Starting phenix.real_space_refine on Tue Aug 6 16:50:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfl_60064/08_2024/8zfl_60064.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfl_60064/08_2024/8zfl_60064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfl_60064/08_2024/8zfl_60064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfl_60064/08_2024/8zfl_60064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfl_60064/08_2024/8zfl_60064.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfl_60064/08_2024/8zfl_60064.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 11140 2.51 5 N 2715 2.21 5 O 3110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 529": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 529": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17070 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "B" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "C" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "D" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.50, per 1000 atoms: 0.62 Number of scatterers: 17070 At special positions: 0 Unit cell: (106.144, 106.144, 156.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3110 8.00 N 2715 7.00 C 11140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 97 " " NAG B 601 " - " ASN B 97 " " NAG C 601 " - " ASN C 97 " " NAG D 601 " - " ASN D 97 " " NAG E 601 " - " ASN E 97 " " NAG G 1 " - " ASN A 228 " " NAG I 1 " - " ASN B 228 " " NAG K 1 " - " ASN C 228 " " NAG M 1 " - " ASN D 228 " " NAG O 1 " - " ASN E 228 " Time building additional restraints: 6.55 Conformation dependent library (CDL) restraints added in 3.0 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 43.4% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.910A pdb=" N GLU A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP A 96 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 295 removed outlier: 3.531A pdb=" N PHE A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 344 through 359 removed outlier: 3.798A pdb=" N ARG A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 363 through 385 Processing helix chain 'A' and resid 487 through 532 Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.909A pdb=" N GLU B 29 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP B 96 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.530A pdb=" N PHE B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 339 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.799A pdb=" N ARG B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 363 through 385 Processing helix chain 'B' and resid 487 through 532 Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.911A pdb=" N GLU C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP C 96 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 295 removed outlier: 3.531A pdb=" N PHE C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 339 Processing helix chain 'C' and resid 344 through 359 removed outlier: 3.799A pdb=" N ARG C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Proline residue: C 356 - end of helix Processing helix chain 'C' and resid 363 through 385 Processing helix chain 'C' and resid 487 through 532 Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.910A pdb=" N GLU D 29 " --> pdb=" O PRO D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP D 96 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.531A pdb=" N PHE D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 344 through 359 removed outlier: 3.798A pdb=" N ARG D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Proline residue: D 356 - end of helix Processing helix chain 'D' and resid 363 through 385 Processing helix chain 'D' and resid 487 through 532 Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.909A pdb=" N GLU E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP E 96 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE E 265 " --> pdb=" O ILE E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 295 removed outlier: 3.531A pdb=" N PHE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 344 through 359 removed outlier: 3.799A pdb=" N ARG E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Proline residue: E 356 - end of helix Processing helix chain 'E' and resid 363 through 385 Processing helix chain 'E' and resid 487 through 532 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 104 removed outlier: 6.021A pdb=" N HIS A 131 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A 148 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 65 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 76 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE A 63 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP A 78 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR A 61 " --> pdb=" O TRP A 78 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL A 80 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN A 59 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG A 82 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER A 57 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL A 84 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR A 55 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 52 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE A 188 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 54 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 104 removed outlier: 6.021A pdb=" N HIS A 131 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A 148 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 65 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 76 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE