Starting phenix.real_space_refine on Sun Dec 29 00:31:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bly_16115/12_2024/8bly_16115.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bly_16115/12_2024/8bly_16115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bly_16115/12_2024/8bly_16115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bly_16115/12_2024/8bly_16115.map" model { file = "/net/cci-nas-00/data/ceres_data/8bly_16115/12_2024/8bly_16115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bly_16115/12_2024/8bly_16115.cif" } resolution = 3.2 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= 0.002 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 42 5.49 5 Mg 14 5.21 5 S 280 5.16 5 C 33628 2.51 5 N 9380 2.21 5 O 10990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 54334 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="MG MG A 601 " occ=0.00 residue: pdb="MG MG B 601 " occ=0.00 residue: pdb="MG MG C 601 " occ=0.00 residue: pdb="MG MG D 601 " occ=0.00 residue: pdb="MG MG E 601 " occ=0.00 residue: pdb="MG MG F 601 " occ=0.00 residue: pdb="MG MG G 601 " occ=0.00 residue: pdb="MG MG H 601 " occ=0.00 residue: pdb="MG MG I 601 " occ=0.00 residue: pdb="MG MG J 601 " occ=0.00 residue: pdb="MG MG K 601 " occ=0.00 residue: pdb="MG MG L 601 " occ=0.00 ... (remaining 2 not shown) Time building chain proxies: 23.93, per 1000 atoms: 0.44 Number of scatterers: 54334 At special positions: 0 Unit cell: (151.41, 154.35, 163.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 280 16.00 P 42 15.00 Mg 14 11.99 O 10990 8.00 N 9380 7.00 C 33628 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.01 Conformation dependent library (CDL) restraints added in 5.7 seconds 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13244 Finding SS restraints... Secondary structure from input PDB file: 299 helices and 86 sheets defined 59.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.892A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.595A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 removed outlier: 4.028A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 152 Processing helix chain 'A' and resid 155 through 169 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.567A pdb=" N ILE A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.562A pdb=" N GLU A 232 " --> pdb=" O ASN A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.206A pdb=" N GLY A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 385 through 410 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 497 through 515 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.839A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 64 through 86 removed outlier: 4.114A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.724A pdb=" N ILE B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 removed outlier: 4.143A pdb=" N GLY B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 267 removed outlier: 3.581A pdb=" N MET B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 385 through 410 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 515 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.882A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 64 through 86 removed outlier: 4.029A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.614A 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 137 through 142 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 155 through 169 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.563A pdb=" N PHE C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 205' Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.548A pdb=" N GLU C 232 " --> pdb=" O ASN C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 233 through 244 removed outlier: 4.123A pdb=" N GLY C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 267 Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 425 Processing helix chain 'C' and resid 433 through 446 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 497 through 515 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.853A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.792A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.808A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.507A pdb=" N PHE D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 201 through 205' Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 259 through 267 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 375 Processing helix chain 'D' and resid 385 through 410 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 458 Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.806A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.848A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.714A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 removed outlier: 4.020A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.775A 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 137 through 142 Processing helix chain 'E' and resid 143 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 removed outlier: 3.574A pdb=" N ILE E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.975A pdb=" N MET E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.022A pdb=" N GLY E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 267 removed outlier: 3.769A 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 308 through 312 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 375 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 458 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.869A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.914A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.747A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.846A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 143 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.575A pdb=" N PHE F 204 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 205' Processing helix chain 'F' and resid 229 through 232 removed outlier: 3.766A pdb=" N GLU F 232 " --> pdb=" O ASN F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 229 through 232' Processing helix chain 'F' and resid 233 through 244 removed outlier: 3.998A pdb=" N GLY F 244 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 267 Processing helix chain 'F' and resid 282 through 297 Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 338 through 356 Processing helix chain 'F' and resid 358 through 375 removed outlier: 3.533A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 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 458 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 497 through 515 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.905A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.715A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.885A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.569A 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 137 through 142 Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 155 through 169 Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.772A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 244 removed outlier: 4.083A pdb=" N GLY G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 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 447 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 'H' and resid 9 through 29 removed outlier: 3.924A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.668A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 removed outlier: 4.097A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.847A 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 137 through 142 Processing helix chain 'H' and resid 143 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.502A pdb=" N ILE H 205 " --> pdb=" O PRO H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 241 removed outlier: 3.920A pdb=" N MET H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 259 through 267 removed