 267 MET cc_start: -0.2484 (mpp) cc_final: -0.2715 (mpp) outliers start: 77 outliers final: 41 residues processed: 379 average time/residue: 0.5940 time to fit residues: 396.4112 Evaluate side-chains 355 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 307 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 401 optimal weight: 10.0000 chunk 514 optimal weight: 0.9990 chunk 398 optimal weight: 7.9990 chunk 592 optimal weight: 0.5980 chunk 393 optimal weight: 20.0000 chunk 701 optimal weight: 2.9990 chunk 439 optimal weight: 40.0000 chunk 427 optimal weight: 3.9990 chunk 323 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 54789 Z= 0.157 Angle : 0.530 12.905 74074 Z= 0.277 Chirality : 0.041 0.197 8988 Planarity : 0.003 0.029 9618 Dihedral : 7.366 71.254 8204 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.92 % Allowed : 12.94 % Favored : 86.14 % 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: 1.01 (0.10), residues: 7308 helix: 1.56 (0.08), residues: 4158 sheet: -0.12 (0.15), residues: 1008 loop : -0.59 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 401 PHE 0.010 0.001 PHE B 195 TYR 0.013 0.001 TYR N 485 ARG 0.002 0.000 ARG K 368 *********************** 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 391 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 6.320 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 14 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8631 (m) REVERT: G 267 MET cc_start: -0.2925 (OUTLIER) cc_final: -0.3207 (mpp) REVERT: B 267 MET cc_start: 0.0224 (OUTLIER) cc_final: -0.0284 (mtp) REVERT: C 59 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: C 387 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7499 (m) REVERT: F 195 PHE cc_start: 0.7383 (p90) cc_final: 0.6703 (p90) REVERT: F 232 GLU cc_start: 0.4037 (OUTLIER) cc_final: 0.3313 (mp0) REVERT: F 488 MET cc_start: 0.8953 (mmm) cc_final: 0.8088 (mmm) REVERT: H 267 MET cc_start: 0.0878 (ptt) cc_final: 0.0082 (mpp) REVERT: H 288 MET cc_start: 0.7382 (ptp) cc_final: 0.7161 (ptp) REVERT: H 389 MET cc_start: 0.7129 (tpp) cc_final: 0.6101 (ttp) REVERT: J 233 MET cc_start: 0.4258 (ppp) cc_final: 0.3419 (ptt) REVERT: K 267 MET cc_start: -0.0452 (OUTLIER) cc_final: -0.0951 (mtp) REVERT: K 327 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7400 (mmmt) REVERT: K 363 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: K 514 MET cc_start: 0.8379 (ttp) cc_final: 0.8147 (ttp) REVERT: L 288 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7613 (ptp) REVERT: L 520 MET cc_start: 0.7632 (mtt) cc_final: 0.7297 (mtt) REVERT: M 69 MET cc_start: 0.6454 (tpp) cc_final: 0.5920 (tpp) REVERT: M 90 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8654 (m) REVERT: M 195 PHE cc_start: 0.7384 (p90) cc_final: 0.6765 (p90) REVERT: N 267 MET cc_start: -0.2657 (mpp) cc_final: -0.2901 (mpp) outliers start: 52 outliers final: 33 residues processed: 376 average time/residue: 0.6042 time to fit residues: 398.5797 Evaluate side-chains 363 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 6.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 9.9990 chunk 280 optimal weight: 0.0170 chunk 419 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 135 optimal weight: 50.0000 chunk 446 optimal weight: 1.9990 chunk 478 optimal weight: 1.9990 chunk 346 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 551 optimal weight: 50.0000 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 54789 Z= 0.208 Angle : 0.545 14.114 74074 Z= 0.284 Chirality : 0.041 0.177 8988 Planarity : 0.003 0.029 9618 Dihedral : 7.294 71.524 8204 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.17 % Allowed : 13.03 % Favored : 85.80 % 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: 1.02 (0.10), residues: 7308 helix: 1.57 (0.08), residues: 4158 sheet: -0.07 (0.16), residues: 994 loop : -0.61 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 401 PHE 0.033 0.001 PHE D 66 TYR 0.019 0.001 TYR M 485 ARG 0.003 0.000 ARG B 58 *********************** 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 386 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 320 time to evaluate : 6.244 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: G 267 MET cc_start: -0.3118 (OUTLIER) cc_final: -0.3430 (mpp) REVERT: B 267 MET cc_start: 0.0231 (OUTLIER) cc_final: -0.0277 (mtp) REVERT: C 59 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: F 232 GLU cc_start: 0.4034 (OUTLIER) cc_final: 0.3316 (mp0) REVERT: F 488 MET cc_start: 0.8936 (mmm) cc_final: 0.8014 (mmm) REVERT: H 267 MET cc_start: 0.0807 (ptt) cc_final: 0.0040 (mpp) REVERT: H 288 MET cc_start: 0.7395 (ptp) cc_final: 0.7184 (ptp) REVERT: H 389 MET cc_start: 0.7110 (tpp) cc_final: 0.6028 (ttp) REVERT: I 69 MET cc_start: 0.6668 (tpp) cc_final: 0.6262 (tpp) REVERT: I 195 PHE cc_start: 0.7219 (p90) cc_final: 0.6605 (p90) REVERT: J 233 MET cc_start: 0.4283 (ppp) cc_final: 0.3279 (ptt) REVERT: K 267 MET cc_start: -0.0469 (OUTLIER) cc_final: -0.0960 (mtp) REVERT: K 363 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: L 288 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7601 (ptp) REVERT: L 520 MET cc_start: 0.7713 (mtt) cc_final: 0.7497 (mtt) REVERT: M 69 MET cc_start: 0.6515 (tpp) cc_final: 0.6154 (tpp) REVERT: M 90 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8694 (m) REVERT: M 195 PHE cc_start: 0.7362 (p90) cc_final: 0.6739 (p90) REVERT: N 267 MET cc_start: -0.2795 (mpp) cc_final: -0.3033 (mpp) outliers start: 66 outliers final: 44 residues processed: 367 average time/residue: 0.6315 time to fit residues: 408.4643 Evaluate side-chains 363 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 5.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain I residue 8 PHE Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 8 PHE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 5.9990 chunk 672 optimal weight: 3.9990 chunk 613 optimal weight: 0.9980 chunk 653 optimal weight: 8.9990 chunk 393 optimal weight: 40.0000 chunk 284 optimal weight: 10.0000 chunk 513 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 590 optimal weight: 8.9990 chunk 618 optimal weight: 0.9980 chunk 651 optimal weight: 8.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 54789 Z= 0.208 Angle : 0.555 15.812 74074 Z= 0.288 Chirality : 0.041 0.193 8988 Planarity : 0.003 0.029 9618 Dihedral : 7.272 71.667 8204 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.10 % Allowed : 13.19 % Favored : 85.71 % 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: 1.01 (0.10), residues: 7308 helix: 1.54 (0.08), residues: 4172 sheet: -0.05 (0.16), residues: 994 loop : -0.62 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 401 PHE 0.023 0.001 PHE D 66 TYR 0.019 0.001 TYR M 485 ARG 0.003 0.000 ARG K 368 *********************** 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 386 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 324 time to evaluate : 6.089 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: G 267 MET cc_start: -0.3061 (OUTLIER) cc_final: -0.3381 (mpp) REVERT: G 288 MET cc_start: 0.7767 (mpp) cc_final: 0.7284 (pmm) REVERT: B 267 MET cc_start: 0.0233 (OUTLIER) cc_final: -0.0296 (mtp) REVERT: C 59 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: D 519 CYS cc_start: 0.8089 (m) cc_final: 0.7864 (t) REVERT: E 288 MET cc_start: 0.7442 (mpp) cc_final: 0.6926 (pmm) REVERT: F 232 GLU cc_start: 0.4174 (OUTLIER) cc_final: 0.3474 (mp0) REVERT: H 267 MET cc_start: 0.0835 (ptt) cc_final: 0.0151 (mpp) REVERT: H 288 MET cc_start: 0.7393 (ptp) cc_final: 0.7182 (ptp) REVERT: H 389 MET cc_start: 0.7096 (tpp) cc_final: 0.6015 (ttp) REVERT: I 69 MET cc_start: 0.6800 (tpp) cc_final: 0.6504 (tpp) REVERT: I 195 PHE cc_start: 0.7188 (p90) cc_final: 0.6613 (p90) REVERT: J 233 MET cc_start: 0.3857 (ppp) cc_final: 0.2871 (ptt) REVERT: K 267 MET cc_start: -0.0307 (OUTLIER) cc_final: -0.0836 (mtp) REVERT: K 327 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7321 (mmmt) REVERT: K 363 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: L 288 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7625 (ptp) REVERT: L 520 MET cc_start: 0.7693 (mtt) cc_final: 0.7479 (mtt) REVERT: M 69 MET cc_start: 0.6587 (tpp) cc_final: 0.6114 (tpp) REVERT: M 90 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8716 (m) REVERT: M 195 PHE cc_start: 0.7354 (p90) cc_final: 0.6709 (p90) outliers start: 62 outliers final: 43 residues processed: 366 average time/residue: 0.6139 time to fit residues: 393.8204 Evaluate side-chains 365 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 314 time to evaluate : 6.