A 63 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP A 78 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR A 61 " --> pdb=" O TRP A 78 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL A 80 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN A 59 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG A 82 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER A 57 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL A 84 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR A 55 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 removed outlier: 4.487A pdb=" N SER A 177 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 212 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN A 239 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 210 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.019A pdb=" N HIS B 131 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU B 148 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 65 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN B 76 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE B 63 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N TRP B 78 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR B 61 " --> pdb=" O TRP B 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL B 80 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN B 59 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG B 82 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER B 57 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL B 84 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR B 55 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 52 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE B 188 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 54 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.019A pdb=" N HIS B 131 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU B 148 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 65 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN B 76 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE B 63 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N TRP B 78 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR B 61 " --> pdb=" O TRP B 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL B 80 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN B 59 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG B 82 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER B 57 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL B 84 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR B 55 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 115 removed outlier: 4.488A pdb=" N SER B 177 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY B 212 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN B 239 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL B 210 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.020A pdb=" N HIS C 131 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU C 148 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 65 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN C 76 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE C 63 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N TRP C 78 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR C 61 " --> pdb=" O TRP C 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL C 80 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN C 59 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG C 82 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER C 57 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL C 84 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR C 55 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE C 52 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE C 188 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 54 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.020A pdb=" N HIS C 131 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU C 148 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 65 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN C 76 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE C 63 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N TRP C 78 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR C 61 " --> pdb=" O TRP C 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL C 80 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN C 59 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG C 82 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER C 57 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL C 84 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR C 55 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 113 through 115 removed outlier: 4.487A pdb=" N SER C 177 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY C 212 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN C 239 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL C 210 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.020A pdb=" N HIS D 131 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU D 148 " --> pdb=" O HIS D 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 65 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 76 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 63 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP D 78 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR D 61 " --> pdb=" O TRP D 78 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL D 80 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLN D 59 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG D 82 