outlier: 3.635A 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 308 through 312 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 375 Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 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 497 through 515 Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.922A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.651A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 removed outlier: 4.135A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 137 through 142 Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 155 through 169 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.690A pdb=" N ILE I 205 " --> pdb=" O PRO I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 232 removed outlier: 3.671A pdb=" N GLU I 232 " --> pdb=" O ASN I 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 229 through 232' Processing helix chain 'I' and resid 233 through 244 removed outlier: 4.094A pdb=" N GLY I 244 " --> pdb=" O VAL I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 267 Processing helix chain 'I' and resid 282 through 297 Processing helix chain 'I' and resid 308 through 312 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 375 Processing helix chain 'I' and resid 385 through 410 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 497 through 515 Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.924A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.740A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.953A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.578A 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 137 through 142 Processing helix chain 'J' and resid 143 through 152 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.539A pdb=" N PHE J 204 " --> pdb=" O SER J 201 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 205 " --> pdb=" O PRO J 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 201 through 205' Processing helix chain 'J' and resid 229 through 244 removed outlier: 3.912A pdb=" N MET J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) Proline residue: J 235 - end of helix removed outlier: 3.998A pdb=" N GLY J 244 " --> pdb=" O VAL J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 267 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 Processing helix chain 'J' and resid 385 through 410 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 458 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 497 through 515 Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.838A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.751A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 removed outlier: 4.010A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 137 through 142 Processing helix chain 'K' and resid 143 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.789A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 removed outlier: 4.334A pdb=" N GLY K 244 " --> pdb=" O VAL K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 267 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 308 through 312 Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 375 Processing helix chain 'K' and resid 385 through 410 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 458 Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 497 through 515 Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.869A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.776A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 removed outlier: 3.866A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.647A 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 137 through 142 Processing helix chain 'L' and resid 143 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.508A pdb=" N ILE L 205 " --> pdb=" O PRO L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 241 Processing helix chain 'L' and resid 259 through 267 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 458 Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 497 through 516 removed outlier: 3.874A pdb=" N THR L 516 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 29 removed outlier: 3.878A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 60 removed outlier: 3.501A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 removed outlier: 3.992A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA M 78 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 137 through 142 Processing helix chain 'M' and resid 143 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 removed outlier: 3.813A pdb=" N ILE M 205 " --> pdb=" O PRO M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 232 No H-bonds generated for 'chain 'M' and resid 230 through 232' Processing helix chain 'M' and resid 233 through 244 removed outlier: 3.926A pdb=" N GLY M 244 " --> pdb=" O VAL M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 267 Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 308 through 312 Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 358 through 375 Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 425 Processing helix chain 'M' and resid 433 through 446 Processing helix chain 'M' and resid 448 through 459 Processing helix chain 'M' and resid 461 through 472 Processing helix chain 'M' and resid 497 through 515 Processing helix chain 'N' and resid 9 through 29 removed outlier: 3.834A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 removed outlier: 3.570A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 86 removed outlier: 3.824A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.542A 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 137 through 142 Processing helix chain 'N' and resid 143 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 removed outlier: 3.590A pdb=" N ILE N 205 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 244 removed outlier: 4.146A pdb=" N GLY N 244 " --> pdb=" O VAL N 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 267 Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 308 through 312 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 375 Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 425 Processing helix chain 'N' and resid 433 through 447 Processing helix chain 'N' and resid 448 through 459 Processing helix chain 'N' and resid 461 through 472 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: 7.417A pdb=" N VAL C 39 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N MET A 520 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.986A pdb=" N ASN A 37 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL N 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 39 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ASP N 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.654A pdb=" N THR A 330 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 325 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 332 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 323 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP A 334 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.635A pdb=" N VAL A 323 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.974A 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 'B' and resid 4 through 8 removed outlier: 7.229A pdb=" N VAL G 39 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET B 520 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 7.449A pdb=" N ASN B 37 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET D 520 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 39 " --> pdb=" O MET D 520 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR D 522 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.624A pdb=" N THR B 330 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 325 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE B 332 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 323 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 334 