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 8 PHE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.5980 chunk 691 optimal weight: 5.9990 chunk 422 optimal weight: 0.9980 chunk 328 optimal weight: 6.9990 chunk 480 optimal weight: 0.9990 chunk 725 optimal weight: 4.9990 chunk 667 optimal weight: 1.9990 chunk 577 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 446 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 54789 Z= 0.169 Angle : 0.550 12.924 74074 Z= 0.284 Chirality : 0.041 0.185 8988 Planarity : 0.003 0.029 9618 Dihedral : 7.151 71.265 8204 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.96 % Allowed : 13.33 % Favored : 85.71 % 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: 1.06 (0.10), residues: 7308 helix: 1.60 (0.08), residues: 4172 sheet: -0.06 (0.16), residues: 994 loop : -0.63 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 401 PHE 0.016 0.001 PHE B 195 TYR 0.016 0.001 TYR M 485 ARG 0.004 0.000 ARG F 350 ********************** 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 389 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 335 time to evaluate : 6.013 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: A 14 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8584 (m) REVERT: A 519 CYS cc_start: 0.8015 (m) cc_final: 0.7785 (t) REVERT: G 267 MET cc_start: -0.3204 (OUTLIER) cc_final: -0.3527 (mpp) REVERT: G 288 MET cc_start: 0.7720 (mpp) cc_final: 0.7210 (pmm) REVERT: B 90 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8209 (m) REVERT: B 195 PHE cc_start: 0.7351 (p90) cc_final: 0.6729 (p90) REVERT: B 267 MET cc_start: 0.0225 (OUTLIER) cc_final: -0.0302 (mtp) REVERT: C 59 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: C 387 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7528 (m) REVERT: E 288 MET cc_start: 0.7537 (mpp) cc_final: 0.7053 (pmm) REVERT: F 195 PHE cc_start: 0.7344 (p90) cc_final: 0.6571 (p90) REVERT: F 232 GLU cc_start: 0.4183 (OUTLIER) cc_final: 0.3469 (mp0) REVERT: F 488 MET cc_start: 0.8745 (mmm) cc_final: 0.7788 (mmm) REVERT: H 267 MET cc_start: 0.0844 (ptt) cc_final: 0.0168 (mpp) REVERT: H 389 MET cc_start: 0.7077 (tpp) cc_final: 0.6004 (ttp) REVERT: I 195 PHE cc_start: 0.7166 (p90) cc_final: 0.6609 (p90) REVERT: J 233 MET cc_start: 0.3646 (ppp) cc_final: 0.2797 (ptt) REVERT: J 288 MET cc_start: 0.7324 (pmm) cc_final: 0.6805 (pmm) REVERT: K 267 MET cc_start: -0.0285 (OUTLIER) cc_final: -0.0530 (mpp) REVERT: K 363 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: L 288 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7672 (ptp) REVERT: L 520 MET cc_start: 0.7604 (mtt) cc_final: 0.7384 (mtt) REVERT: M 90 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8682 (m) REVERT: M 195 PHE cc_start: 0.7390 (p90) cc_final: 0.6817 (p90) REVERT: M 491 MET cc_start: 0.7847 (ptp) cc_final: 0.7368 (ptp) REVERT: N 288 MET cc_start: 0.6977 (ptp) cc_final: 0.6772 (ptp) outliers start: 54 outliers final: 38 residues processed: 372 average time/residue: 0.6061 time to fit residues: 397.4596 Evaluate side-chains 370 residues out of total 5663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 6.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 8 PHE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 3.9990 chunk 615 optimal weight: 10.0000 chunk 176 optimal weight: 0.0060 chunk 532 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 578 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 593 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN F 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.123400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.086131 restraints weight = 135168.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082257 restraints weight = 130803.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.082959 restraints weight = 106960.926| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1954 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= 0.209 Angle : 0.564 15.412 74074 Z= 0.291 Chirality : 0.041 0.195 8988 Planarity : 0.003 0.031 9618 Dihedral : 7.123 71.510 8204 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.08 % Allowed : 13.38 % Favored : 85.54 % 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: 1.04 (0.10), residues: 7308 helix: 1.59 (0.08), residues: 4172 sheet: -0.05 (0.16), residues: 987 loop : -0.64 (0.12), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 401 PHE 0.012 0.001 PHE D 66 TYR 0.016 0.001 TYR N 485 ARG 0.003 0.000 ARG K 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8749.14 seconds wall clock time: 463 minutes 37.95 seconds (27817.95 seconds total)