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N SER D 57 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL D 84 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR D 55 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE D 52 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE D 188 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 54 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.020A pdb=" N HIS D 131 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU D 148 " --> pdb=" O HIS D 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 65 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 76 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 63 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP D 78 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR D 61 " --> pdb=" O TRP D 78 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL D 80 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLN D 59 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG D 82 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N SER D 57 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL D 84 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR D 55 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 113 through 115 removed outlier: 4.489A pdb=" N SER D 177 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY D 212 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN D 239 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL D 210 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.019A pdb=" N HIS E 131 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU E 148 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 65 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN E 76 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE E 63 " --> pdb=" O ASN E 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP E 78 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR E 61 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL E 80 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN E 59 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG E 82 " --> pdb=" O SER E 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER E 57 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL E 84 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR E 55 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE E 52 " --> pdb=" O ASP E 186 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE E 188 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL E 54 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.019A pdb=" N HIS E 131 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU E 148 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 65 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN E 76 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE E 63 " --> pdb=" O ASN E 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP E 78 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR E 61 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL E 80 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN E 59 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG E 82 " --> pdb=" O SER E 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER E 57 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL E 84 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR E 55 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 115 removed outlier: 4.488A pdb=" N SER E 177 " --> pdb=" O THR E 230 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY E 212 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN E 239 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL E 210 " --> pdb=" O GLN E 239 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2925 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: 5.50 Time building geometry restraints manager: 7.23 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: 5135 1.34 - 1.46: 3931 1.46 - 1.58: 8259 1.58 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 17505 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 17500 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.32: 370 105.32 - 112.48: 9252 112.48 - 119.65: 5621 119.65 - 126.82: 8256 126.82 - 133.99: 316 Bond angle restraints: 23815 Sorted by residual: angle pdb=" N VAL E 295 " pdb=" CA VAL E 295 " pdb=" C VAL E 295 " ideal model delta sigma weight residual 112.17 104.74 7.43 9.50e-01 1.11e+00 6.11e+01 angle pdb=" N VAL B 295 " pdb=" CA VAL B 295 " pdb=" C VAL B 295 " ideal model delta sigma weight residual 112.17 104.79 7.38 9.50e-01 1.11e+00 6.04e+01 angle pdb=" N VAL D 295 " pdb=" CA VAL D 295 " pdb=" C VAL D 295 " ideal model delta sigma weight residual 112.17 104.82 7.35 9.50e-01 1.11e+00 5.98e+01 angle pdb=" N VAL A 295 " pdb=" CA VAL A 295 " pdb=" C VAL A 295 " ideal model delta sigma weight residual 112.17 104.83 7.34 9.50e-01 1.11e+00 5.97e+01 angle pdb=" N VAL C 295 " pdb=" CA VAL C 295 " pdb=" C VAL C 295 " ideal model delta sigma weight residual 112.17 104.84 7.33 9.50e-01 1.11e+00 5.95e+01 ... (remaining 23810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 9195 16.82 - 33.63: 1078 33.63 - 50.45: 337 50.45 - 67.27: 110 67.27 - 84.08: 10 Dihedral angle restraints: 10730 sinusoidal: 4625 harmonic: 6105 Sorted by residual: dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual 93.00 33.82 59.18 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS A 157 " pdb=" SG CYS A 157 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 33.84 59.16 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS E 157 " pdb=" SG CYS E 157 " pdb=" SG CYS E 171 " pdb=" CB CYS E 171 " ideal model delta sinusoidal