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 213 through 216 removed outlier: 3.621A pdb=" N VAL B 323 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 8 removed outlier: 7.326A pdb=" N VAL E 39 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET C 520 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.651A pdb=" N THR C 330 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 325 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE C 332 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 323 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP C 334 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 213 through 216 removed outlier: 3.605A pdb=" N VAL C 323 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC2, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC3, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.659A pdb=" N ASN D 37 " --> pdb=" O GLU F 518 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET F 520 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL D 39 " --> pdb=" O MET F 520 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR F 522 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 174 through 179 Processing sheet with id=AC5, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.639A pdb=" N THR D 330 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE D 325 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE D 332 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 323 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP D 334 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 213 through 216 removed outlier: 3.587A pdb=" N VAL D 323 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AC8, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.014A pdb=" N ASN H 37 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS E 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 175 through 179 Processing sheet with id=AD2, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.647A pdb=" N THR E 330 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE E 325 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE E 332 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL E 323 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP E 334 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 323 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.647A pdb=" N THR E 330 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE E 325 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE E 332 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL E 323 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP E 334 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU E 247 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD5, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AD6, first strand: chain 'F' and resid 48 through 50 removed outlier: 7.738A pdb=" N ASN F 37 " --> pdb=" O GLU I 518 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET I 520 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL F 39 " --> pdb=" O MET I 520 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR I 522 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 174 through 179 Processing sheet with id=AD8, first strand: chain 'F' and resid 193 through 195 removed outlier: 6.378A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 323 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 274 through 276 removed outlier: 6.049A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 274 through 276 removed outlier: 6.049A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE3, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AE4, first strand: chain 'G' and resid 4 through 8 removed outlier: 4.259A pdb=" N THR G 517 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL M 39 " --> pdb=" O THR G 517 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS G 519 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 174 through 179 Processing sheet with id=AE6, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.669A pdb=" N THR G 330 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE G 325 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE G 332 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 323 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP G 334 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU G 247 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 213 through 216 removed outlier: 3.602A pdb=" N VAL G 323 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE9, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 8 removed outlier: 5.949A pdb=" N ASN J 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS H 519 " --> pdb=" O ASN J 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 175 through 179 Processing sheet with id=AF3, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.645A pdb=" N THR H 330 " --> pdb=" O ILE H 325 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE H 325 " --> pdb=" O THR H 330 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE H 332 " --> pdb=" O VAL H 323 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL H 323 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP H 334 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 323 " --> pdb=" O LEU H 215 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.645A pdb=" N THR H 330 " --> pdb=" O ILE H 325 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE H 325 " --> pdb=" O THR H 330 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE H 332 " --> pdb=" O VAL H 323 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL H 323 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP H 334 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF6, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AF7, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.923A pdb=" N ASN I 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N VAL K 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL I 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASP K 523 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 174 through 179 Processing sheet with id=AF9, first strand: chain 'I' and resid 193 through 195 removed outlier: 6.606A pdb=" N THR I 330 " --> pdb=" O ILE I 325 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE I 325 " --> pdb=" O THR I 330 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE I 332 " --> pdb=" O VAL I 323 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL I 323 " --> pdb=" O ILE I 332 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP I 334 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 213 through 216 removed outlier: 3.727A pdb=" N VAL I 323 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG3, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AG4, first strand: chain 'J' and resid 4 through 8 removed outlier: 5.982A pdb=" N ASN L 37 " --> pdb=" O THR J 517 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS J 519 " --> pdb=" O ASN L 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AG6, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.617A pdb=" N THR J 330 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE J 325 " --> pdb=" O THR J 330 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE J 332 " --> pdb=" O VAL J 323 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL J 323 " --> pdb=" O ILE J 332 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP J 334 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 323 " --> pdb=" O LEU J 215 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.617A pdb=" N THR J 330 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE J 325 " --> pdb=" O THR J 330 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE J 332 " --> pdb=" O VAL J 323 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL J 323 " --> pdb=" O ILE J 332 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP J 334 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU J 247 " --> pdb=" O ALA J 274 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG9, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AH1, first strand: chain 'K' and resid 48 through 50 removed outlier: 5.418A pdb=" N ASN K 37 " --> pdb=" O THR M 517 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS M 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AH3, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.398A pdb=" N ARG K 322 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL K 323 " --> pdb=" O LEU K 215 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 274 through 277 removed outlier: 6.155A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'K' and resid 274 through 277 removed outlier: 6.155A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH7, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AH8, first strand: chain 'L' and resid 4 through 8 removed outlier: 7.281A pdb=" N VAL N 39 " --> pdb=" O GLU L 518 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET L 520 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 175 through 179 Processing sheet with id=AI1, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.654A pdb=" N THR L 330 " --> pdb=" O ILE L 325 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE L 325 " --> pdb=" O THR L 330 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE L 332 " --> pdb=" O VAL L 323 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL L 323 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP L 334 " --> pdb=" O LYS L 321 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 213 through 216 removed outlier: 3.599A pdb=" N VAL L 323 " --> pdb=" O LEU L 215 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AI4, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AI5, first strand: chain 'M' and resid 174 through 179 Processing sheet with id=AI6, first strand: chain 'M' and resid 193 through 195 removed outlier: 6.654A pdb=" N THR M 330 " --> pdb=" O ILE M 325 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE M 325 " --> pdb=" O THR M 330 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE M 332 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL M 323 " --> pdb=" O ILE M 332 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP M 334 " --> pdb=" O LYS M 321 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU M 247 " --> pdb=" O ALA M 274 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 213 through 216 removed outlier: 3.644A pdb=" N VAL M 323 " --> pdb=" O LEU M 215 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AI9, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AJ1, first strand: chain 'N' and resid 174 through 179 Processing sheet with id=AJ2, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.356A pdb=" N ARG N 322 " --> pdb=" O ILE N 333 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL N 323 " --> pdb=" O LEU N 215 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 274 through 276 removed outlier: 6.156A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AJ5, first strand: chain 'N' and resid 476 through 479 3606 hydrogen bonds defined for protein. 10326 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: 26.59 Time building geometry restraints manager: 12.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 18830 1.34 - 1.46: 9364 1.46 - 1.58: 25958 1.58 - 1.70: 56 1.70 - 1.81: 518 Bond restraints: 54726 Sorted by residual: bond pdb=" CB GLU I 484 " pdb=" CG GLU I 484 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB ARG K 362 " pdb=" CG ARG K 362 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.87e-01 bond pdb=" CB MET K 514 " pdb=" CG MET K 514 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.77e-01 bond pdb=" CA VAL D 189 " pdb=" CB VAL D 189 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.74e-01 bond pdb=" CA VAL F 189 " pdb=" CB VAL F 189 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.67e-01 ... (remaining 54721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 73708 2.75 - 5.50: 263 5.50 - 8.25: 15 8.25 - 11.00: 3 11.00 - 13.75: 1 Bond angle restraints: 73990 Sorted by residual: angle pdb=" CB MET J 111 " pdb=" CG MET J 111 " pdb=" SD MET J 111 " ideal model delta sigma weight residual 112.70 126.45 -13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" CA ARG D 362 " pdb=" CB ARG D 362 " pdb=" CG ARG D 362 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CB MET G 488 " pdb=" CG MET G 488 " pdb=" SD MET G 488 " ideal model delta sigma weight residual 112.70 122.37 -9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET F 69 " pdb=" CG MET F 69 " pdb=" SD MET F 69 " ideal model delta sigma weight residual 112.70 103.30 9.40 3.00e+00 1.11e-01 9.82e+00 angle pdb=" N ILE B 230 " pdb=" CA ILE B 230 " pdb=" C ILE B 230 " ideal model delta sigma weight residual 111.90 109.60 2.30 8.10e-01 1.52e+00 8.08e+00 ... (remaining 73985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 29921 17.88 - 35.77: 3146 35.77 - 53.65: 843 53.65 - 71.53: 190 71.53 - 89.41: 60 Dihedral angle restraints: 34160 sinusoidal: 13510 harmonic: 20650 Sorted by residual: dihedral pdb=" CA THR K 50 " pdb=" C THR K 50 " pdb=" N LYS K 51 " pdb=" CA LYS K 51 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP N 196 " pdb=" CB ASP N 196 " pdb=" CG ASP N 196 " pdb=" OD1 ASP N 196 " ideal model delta sinusoidal sigma weight residual -30.00 -84.78 54.78 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP J 196 " pdb=" CB ASP J 196 " pdb=" CG ASP J 196 " pdb=" OD1 ASP J 196 " ideal model delta sinusoidal sigma weight residual -30.00 -84.32 54.32 1 2.00e+01 2.50e-03 1.00e+01 ... (remaining 34157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 5606 0.027 - 0.054: 1894 0.054 - 0.080: 872 0.080 - 0.107: 443 0.107 - 0.134: 159 Chirality restraints: 8974 Sorted by residual: chirality pdb=" CA VAL L 136 " pdb=" N VAL L 136 " pdb=" C VAL L 136 " pdb=" CB VAL L 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL I 136 " pdb=" N VAL I 136 " pdb=" C VAL I 136 " pdb=" CB VAL I 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL E 136 " pdb=" N VAL E 136 " pdb=" C VAL E 136 " pdb=" CB VAL E 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 8971 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 362 " 0.124 9.50e-02 1.11e+02 5.61e-02 2.41e+00 pdb=" NE ARG D 362 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 362 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 362 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 362 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 449 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 450 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 450 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 450 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA M 449 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO M 450 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO M 450 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO M 450 " -0.019 5.00e-02 4.00e+02 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 383 2.56 - 3.14: 43441 3.14 - 3.73: 90849 3.73 - 4.31: 122470 4.31 - 4.90: 206816 Nonbonded interactions: 463959 Sorted by model distance: nonbonded pdb="MG MG M 601 " pdb=" O2A ATP M 602 " model vdw 1.971 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2A ATP C 602 " model vdw 1.972 2.170 nonbonded pdb="MG MG C 601 " pdb=" O3G ATP C 602 " model vdw 1.976 2.170 nonbonded pdb="MG MG M 601 " pdb=" O3G ATP M 602 " model vdw 1.977 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2A ATP B 602 " model vdw 1.978 2.170 ... (remaining 463954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.490 Check model and map are aligned: 0.320 Set scattering table: 0.380 Process input model: 102.820 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.002 0.032 54726 Z= 0.155 Angle : 0.466 13.747 73990 Z= 0.255 Chirality : 0.039 0.134 8974 Planarity : 0.002 0.056 9618 Dihedral : 16.452 89.414 20916 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.18 % Allowed : 18.03 % Favored : 81.80 % 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: 1.29 (0.10), residues: 7294 helix: 1.71 (0.08), residues: 4088 sheet: 0.46 (0.14), residues: 1176 loop : -0.57 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.008 0.001 PHE I 195 TYR 0.018 0.001 TYR I 203 ARG 0.012 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 243 time to evaluate : 5.260 Fit side-chains revert: symmetry clash REVERT: C 193 MET cc_start: 0.7001 (tpp) cc_final: 0.6708 (tpt) REVERT: C 307 MET cc_start: 0.6875 (tpt) cc_final: 0.6550 (tpt) REVERT: L 362 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6681 (tmm160) outliers start: 10 outliers final: 2 residues processed: 249 average time/residue: 0.5060 time to fit residues: 222.3306 Evaluate side-chains 245 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 242 time to evaluate : 5.