sigma weight residual 93.00 33.85 59.15 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 10727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1921 0.037 - 0.075: 646 0.075 - 0.112: 185 0.112 - 0.149: 33 0.149 - 0.187: 15 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C2 NAG O 1 " pdb=" C1 NAG O 1 " pdb=" C3 NAG O 1 " pdb=" N2 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C2 NAG K 1 " pdb=" C1 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" N2 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C2 NAG I 1 " pdb=" C1 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" N2 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 2797 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 299 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO E 300 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO E 300 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 300 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 299 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO B 300 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 299 " -0.016 5.00e-02 4.00e+02 2.51e-02 1.00e+00 pdb=" N PRO C 300 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 300 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 300 " -0.014 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2636 2.77 - 3.30: 14670 3.30 - 3.83: 27043 3.83 - 4.37: 31867 4.37 - 4.90: 56358 Nonbonded interactions: 132574 Sorted by model distance: nonbonded pdb=" OD2 ASP B 181 " pdb=" OG SER B 183 " model vdw 2.236 3.040 nonbonded pdb=" OD2 ASP A 181 " pdb=" OG SER A 183 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP D 181 " pdb=" OG SER D 183 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP C 181 " pdb=" OG SER C 183 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP E 181 " pdb=" OG SER E 183 " model vdw 2.238 3.040 ... (remaining 132569 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' } ncs_group { reference = 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' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.420 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 46.990 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.003 0.029 17505 Z= 0.165 Angle : 0.509 7.428 23815 Z= 0.293 Chirality : 0.042 0.187 2800 Planarity : 0.003 0.025 2890 Dihedral : 16.533 84.082 6755 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.69 % Allowed : 21.97 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.07 (0.18), residues: 2040 helix: 1.65 (0.17), residues: 785 sheet: 1.77 (0.25), residues: 445 loop : -0.89 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 350 HIS 0.004 0.001 HIS C 352 PHE 0.017 0.001 PHE C 332 TYR 0.008 0.001 TYR E 72 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 390 time to evaluate : 1.859 Fit side-chains REVERT: A 146 GLU cc_start: 0.8381 (tt0) cc_final: 0.8173 (tt0) REVERT: A 162 LYS cc_start: 0.8616 (tttt) cc_final: 0.8401 (ttmt) REVERT: A 227 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7599 (m) REVERT: A 249 LEU cc_start: 0.8051 (mt) cc_final: 0.7365 (tp) REVERT: A 266 THR cc_start: 0.8110 (m) cc_final: 0.7610 (p) REVERT: A 489 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7306 (mt-10) REVERT: A 514 SER cc_start: 0.8470 (m) cc_final: 0.8077 (p) REVERT: B 227 VAL cc_start: 0.7699 (m) cc_final: 0.7376 (m) REVERT: B 249 LEU cc_start: 0.8091 (mt) cc_final: 0.7464 (tp) REVERT: B 266 THR cc_start: 0.8075 (m) cc_final: 0.7700 (p) REVERT: B 291 MET cc_start: 0.7564 (mtp) cc_final: 0.7025 (mtp) REVERT: B 349 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7585 (tppp) REVERT: B 489 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6688 (tt0) REVERT: B 514 SER cc_start: 0.8394 (m) cc_final: 0.8005 (t) REVERT: B 530 ASN cc_start: 0.7922 (t0) cc_final: 0.7691 (t0) REVERT: C 23 ASP cc_start: 0.7799 (p0) cc_final: 0.7399 (p0) REVERT: C 47 ARG cc_start: 0.7534 (mpp-170) cc_final: 0.7328 (mpp-170) REVERT: C 227 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7432 (m) REVERT: C 247 LEU cc_start: 0.8534 (tp) cc_final: 0.8313 (mt) REVERT: C 249 LEU cc_start: 0.7890 (mt) cc_final: 0.7312 (tp) REVERT: C 291 MET cc_start: 0.7674 (mtp) cc_final: 0.7087 (mtp) REVERT: C 489 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7251 (mt-10) REVERT: C 514 SER cc_start: 0.8400 (m) cc_final: 0.7968 (p) REVERT: D 146 GLU cc_start: 0.8419 (tt0) cc_final: 0.8154 (tt0) REVERT: D 227 VAL cc_start: 0.7760 (m) cc_final: 0.7303 (m) REVERT: D 245 TYR cc_start: 0.8775 (m-80) cc_final: 0.8466 (m-80) REVERT: D 249 LEU cc_start: 0.8121 (mt) cc_final: 0.7446 (tp) REVERT: D 291 MET cc_start: 0.7548 (mtp) cc_final: 0.7048 (mtp) REVERT: D 294 MET cc_start: 0.4592 (mmt) cc_final: 0.3339 (mmp) REVERT: D 311 LEU cc_start: 0.8260 (tp) cc_final: 0.8039 (tp) REVERT: D 489 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 493 ASP cc_start: 0.7714 (m-30) cc_final: 0.7433 (m-30) REVERT: D 514 SER cc_start: 0.8544 (m) cc_final: 0.8153 (p) REVERT: E 23 ASP cc_start: 0.7723 (p0) cc_final: 0.7509 (p0) REVERT: E 47 ARG cc_start: 0.7575 (mpp-170) cc_final: 0.7128 (mpp-170) REVERT: E 146 GLU cc_start: 0.8416 (tt0) cc_final: 0.8206 (tt0) REVERT: E 227 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7382 (m) REVERT: E 249 LEU cc_start: 0.7916 (mt) cc_final: 0.7361 (tp) REVERT: E 514 SER cc_start: 0.8375 (m) cc_final: 0.7886 (p) outliers start: 13 outliers final: 1 residues processed: 390 average time/residue: 1.2272 time to fit residues: 532.6348 Evaluate side-chains 237 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 70 GLN B 271 HIS B 361 GLN B 519 ASN C 70 GLN C 352 HIS C 530 ASN D 271 HIS D 352 HIS D 530 ASN E 