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain L residue 362 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 4.9990 chunk 551 optimal weight: 50.0000 chunk 306 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 372 optimal weight: 2.9990 chunk 294 optimal weight: 40.0000 chunk 570 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 chunk 346 optimal weight: 50.0000 chunk 424 optimal weight: 0.9990 chunk 661 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN C 366 GLN H 37 ASN I 37 ASN J 37 ASN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 229 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54726 Z= 0.197 Angle : 0.489 9.390 73990 Z= 0.266 Chirality : 0.040 0.166 8974 Planarity : 0.003 0.035 9618 Dihedral : 8.285 87.058 8196 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.42 % Allowed : 16.27 % Favored : 82.31 % 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: 1.37 (0.10), residues: 7294 helix: 1.77 (0.08), residues: 4116 sheet: 0.31 (0.13), residues: 1246 loop : -0.46 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 401 PHE 0.008 0.001 PHE M 8 TYR 0.010 0.001 TYR H 478 ARG 0.006 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 240 time to evaluate : 4.640 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: B 233 MET cc_start: 0.1559 (ppp) cc_final: 0.0868 (ptp) REVERT: B 447 MET cc_start: 0.9122 (mtt) cc_final: 0.8866 (mtt) REVERT: D 227 ILE cc_start: 0.3274 (OUTLIER) cc_final: 0.2675 (mm) REVERT: D 240 VAL cc_start: 0.5866 (OUTLIER) cc_final: 0.5571 (p) REVERT: E 193 MET cc_start: 0.6652 (tpt) cc_final: 0.6312 (tpt) REVERT: G 63 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: I 366 GLN cc_start: 0.6095 (OUTLIER) cc_final: 0.5874 (pp30) REVERT: J 111 MET cc_start: 0.8682 (mmm) cc_final: 0.8445 (mmp) REVERT: J 193 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6123 (tmm) REVERT: K 233 MET cc_start: 0.2260 (ppp) cc_final: 0.1658 (ptm) REVERT: L 362 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6674 (tmm160) REVERT: L 483 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: N 63 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: N 362 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6650 (tmm160) REVERT: N 447 MET cc_start: 0.9034 (mtt) cc_final: 0.8771 (mtt) outliers start: 80 outliers final: 32 residues processed: 296 average time/residue: 0.4883 time to fit residues: 253.9665 Evaluate side-chains 281 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 4.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 550 optimal weight: 7.9990 chunk 450 optimal weight: 30.0000 chunk 182 optimal weight: 0.9990 chunk 662 optimal weight: 0.0570 chunk 715 optimal weight: 2.9990 chunk 589 optimal weight: 0.9990 chunk 656 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 531 optimal weight: 7.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54726 Z= 0.212 Angle : 0.465 9.779 73990 Z= 0.252 Chirality : 0.040 0.151 8974 Planarity : 0.003 0.036 9618 Dihedral : 7.808 87.187 8195 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.00 % Allowed : 15.58 % Favored : 82.42 % 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: 1.38 (0.10), residues: 7294 helix: 1.79 (0.08), residues: 4116 sheet: 0.34 (0.13), residues: 1232 loop : -0.49 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.007 0.001 PHE M 8 TYR 0.008 0.001 TYR L 478 ARG 0.003 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 240 time to evaluate : 4.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: B 267 MET cc_start: 0.2938 (pmm) cc_final: 0.2605 (pmm) REVERT: C 193 MET cc_start: 0.7018 (tpt) cc_final: 0.6710 (tpt) REVERT: C 219 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.4691 (m-80) REVERT: D 227 ILE cc_start: 0.3148 (OUTLIER) cc_final: 0.2583 (mm) REVERT: D 240 VAL cc_start: 0.5638 (OUTLIER) cc_final: 0.5404 (p) REVERT: E 193 MET cc_start: 0.6557 (tpt) cc_final: 0.6171 (tpt) REVERT: G 63 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: I 366 GLN cc_start: 0.6127 (OUTLIER) cc_final: 0.5906 (pp30) REVERT: J 111 MET cc_start: 0.8766 (mmm) cc_final: 0.8540 (mmp) REVERT: J 193 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6286 (tmm) REVERT: K 233 MET cc_start: 0.2137 (ppp) cc_final: 0.1678 (ptm) REVERT: L 63 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: L 166 MET cc_start: 0.8925 (mtt) cc_final: 0.8542 (mmm) REVERT: L 304 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: L 362 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6654 (tmm160) REVERT: N 63 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: N 362 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6563 (tmm160) outliers start: 113 outliers final: 58 residues processed: 333 average time/residue: 0.5031 time to fit residues: 296.5647 Evaluate side-chains 310 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 4.9990 chunk 497 optimal weight: 9.9990 chunk 343 optimal weight: 50.0000 chunk 73 optimal weight: 8.9990 chunk 316 optimal weight: 3.9990 chunk 444 optimal weight: 30.0000 chunk 664 optimal weight: 4.9990 chunk 703 optimal weight: 40.0000 chunk 347 optimal weight: 30.0000 chunk 629 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 54726 Z= 0.421 Angle : 0.549 10.395 73990 Z= 0.293 Chirality : 0.043 0.149 8974 Planarity : 0.003 0.041 9618 Dihedral : 8.607 88.944 8195 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.50 % Allowed : 15.65 % Favored : 81.85 % 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: 7294 helix: 1.38 (0.08), residues: 4158 sheet: 0.24 (0.13), residues: 1218 loop : -0.70 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 401 PHE 0.013 0.001 PHE M 219 TYR 0.013 0.002 TYR N 476 ARG 0.004 0.001 ARG L 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 241 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 MET cc_start: 0.6491 (tpt) cc_final: 0.6282 (tpt) REVERT: C 219 PHE cc_start: 0.4951 (OUTLIER) cc_final: 0.4365 (m-80) REVERT: D 240 VAL cc_start: 0.5643 (OUTLIER) cc_final: 0.5398 (p) REVERT: E 193 MET cc_start: 0.6422 (tpt) cc_final: 0.5985 (tpt) REVERT: E 301 ILE cc_start: -0.3755 (OUTLIER) cc_final: -0.3980 (tt) REVERT: F 483 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: H 520 MET cc_start: 0.9322 (mtp) cc_final: 0.9114 (mtp) REVERT: I 233 MET cc_start: 0.4309 (ppp) cc_final: 0.3349 (ptp) REVERT: I 267 MET cc_start: 0.2278 (ppp) cc_final: 0.1807 (ptt) REVERT: I 366 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.5906 (pp30) REVERT: J 111 MET cc_start: 0.8898 (mmm) cc_final: 0.8680 (mmm) REVERT: J 483 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: J 520 MET cc_start: 0.9122 (mtp) cc_final: 0.8891 (mtp) REVERT: L 63 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: L 166 MET cc_start: 0.8944 (mtt) cc_final: 0.8587 (mmm) REVERT: L 193 MET cc_start: 0.6383 (tpt) cc_final: 0.6094 (tpp) REVERT: L 304 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: L 362 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6641 (tmm160) REVERT: L 467 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8666 (t0) REVERT: M 378 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8719 (p) REVERT: N 63 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: N 193 MET cc_start: 0.6395 (tpt) cc_final: 0.6133 (tpt) REVERT: N 362 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6659 (tmm160) REVERT: N 389 MET cc_start: 0.7658 (tpp) cc_final: 0.7346 (tpp) outliers start: 141 outliers final: 84 residues processed: 357 average time/residue: 0.4769 time to fit residues: 300.9773 Evaluate side-chains 338 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 241 time to evaluate : 4.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 1.9990 chunk 399 optimal weight: 40.0000 chunk 10 optimal weight: 0.9980 chunk 523 optimal weight: 0.9980 chunk 290 optimal weight: 7.9990 chunk 600 optimal weight: 9.9990 chunk 486 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 359 optimal weight: 0.7980 chunk 631 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8396 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54726 Z= 0.165 Angle : 0.454 9.814 73990 Z= 0.246 Chirality : 0.039 0.155 8974 Planarity : 0.002 0.035 9618 Dihedral : 7.719 88.085 8195 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.02 % Allowed : 16.36 % Favored : 81.62 % 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: 1.30 (0.10), residues: 7294 helix: 1.73 (0.08), residues: 4158 sheet: 0.29 (0.14), residues: 1232 loop : -0.61 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 401 PHE 0.015 0.001 PHE F 195 TYR 0.008 0.001 TYR L 478 ARG 0.002 0.000 ARG J 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 241 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 219 PHE cc_start: 0.4973 (OUTLIER) cc_final: 0.4398 (m-80) REVERT: C 514 MET cc_start: 0.9123 (ttm) cc_final: 0.8696 (ttp) REVERT: D 240 VAL cc_start: 0.5631 (OUTLIER) cc_final: 0.5388 (p) REVERT: E 193 MET cc_start: 0.6355 (tpt) cc_final: 0.6076 (tpt) REVERT: E 219 PHE cc_start: 0.6332 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: E 301 ILE cc_start: -0.3756 (OUTLIER) cc_final: -0.4029 (tt) REVERT: G 63 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: I 233 MET cc_start: 0.3496 (ppp) cc_final: 0.2601 (ptp) REVERT: I 267 MET cc_start: 0.2270 (ppp) cc_final: 0.1775 (ptt) REVERT: I 366 GLN cc_start: 0.6131 (OUTLIER) cc_final: 0.5906 (pp30) REVERT: J 69 MET cc_start: 0.9270 (mtt) cc_final: 0.9064 (mtt) REVERT: J 111 MET cc_start: 0.8826 (mmm) cc_final: 0.8616 (mmm) REVERT: J 219 PHE cc_start: 0.6095 (OUTLIER) cc_final: 0.5378 (m-80) REVERT: J 227 ILE cc_start: 0.0611 (OUTLIER) cc_final: 0.0343 (pp) REVERT: J 483 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7938 (mm-30) REVERT: J 520 MET cc_start: 0.9012 (mtp) cc_final: 0.8728 (mtp) REVERT: L 63 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: L 166 MET cc_start: 0.8907 (mtt) cc_final: 0.8608 (mmm) REVERT: L 304 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: L 362 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6641 (tmm160) REVERT: L 467 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8529 (t0) REVERT: L 517 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9057 (p) REVERT: M 484 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7917 (pp20) REVERT: M 514 MET cc_start: 0.9076 (ttm) cc_final: 0.8702 (ttp) REVERT: N 63 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: N 193 MET cc_start: 0.6304 (tpt) cc_final: 0.6099 (tpt) REVERT: N 362 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6589 (tmm160) outliers start: 114 outliers final: 64 residues processed: 336 average time/residue: 0.4922 time to fit residues: 292.0066 Evaluate side-chains 322 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 241 time to evaluate : 4.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 353 ILE Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 219 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 20.0000 chunk 633 optimal weight: 2.9990 chunk 139 optimal weight: 40.0000 chunk 413 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 704 optimal weight: 9.9990 chunk 584 optimal weight: 0.4980 chunk 326 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 369 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.8406 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54726 Z= 0.217 Angle : 0.462 9.557 73990 Z= 0.248 Chirality : 0.040 0.140 8974 Planarity : 0.003 0.076 9618 Dihedral : 7.764 87.588 8195 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.39 % Allowed : 16.00 % Favored : 81.60 % 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: 1.33 (0.10), residues: 7294 helix: 1.76 (0.08), residues: 4158 sheet: 0.30 (0.14), residues: 1232 loop : -0.60 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.014 0.001 PHE F 219 TYR 0.008 0.001 TYR N 476 ARG 0.016 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 241 time to evaluate : 4.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: B 483 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: C 193 MET cc_start: 0.6757 (tpt) cc_final: 0.6272 (tpt) REVERT: C 219 PHE cc_start: 0.5019 (OUTLIER) cc_final: 0.4388 (m-80) REVERT: D 240 VAL cc_start: 0.5618 (OUTLIER) cc_final: 0.5372 (p) REVERT: E 193 MET cc_start: 0.6368 (tpt) cc_final: 0.6083 (tpt) REVERT: E 219 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: E 301 ILE cc_start: -0.3706 (OUTLIER) cc_final: -0.4023 (tt) REVERT: F 483 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7927 (mm-30) REVERT: G 63 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: G 142 LYS cc_start: 0.1733 (OUTLIER) cc_final: 0.1529 (tptp) REVERT: H 272 LYS cc_start: 0.3473 (OUTLIER) cc_final: 0.3166 (tttp) REVERT: I 233 MET cc_start: 0.3494 (ppp) cc_final: 0.2617 (ptp) REVERT: I 267 MET cc_start: 0.2315 (ppp) cc_final: 0.1848 (ptt) REVERT: I 366 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5903 (pp30) REVERT: J 111 MET cc_start: 0.8884 (mmm) cc_final: 0.8648 (mmm) REVERT: J 219 PHE cc_start: 0.6095 (OUTLIER) cc_final: 0.5376 (m-80) REVERT: J 227 ILE cc_start: 0.0598 (OUTLIER) cc_final: 0.0322 (pp) REVERT: J 483 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: J 520 MET cc_start: 0.9055 (mtp) cc_final: 0.8768 (mtp) REVERT: L 63 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: L 166 MET cc_start: 0.8914 (mtt) cc_final: 0.8619 (mmm) REVERT: L 193 MET cc_start: 0.6255 (tpt) cc_final: 0.5959 (tpp) REVERT: L 304 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: L 467 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8537 (t0) REVERT: L 483 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7604 (mm-30) REVERT: L 517 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9070 (p) REVERT: M 378 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8638 (p) REVERT: M 484 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7901 (pp20) REVERT: N 362 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6636 (tmm160) REVERT: N 389 MET cc_start: 0.7581 (tpp) cc_final: 0.7275 (tpp) REVERT: N 483 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8075 (mm-30) outliers start: 135 outliers final: 89 residues processed: 357 average time/residue: 0.5011 time to fit residues: 315.1093 Evaluate side-chains 353 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 241 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 272 LYS Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain H residue 467 ASN Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 353 ILE Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 467 ASN Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 219 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 483 GLU Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 483 GLU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 401 optimal weight: 0.9990 chunk 514 optimal weight: 1.9990 chunk 398 optimal weight: 30.0000 chunk 592 optimal weight: 4.9990 chunk 393 optimal weight: 50.0000 chunk 701 optimal weight: 30.0000 chunk 439 optimal weight: 9.9990 chunk 427 optimal weight: 0.9990 chunk 323 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54726 Z= 0.160 Angle : 0.444 10.411 73990 Z= 0.239 Chirality : 0.039 0.148 8974 Planarity : 0.002 0.039 9618 Dihedral : 7.417 86.087 8191 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.36 % Allowed : 16.00 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.10), residues: 7294 helix: 1.92 (0.08), residues: 4116 sheet: 0.31 (0.14), residues: 1232 loop : -0.51 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E 401 PHE 0.010 0.001 PHE F 195 TYR 0.008 0.001 TYR L 478 ARG 0.012 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 243 time to evaluate : 5.