70 GLN E 352 HIS E 530 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17505 Z= 0.252 Angle : 0.692 11.828 23815 Z= 0.349 Chirality : 0.049 0.266 2800 Planarity : 0.005 0.038 2890 Dihedral : 7.267 55.961 2746 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.52 % Allowed : 18.03 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.90 (0.18), residues: 2040 helix: 2.65 (0.17), residues: 835 sheet: 1.61 (0.24), residues: 470 loop : -0.68 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 494 HIS 0.006 0.002 HIS B 131 PHE 0.010 0.001 PHE E 312 TYR 0.015 0.002 TYR B 245 ARG 0.005 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 257 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8787 (pttm) REVERT: A 162 LYS cc_start: 0.8661 (tttt) cc_final: 0.8455 (ttmt) REVERT: A 227 VAL cc_start: 0.8039 (m) cc_final: 0.7761 (m) REVERT: A 247 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 266 THR cc_start: 0.8185 (m) cc_final: 0.7737 (p) REVERT: A 291 MET cc_start: 0.7203 (mtp) cc_final: 0.6885 (mtp) REVERT: A 489 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6805 (mt-10) REVERT: A 493 ASP cc_start: 0.7651 (m-30) cc_final: 0.7331 (m-30) REVERT: A 514 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 40 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8819 (pttm) REVERT: B 47 ARG cc_start: 0.7698 (mpp-170) cc_final: 0.7369 (mpp-170) REVERT: B 104 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7970 (mtm180) REVERT: B 266 THR cc_start: 0.8211 (m) cc_final: 0.7840 (p) REVERT: B 291 MET cc_start: 0.7306 (mtp) cc_final: 0.6942 (mtp) REVERT: B 349 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7576 (tppp) REVERT: B 353 ARG cc_start: 0.7308 (ptt180) cc_final: 0.6884 (ptt90) REVERT: B 514 SER cc_start: 0.8067 (m) cc_final: 0.7765 (p) REVERT: B 530 ASN cc_start: 0.7710 (t0) cc_final: 0.7478 (t0) REVERT: C 23 ASP cc_start: 0.7882 (p0) cc_final: 0.7458 (p0) REVERT: C 40 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8754 (pttm) REVERT: C 47 ARG cc_start: 0.7793 (mpp-170) cc_final: 0.7325 (mpp-170) REVERT: C 227 VAL cc_start: 0.7883 (m) cc_final: 0.7623 (m) REVERT: C 288 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7498 (mmm) REVERT: C 291 MET cc_start: 0.7459 (mtp) cc_final: 0.7023 (mtp) REVERT: C 292 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6735 (mt) REVERT: C 489 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6912 (mt-10) REVERT: C 514 SER cc_start: 0.8105 (m) cc_final: 0.7781 (p) REVERT: D 146 GLU cc_start: 0.8384 (tt0) cc_final: 0.8138 (tt0) REVERT: D 291 MET cc_start: 0.7325 (mtp) cc_final: 0.6806 (mtp) REVERT: D 294 MET cc_start: 0.5202 (mmp) cc_final: 0.3973 (mmp) REVERT: D 353 ARG cc_start: 0.7147 (ptt180) cc_final: 0.6720 (ptt90) REVERT: D 489 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6784 (mt-10) REVERT: D 493 ASP cc_start: 0.7635 (m-30) cc_final: 0.7327 (m-30) REVERT: D 514 SER cc_start: 0.8165 (m) cc_final: 0.7816 (p) REVERT: E 23 ASP cc_start: 0.7735 (p0) cc_final: 0.7496 (p0) REVERT: E 47 ARG cc_start: 0.7749 (mpp-170) cc_final: 0.7341 (mpp-170) REVERT: E 146 GLU cc_start: 0.8408 (tt0) cc_final: 0.8188 (tt0) REVERT: E 227 VAL cc_start: 0.8212 (m) cc_final: 0.7981 (m) REVERT: E 292 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6637 (mt) REVERT: E 353 ARG cc_start: 0.7113 (ptt180) cc_final: 0.6837 (ptt90) REVERT: E 493 ASP cc_start: 0.7763 (m-30) cc_final: 0.7486 (m-30) REVERT: E 514 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7668 (p) REVERT: E 529 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7247 (tt0) outliers start: 66 outliers final: 25 residues processed: 292 average time/residue: 1.2298 time to fit residues: 401.8782 Evaluate side-chains 267 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 232 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 529 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 186 optimal weight: 0.0870 chunk 201 optimal weight: 4.9990 chunk 166 optimal weight: 0.0040 chunk 184 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17505 Z= 0.173 Angle : 0.608 9.986 23815 Z= 0.305 Chirality : 0.046 0.341 2800 Planarity : 0.004 0.035 2890 Dihedral : 6.887 56.254 2740 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.15 % Allowed : 20.11 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.27 (0.18), residues: 2040 helix: 3.31 (0.17), residues: 820 sheet: 1.78 (0.25), residues: 425 loop : -0.69 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 494 HIS 0.003 0.001 HIS B 271 PHE 0.009 0.001 PHE E 312 TYR 0.012 0.001 TYR C 72 ARG 0.002 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 237 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8537 (mpp) REVERT: A 162 LYS cc_start: 0.8632 (tttt) cc_final: 0.8424 (ttmt) REVERT: A 227 VAL cc_start: 0.8065 (m) cc_final: 0.7774 (m) REVERT: A 249 LEU cc_start: 0.7553 (mp) cc_final: 0.6669 (tp) REVERT: A 266 THR cc_start: 0.8195 (m) cc_final: 0.7673 (p) REVERT: A 291 MET cc_start: 0.7149 (mtp) cc_final: 0.6838 (mtp) REVERT: A 514 SER cc_start: 0.8052 (m) cc_final: 0.7837 (p) REVERT: B 40 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8757 (pttm) REVERT: B 47 ARG cc_start: 0.7739 (mpp-170) cc_final: 0.7486 (mpp-170) REVERT: B 106 ASP cc_start: 0.8225 (m-30) cc_final: 0.7928 (p0) REVERT: B 266 THR cc_start: 0.8231 (m) cc_final: 0.7857 (p) REVERT: B 291 MET cc_start: 0.7206 (mtp) cc_final: 0.6877 (mtp) REVERT: B 292 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6791 (mt) REVERT: B 349 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7677 (tppp) REVERT: B 353 ARG cc_start: 0.7318 (ptt180) cc_final: 0.6849 (ptt90) REVERT: B 493 ASP cc_start: 0.7659 (m-30) cc_final: 0.7405 (m-30) REVERT: C 23 ASP cc_start: 0.7851 (p0) cc_final: 0.7440 (p0) REVERT: C 40 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8791 (pttm) REVERT: C 47 ARG cc_start: 0.7790 (mpp-170) cc_final: 0.7180 (mtm180) REVERT: C 227 VAL cc_start: 0.7923 (m) cc_final: 0.7645 (m) REVERT: C 249 LEU cc_start: 0.7599 (mp) cc_final: 0.6799 (tp) REVERT: C 288 MET cc_start: 0.7921 (ttm) cc_final: 0.7465 (mmm) REVERT: C 291 MET cc_start: 0.7195 (mtp) cc_final: 0.6839 (mtp) REVERT: C 292 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6561 (mt) REVERT: C 493 ASP cc_start: 0.7586 (m-30) cc_final: 0.7296 (m-30) REVERT: C 514 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7904 (p) REVERT: D 40 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (pttm) REVERT: D 146 GLU cc_start: 0.8347 (tt0) cc_final: 0.8101 (tt0) REVERT: D 288 MET cc_start: 0.7912 (mtm) cc_final: 0.7632 (mmm) REVERT: D 291 MET cc_start: 0.7232 (mtp) cc_final: 0.6800 (mtp) REVERT: D 294 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.4164 (mmp) REVERT: D 353 ARG cc_start: 0.7178 (ptt180) cc_final: 0.6884 (ptt90) REVERT: D 514 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7771 (p) REVERT: E 23 ASP cc_start: 0.7754 (p0) cc_final: 0.7498 (p0) REVERT: E 47 ARG cc_start: 0.7731 (mpp-170) cc_final: 0.7286 (mpp-170) REVERT: E 102 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8477 (mpp) REVERT: E 146 GLU cc_start: 0.8364 (tt0) cc_final: 0.8155 (tt0) REVERT: E 227 VAL cc_start: 0.8227 (m) cc_final: 0.7978 (m) REVERT: E 247 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8206 (mp) REVERT: E 288 MET cc_start: 0.7784 (mtm) cc_final: 0.7515 (mmm) REVERT: E 291 MET cc_start: 0.7164 (mtp) cc_final: 0.6798 (mtp) REVERT: E 292 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6548 (mt) REVERT: E 493 ASP cc_start: 0.7702 (m-30) cc_final: 0.7405 (m-30) outliers start: 59 outliers final: 12 residues processed: 276 average time/residue: 1.1476 time to fit residues: 356.4119 Evaluate side-chains 253 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 0.0870 chunk 125 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN B 271 HIS B 361 GLN C 352 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17505 Z= 0.160 Angle : 0.584 9.734 23815 Z= 0.290 Chirality : 0.045 0.317 2800 Planarity : 0.004 0.037 2890 Dihedral : 6.633 56.898 2740 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.84 % Allowed : 19.95 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.38 (0.19), residues: 2040 helix: 3.45 (0.17), residues: 820 sheet: 1.77 (0.25), residues: 425 loop : -0.65 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 494 HIS 0.003 0.001 HIS B 271 PHE 0.010 0.001 PHE E 312 TYR 0.012 0.001 TYR C 72 ARG 0.002 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 236 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8534 (mpp) REVERT: A 104 ARG cc_start: 0.8252 (mtm110) cc_final: 0.8048 (mtm180) REVERT: A 162 LYS cc_start: 0.8646 (tttt) cc_final: 0.8444 (ttmt) REVERT: A 227 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7779 (m) REVERT: A 266 THR cc_start: 0.8176 (m) cc_final: 0.7664 (p) REVERT: A 288 MET cc_start: 0.7775 (mmm) cc_final: 0.7568 (mmm) REVERT: A 291 MET cc_start: 0.7145 (mtp) cc_final: 0.6827 (mtp) REVERT: A 493 ASP cc_start: 0.7520 (m-30) cc_final: 0.7125 (m-30) REVERT: B 47 ARG cc_start: 0.7770 (mpp-170) cc_final: 0.7558 (mpp-170) REVERT: B 291 MET cc_start: 0.7044 (mtp) cc_final: 0.6727 (mtp) REVERT: B 349 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7544 (tppp) REVERT: B 493 ASP cc_start: 0.7617 (m-30) cc_final: 0.7320 (m-30) REVERT: B 516 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7241 (mp) REVERT: C 23 ASP cc_start: 0.7791 (p0) cc_final: 0.7371 (p0) REVERT: C 40 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8784 (pttm) REVERT: C 47 ARG cc_start: 0.7801 (mpp-170) cc_final: 0.7161 (mtm180) REVERT: C 104 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7938 (mtm180) REVERT: C 227 VAL cc_start: 0.7923 (m) cc_final: 0.7629 (m) REVERT: C 288 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7437 (mmm) REVERT: C 291 MET cc_start: 0.7067 (mtp) cc_final: 0.6724 (mtp) REVERT: C 292 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6451 (mt) REVERT: C 493 ASP cc_start: 0.7534 (m-30) cc_final: 0.7163 (m-30) REVERT: D 40 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8718 (pttm) REVERT: D 146 GLU cc_start: 0.8329 (tt0) cc_final: 0.8097 (tt0) REVERT: D 288 MET cc_start: 0.7897 (mtm) cc_final: 0.7615 (mmm) REVERT: D 291 MET cc_start: 0.7097 (mtp) cc_final: 0.6788 (mtp) REVERT: D 294 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.4210 (mmp) REVERT: D 353 ARG cc_start: 0.7195 (ptt180) cc_final: 0.6898 (ptt90) REVERT: D 383 MET cc_start: 0.2344 (OUTLIER) cc_final: 0.1220 (mmt) REVERT: E 23 ASP cc_start: 0.7712 (p0) cc_final: 0.7438 (p0) REVERT: E 47 ARG cc_start: 0.7712 (mpp-170) cc_final: 0.7285 (mpp-170) REVERT: E 102 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8473 (mpp) REVERT: E 146 GLU cc_start: 0.8369 (tt0) cc_final: 0.8151 (tt0) REVERT: E 227 VAL cc_start: 0.8240 (m) cc_final: 0.7995 (m) REVERT: E 247 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8205 (mp) REVERT: E 288 MET cc_start: 0.7843 (mtm) cc_final: 0.7438 (mmm) REVERT: E 291 MET cc_start: 0.6976 (mtp) cc_final: 0.6576 (mtp) REVERT: E 292 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6583 (mt) REVERT: E 493 ASP cc_start: 0.7630 (m-30) cc_final: 0.7316 (m-30) outliers start: 72 outliers final: 14 residues processed: 282 average time/residue: 1.1539 time to fit residues: 367.6517 Evaluate side-chains 249 