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: A 389 MET cc_start: 0.7833 (tpp) cc_final: 0.7502 (tpp) REVERT: B 483 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: C 193 MET cc_start: 0.6762 (tpt) cc_final: 0.6287 (tpt) REVERT: C 219 PHE cc_start: 0.5039 (OUTLIER) cc_final: 0.4406 (m-80) REVERT: C 514 MET cc_start: 0.9131 (ttm) cc_final: 0.8737 (ttp) REVERT: D 240 VAL cc_start: 0.5600 (OUTLIER) cc_final: 0.5364 (p) REVERT: E 161 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8661 (mp) REVERT: E 193 MET cc_start: 0.6367 (tpt) cc_final: 0.6078 (tpt) REVERT: E 301 ILE cc_start: -0.3717 (OUTLIER) cc_final: -0.4070 (tt) REVERT: F 456 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8940 (tp) REVERT: F 483 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: G 63 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: H 272 LYS cc_start: 0.3346 (OUTLIER) cc_final: 0.3013 (tttp) REVERT: I 203 TYR cc_start: 0.0791 (t80) cc_final: 0.0548 (t80) REVERT: I 267 MET cc_start: 0.1791 (ppp) cc_final: 0.1373 (ptt) REVERT: I 366 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5902 (pp30) REVERT: J 69 MET cc_start: 0.9266 (mtt) cc_final: 0.9033 (mtt) REVERT: J 111 MET cc_start: 0.8757 (mmm) cc_final: 0.8525 (mmm) REVERT: J 219 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5370 (m-80) REVERT: J 227 ILE cc_start: 0.0585 (OUTLIER) cc_final: 0.0298 (pp) REVERT: L 63 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: L 73 MET cc_start: 0.9035 (mtm) cc_final: 0.8643 (mtp) REVERT: L 166 MET cc_start: 0.8906 (mtt) cc_final: 0.8637 (mmm) REVERT: L 193 MET cc_start: 0.6385 (tpt) cc_final: 0.6148 (tpt) REVERT: L 467 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8501 (t0) REVERT: L 517 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8981 (p) REVERT: M 484 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7922 (pp20) REVERT: N 193 MET cc_start: 0.6311 (tpt) cc_final: 0.5928 (tpt) REVERT: N 483 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8071 (mm-30) outliers start: 133 outliers final: 82 residues processed: 362 average time/residue: 0.4900 time to fit residues: 309.7323 Evaluate side-chains 343 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 243 time to evaluate : 5.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 272 LYS Chi-restraints excluded: chain H residue 467 ASN Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 353 ILE Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 467 ASN Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 219 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 483 GLU Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 483 GLU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 20.0000 chunk 280 optimal weight: 1.9990 chunk 419 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 135 optimal weight: 50.0000 chunk 446 optimal weight: 0.6980 chunk 478 optimal weight: 0.6980 chunk 346 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 551 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8391 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54726 Z= 0.185 Angle : 0.455 9.931 73990 Z= 0.243 Chirality : 0.039 0.141 8974 Planarity : 0.002 0.035 9618 Dihedral : 7.486 85.095 8191 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.18 % Allowed : 16.04 % Favored : 81.78 % 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: 1.50 (0.10), residues: 7294 helix: 1.93 (0.08), residues: 4116 sheet: 0.33 (0.14), residues: 1232 loop : -0.51 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.011 0.001 PHE D 219 TYR 0.008 0.001 TYR N 476 ARG 0.009 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 244 time to evaluate : 4.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: A 389 MET cc_start: 0.7821 (tpp) cc_final: 0.7538 (tpp) REVERT: B 483 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8173 (mm-30) REVERT: C 193 MET cc_start: 0.6530 (tpt) cc_final: 0.6056 (tpt) REVERT: C 219 PHE cc_start: 0.5046 (OUTLIER) cc_final: 0.4410 (m-80) REVERT: C 514 MET cc_start: 0.9164 (ttm) cc_final: 0.8742 (ttp) REVERT: D 240 VAL cc_start: 0.5621 (OUTLIER) cc_final: 0.5372 (p) REVERT: E 161 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8670 (mp) REVERT: E 193 MET cc_start: 0.6172 (tpt) cc_final: 0.5911 (tpt) REVERT: E 301 ILE cc_start: -0.3694 (OUTLIER) cc_final: -0.4096 (tt) REVERT: F 456 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8946 (tp) REVERT: F 483 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: H 272 LYS cc_start: 0.3427 (OUTLIER) cc_final: 0.3013 (tttp) REVERT: I 203 TYR cc_start: 0.0798 (t80) cc_final: 0.0549 (t80) REVERT: I 267 MET cc_start: 0.1772 (ppp) cc_final: 0.1339 (ptt) REVERT: I 366 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.5899 (pp30) REVERT: J 111 MET cc_start: 0.8891 (mmm) cc_final: 0.8594 (mmm) REVERT: J 227 ILE cc_start: 0.0481 (OUTLIER) cc_final: 0.0123 (pp) REVERT: J 456 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8944 (tp) REVERT: J 483 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: J 520 MET cc_start: 0.8954 (mtp) cc_final: 0.8653 (mtp) REVERT: K 483 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: L 63 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: L 166 MET cc_start: 0.8912 (mtt) cc_final: 0.8639 (mmm) REVERT: L 467 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8509 (t0) REVERT: L 517 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8915 (p) REVERT: M 484 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7919 (pp20) REVERT: M 514 MET cc_start: 0.9098 (ttm) cc_final: 0.8685 (ttp) REVERT: N 142 LYS cc_start: -0.0067 (OUTLIER) cc_final: -0.0382 (tptt) REVERT: N 193 MET cc_start: 0.6270 (tpt) cc_final: 0.5791 (tpt) REVERT: N 267 MET cc_start: 0.2202 (ppp) cc_final: 0.1838 (ptt) REVERT: N 483 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8054 (mm-30) outliers start: 123 outliers final: 92 residues processed: 357 average time/residue: 0.4801 time to fit residues: 302.0577 Evaluate side-chains 355 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 243 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 272 LYS Chi-restraints excluded: chain H residue 467 ASN Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 353 ILE Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 467 ASN Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 483 GLU Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 483 GLU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 2.9990 chunk 672 optimal weight: 8.9990 chunk 613 optimal weight: 4.9990 chunk 653 optimal weight: 50.0000 chunk 393 optimal weight: 40.0000 chunk 284 optimal weight: 7.9990 chunk 513 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 590 optimal weight: 10.0000 chunk 618 optimal weight: 0.8980 chunk 651 optimal weight: 30.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54726 Z= 0.287 Angle : 0.495 10.473 73990 Z= 0.262 Chirality : 0.041 0.148 8974 Planarity : 0.003 0.037 9618 Dihedral : 7.895 86.067 8191 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.25 % Allowed : 15.95 % Favored : 81.80 % 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: 1.26 (0.10), residues: 7294 helix: 1.70 (0.08), residues: 4158 sheet: 0.29 (0.14), residues: 1232 loop : -0.62 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 401 PHE 0.010 0.001 PHE M 8 TYR 0.011 0.001 TYR B 476 ARG 0.008 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 244 time to evaluate : 4.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: A 389 MET cc_start: 0.7880 (tpp) cc_final: 0.7585 (tpp) REVERT: B 483 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8167 (mm-30) REVERT: C 193 MET cc_start: 0.6549 (tpt) cc_final: 0.6093 (tpt) REVERT: C 219 PHE cc_start: 0.5037 (OUTLIER) cc_final: 0.4399 (m-80) REVERT: C 467 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8509 (t0) REVERT: D 240 VAL cc_start: 0.5633 (OUTLIER) cc_final: 0.5383 (p) REVERT: D 467 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8608 (t0) REVERT: E 161 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8702 (mp) REVERT: E 193 MET cc_start: 0.6201 (tpt) cc_final: 0.5931 (tpt) REVERT: E 301 ILE cc_start: -0.3643 (OUTLIER) cc_final: -0.4069 (tt) REVERT: F 456 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8964 (tp) REVERT: F 483 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: H 272 LYS cc_start: 0.3399 (OUTLIER) cc_final: 0.3180 (tttp) REVERT: I 203 TYR cc_start: 0.0846 (t80) cc_final: 0.0583 (t80) REVERT: I 267 MET cc_start: 0.1762 (ppp) cc_final: 0.1368 (ptt) REVERT: I 366 GLN cc_start: 0.6127 (OUTLIER) cc_final: 0.5905 (pp30) REVERT: J 227 ILE cc_start: -0.0059 (OUTLIER) cc_final: -0.0414 (pp) REVERT: J 456 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8959 (tp) REVERT: J 483 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: J 520 MET cc_start: 0.8905 (mtp) cc_final: 0.8650 (mtp) REVERT: K 483 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: L 63 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: L 166 MET cc_start: 0.8920 (mtt) cc_final: 0.8628 (mmm) REVERT: L 193 MET cc_start: 0.6733 (tpt) cc_final: 0.6369 (tpp) REVERT: L 467 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8533 (t0) REVERT: L 517 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9068 (p) REVERT: M 378 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8708 (p) REVERT: M 484 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7901 (pp20) REVERT: N 142 LYS cc_start: 0.0083 (OUTLIER) cc_final: -0.0229 (tptt) REVERT: N 193 MET cc_start: 0.6141 (tpt) cc_final: 0.5733 (tpt) REVERT: N 267 MET cc_start: 0.2237 (ppp) cc_final: 0.1879 (ptt) REVERT: N 483 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8058 (mm-30) outliers start: 127 outliers final: 91 residues processed: 361 average time/residue: 0.4705 time to fit residues: 300.3268 Evaluate side-chains 357 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 243 time to evaluate : 4.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 272 LYS Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain H residue 467 ASN Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 353 ILE Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 467 ASN Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 483 GLU Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 483 GLU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.7980 chunk 691 optimal weight: 2.9990 chunk 422 optimal weight: 5.9990 chunk 328 optimal weight: 4.9990 chunk 480 optimal weight: 4.9990 chunk 725 optimal weight: 0.9990 chunk 667 optimal weight: 4.9990 chunk 577 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 446 optimal weight: 50.0000 chunk 354 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8393 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54726 Z= 0.191 Angle : 0.467 10.416 73990 Z= 0.248 Chirality : 0.040 0.140 8974 Planarity : 0.002 0.035 9618 Dihedral : 7.546 85.866 8191 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.97 % Allowed : 16.22 % Favored : 81.81 % 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: 1.40 (0.10), residues: 7294 helix: 1.84 (0.08), residues: 4116 sheet: 0.28 (0.14), residues: 1232 loop : -0.53 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.009 0.001 PHE D 219 TYR 0.009 0.001 TYR L 478 ARG 0.007 0.000 ARG F 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 242 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: A 389 MET cc_start: 0.7882 (tpp) cc_final: 0.7589 (tpp) REVERT: B 447 MET cc_start: 0.9157 (mtm) cc_final: 0.8953 (mtt) REVERT: B 483 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8166 (mm-30) REVERT: C 193 MET cc_start: 0.6662 (tpt) cc_final: 0.6256 (tpt) REVERT: C 219 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4406 (m-80) REVERT: C 467 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8571 (t0) REVERT: D 467 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8591 (t0) REVERT: E 161 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8679 (mp) REVERT: E 193 MET cc_start: 0.6194 (tpt) cc_final: 0.5919 (tpt) REVERT: E 301 ILE cc_start: -0.3068 (OUTLIER) cc_final: -0.3546 (tt) REVERT: F 483 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: H 272 LYS cc_start: 0.3468 (OUTLIER) cc_final: 0.3164 (tttp) REVERT: I 203 TYR cc_start: 0.0732 (t80) cc_final: 0.0398 (t80) REVERT: I 267 MET cc_start: 0.1747 (ppp) cc_final: 0.1392 (ptt) REVERT: I 366 GLN cc_start: 0.6125 (OUTLIER) cc_final: 0.5904 (pp30) REVERT: J 227 ILE cc_start: -0.0083 (OUTLIER) cc_final: -0.0468 (pp) REVERT: J 483 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: L 63 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: L 73 MET cc_start: 0.9027 (mtm) cc_final: 0.8634 (mtp) REVERT: L 166 MET cc_start: 0.8901 (mtt) cc_final: 0.8636 (mmm) REVERT: L 193 MET cc_start: 0.6494 (tpt) cc_final: 0.6192 (tpp) REVERT: L 467 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8511 (t0) REVERT: L 517 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8975 (p) REVERT: M 484 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7919 (pp20) REVERT: M 514 MET cc_start: 0.9035 (ttm) cc_final: 0.8608 (ttp) REVERT: N 142 LYS cc_start: -0.0042 (OUTLIER) cc_final: -0.0344 (tptt) REVERT: N 193 MET cc_start: 0.6120 (tpt) cc_final: 0.5711 (tpt) REVERT: N 267 MET cc_start: 0.2209 (ppp) cc_final: 0.1862 (ptt) REVERT: N 483 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8047 (mm-30) outliers start: 111 outliers final: 88 residues processed: 344 average time/residue: 0.4814 time to fit residues: 292.8460 Evaluate side-chains 348 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 242 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 272 LYS Chi-restraints excluded: chain H residue 467 ASN Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 353 ILE Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 467 ASN Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 483 GLU Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 483 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 5.9990 chunk 615 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 532 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 578 optimal weight: 0.6980 chunk 242 optimal weight: 30.0000 chunk 593 optimal weight: 0.3980 chunk 73 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.137020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093934 restraints weight = 105632.477| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.43 r_work: 0.3066 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 54726 Z= 0.168 Angle : 0.456 10.132 73990 Z= 0.242 Chirality : 0.039 0.137 8974 Planarity : 0.002 0.035 9618 Dihedral : 7.389 84.169 8191 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.88 % Allowed : 16.43 % Favored : 81.69 % 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: 1.44 (0.10), residues: 7294 helix: 1.92 (0.08), residues: 4116 sheet: 0.79 (0.15), residues: 980 loop : -0.82 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.009 0.001 PHE D 219 TYR 0.008 0.001 TYR L 478 ARG 0.007 0.000 ARG F 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7545.19 seconds wall clock time: 136 minutes 59.97 seconds (8219.97 seconds total)