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 519 ASN B 271 HIS C 352 HIS C 519 ASN D 519 ASN E 519 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17505 Z= 0.250 Angle : 0.671 9.819 23815 Z= 0.335 Chirality : 0.048 0.283 2800 Planarity : 0.004 0.038 2890 Dihedral : 6.633 55.871 2740 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.32 % Allowed : 19.25 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.16 (0.18), residues: 2040 helix: 3.23 (0.17), residues: 825 sheet: 1.58 (0.23), residues: 470 loop : -0.86 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 494 HIS 0.005 0.001 HIS E 131 PHE 0.012 0.001 PHE E 312 TYR 0.013 0.002 TYR B 245 ARG 0.004 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 221 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8044 (mpp-170) cc_final: 0.7833 (mtm180) REVERT: A 104 ARG cc_start: 0.8281 (mtm110) cc_final: 0.8069 (mtm180) REVERT: A 162 LYS cc_start: 0.8655 (tttt) cc_final: 0.8433 (ttmt) REVERT: A 203 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8088 (mp) REVERT: A 249 LEU cc_start: 0.7711 (mp) cc_final: 0.6894 (tp) REVERT: A 266 THR cc_start: 0.8339 (m) cc_final: 0.7848 (p) REVERT: A 288 MET cc_start: 0.7839 (mmm) cc_final: 0.7615 (mmm) REVERT: A 291 MET cc_start: 0.7211 (mtp) cc_final: 0.6789 (mtp) REVERT: A 493 ASP cc_start: 0.7703 (m-30) cc_final: 0.7337 (m-30) REVERT: A 516 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7107 (mp) REVERT: A 529 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7151 (tp30) REVERT: B 40 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8842 (pttm) REVERT: B 47 ARG cc_start: 0.8035 (mpp-170) cc_final: 0.7813 (mtm180) REVERT: B 203 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 266 THR cc_start: 0.8380 (m) cc_final: 0.7963 (p) REVERT: B 291 MET cc_start: 0.7105 (mtp) cc_final: 0.6810 (mtp) REVERT: B 349 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7563 (tppp) REVERT: B 493 ASP cc_start: 0.7685 (m-30) cc_final: 0.7425 (m-30) REVERT: B 516 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7258 (mp) REVERT: C 23 ASP cc_start: 0.7807 (p0) cc_final: 0.7377 (p0) REVERT: C 40 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8677 (pttm) REVERT: C 47 ARG cc_start: 0.7979 (mpp-170) cc_final: 0.7392 (mtm180) REVERT: C 104 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7995 (mtm180) REVERT: C 203 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8003 (mp) REVERT: C 227 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7828 (m) REVERT: C 288 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7500 (mmm) REVERT: C 291 MET cc_start: 0.7149 (mtp) cc_final: 0.6654 (mtp) REVERT: C 292 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6502 (mt) REVERT: D 146 GLU cc_start: 0.8377 (tt0) cc_final: 0.8141 (tt0) REVERT: D 203 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7987 (mp) REVERT: D 288 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7605 (mmm) REVERT: D 291 MET cc_start: 0.7192 (mtp) cc_final: 0.6843 (mtp) REVERT: D 294 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4055 (mmp) REVERT: D 346 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7116 (ptpt) REVERT: D 353 ARG cc_start: 0.7146 (ptt180) cc_final: 0.6825 (ptt90) REVERT: E 23 ASP cc_start: 0.7660 (p0) cc_final: 0.7330 (p0) REVERT: E 47 ARG cc_start: 0.7909 (mpp-170) cc_final: 0.7560 (mpp-170) REVERT: E 146 GLU cc_start: 0.8421 (tt0) cc_final: 0.8194 (tt0) REVERT: E 203 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8101 (mp) REVERT: E 227 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7907 (m) REVERT: E 247 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8258 (mp) REVERT: E 291 MET cc_start: 0.7129 (mtp) cc_final: 0.6686 (mtp) REVERT: E 292 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6448 (mt) REVERT: E 493 ASP cc_start: 0.7795 (m-30) cc_final: 0.7528 (m-30) outliers start: 81 outliers final: 35 residues processed: 275 average time/residue: 1.1901 time to fit residues: 367.2228 Evaluate side-chains 269 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 215 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS C 352 HIS D 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17505 Z= 0.166 Angle : 0.593 9.624 23815 Z= 0.296 Chirality : 0.046 0.297 2800 Planarity : 0.004 0.034 2890 Dihedral : 6.507 56.001 2740 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.47 % Allowed : 19.89 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.31 (0.19), residues: 2040 helix: 3.39 (0.17), residues: 825 sheet: 1.77 (0.25), residues: 425 loop : -0.75 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 494 HIS 0.003 0.001 HIS B 271 PHE 0.010 0.001 PHE E 312 TYR 0.012 0.001 TYR D 72 ARG 0.001 0.000 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 229 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8547 (mpp) REVERT: A 104 ARG cc_start: 0.8255 (mtm110) cc_final: 0.8036 (mtm180) REVERT: A 162 LYS cc_start: 0.8660 (tttt) cc_final: 0.8430 (ttmt) REVERT: A 227 VAL cc_start: 0.8150 (m) cc_final: 0.7886 (m) REVERT: A 266 THR cc_start: 0.8292 (m) cc_final: 0.7819 (p) REVERT: A 288 MET cc_start: 0.7762 (mmm) cc_final: 0.7181 (mmm) REVERT: A 291 MET cc_start: 0.7140 (mtp) cc_final: 0.6787 (mtp) REVERT: A 346 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6767 (ptpt) REVERT: B 40 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8811 (pttm) REVERT: B 203 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8051 (mp) REVERT: B 291 MET cc_start: 0.7043 (mtp) cc_final: 0.6639 (mtp) REVERT: B 349 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7582 (tppp) REVERT: B 493 ASP cc_start: 0.7692 (m-30) cc_final: 0.7359 (m-30) REVERT: C 47 ARG cc_start: 0.7962 (mpp-170) cc_final: 0.7387 (mtm180) REVERT: C 227 VAL cc_start: 0.8073 (m) cc_final: 0.7752 (m) REVERT: C 288 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7465 (mmm) REVERT: C 291 MET cc_start: 0.7111 (mtp) cc_final: 0.6733 (mtp) REVERT: C 292 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6528 (mt) REVERT: C 493 ASP cc_start: 0.7552 (m-30) cc_final: 0.7239 (m-30) REVERT: D 36 GLU cc_start: 0.7783 (tt0) cc_final: 0.7405 (mt-10) REVERT: D 40 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (pttm) REVERT: D 146 GLU cc_start: 0.8352 (tt0) cc_final: 0.8114 (tt0) REVERT: D 203 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7935 (mp) REVERT: D 288 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7599 (mmm) REVERT: D 291 MET cc_start: 0.7101 (mtp) cc_final: 0.6724 (mtp) REVERT: D 294 MET cc_start: 0.5086 (OUTLIER) cc_final: 0.4276 (tmm) REVERT: D 346 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7047 (ptpt) REVERT: D 383 MET cc_start: 0.2451 (OUTLIER) cc_final: 0.1397 (mmt) REVERT: E 23 ASP cc_start: 0.7627 (p0) cc_final: 0.7289 (p0) REVERT: E 47 ARG cc_start: 0.7875 (mpp-170) cc_final: 0.7421 (mpp-170) REVERT: E 102 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8462 (mpp) REVERT: E 146 GLU cc_start: 0.8378 (tt0) cc_final: 0.8154 (tt0) REVERT: E 203 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8083 (mp) REVERT: E 227 VAL cc_start: 0.8185 (m) cc_final: 0.7931 (m) REVERT: E 288 MET cc_start: 0.7844 (mtm) cc_final: 0.7583 (mmm) REVERT: E 291 MET cc_start: 0.7000 (mtp) cc_final: 0.6660 (mtp) REVERT: E 292 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6362 (mt) REVERT: E 493 ASP cc_start: 0.7663 (m-30) cc_final: 0.7360 (m-30) outliers start: 65 outliers final: 20 residues processed: 271 average time/residue: 1.1496 time to fit residues: 350.5742 Evaluate side-chains 255 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 220 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.0030 chunk 22 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN B 271 HIS C 352 HIS D 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17505 Z= 0.173 Angle : 0.613 18.662 23815 Z= 0.301 Chirality : 0.047 0.313 2800 Planarity : 0.004 0.034 2890 Dihedral : 6.430 55.544 2740 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.31 % Allowed : 20.11 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.31 (0.19), residues: 2040 helix: 3.39 (0.17), residues: 825 sheet: 1.74 (0.25), residues: 425 loop : -0.73 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 494 HIS 0.003 0.001 HIS E 131 PHE 0.010 0.001 PHE C 293 TYR 0.013 0.001 TYR E 229 ARG 0.001 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 224 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8541 (mpp) REVERT: A 162 LYS cc_start: 0.8659 (tttt) cc_final: 0.8431 (ttmt) REVERT: A 227 VAL cc_start: 0.8176 (m) cc_final: 0.7923 (m) REVERT: A 288 MET cc_start: 0.7755 (mmm) cc_final: 0.7182 (mmm) REVERT: A 291 MET cc_start: 0.7156 (mtp) cc_final: 0.6818 (mtp) REVERT: A 346 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6778 (ptpt) REVERT: A 516 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7039 (mp) REVERT: B 40 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8825 (pttm) REVERT: B 102 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8515 (mpp) REVERT: B 148 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8833 (tp) REVERT: B 203 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8057 (mp) REVERT: B 249 LEU cc_start: 0.7568 (mt) cc_final: 0.7151 (mt) REVERT: B 291 MET cc_start: 0.6874 (mtp) cc_final: 0.6474 (mtp) REVERT: B 349 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7709 (tppp) REVERT: B 493 ASP cc_start: 0.7657 (m-30) cc_final: 0.7327 (m-30) REVERT: C 47 ARG cc_start: 0.7946 (mpp-170) cc_final: 0.7410 (mtm180) REVERT: C 227 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7766 (m) REVERT: C 288 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7495 (mmm) REVERT: C 291 MET cc_start: 0.7100 (mtp) cc_final: 0.6736 (mtp) REVERT: C 292 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6448 (mt) REVERT: C 493 ASP cc_start: 0.7584 (m-30) cc_final: 0.7221 (m-30) REVERT: D 36 GLU cc_start: 0.7747 (tt0) cc_final: 0.7389 (mt-10) REVERT: D 40 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8702 (pttm) REVERT: D 146 GLU cc_start: 0.8349 (tt0) cc_final: 0.8092 (tt0) REVERT: D 203 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7946 (mp) REVERT: D 288 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7626 (mmm) REVERT: D 291 MET cc_start: 0.6915 (mtp) cc_final: 0.6677 (mtp) REVERT: D 294 MET cc_start: 0.4877 (OUTLIER) cc_final: 0.4522 (ttp) REVERT: D 383 MET cc_start: 0.2454 (OUTLIER) cc_final: 0.1420 (mmt) REVERT: E 23 ASP cc_start: 0.7609 (p0) cc_final: 0.7237 (p0) REVERT: E 47 ARG cc_start: 0.7880 (mpp-170) cc_final: 0.7429 (mpp-170) REVERT: E 102 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8459 (mpp) REVERT: E 146 GLU cc_start: 0.8375 (tt0) cc_final: 0.8148 (tt0) REVERT: E 203 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (mp) REVERT: E 227 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7879 (m) REVERT: E 288 MET cc_start: 0.7855 (mtm) cc_final: 0.7326 (mmm) REVERT: E 291 MET cc_start: 0.7019 (mtp) cc_final: 0.6702 (mtp) REVERT: E 292 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6345 (mt) REVERT: E 493 ASP cc_start: 0.7655 (m-30) cc_final: 0.7347 (m-30) outliers start: 62 outliers final: 18 residues processed: 262 average time/residue: 1.1296 time to fit residues: 334.0714 Evaluate side-chains 257 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS C 352 HIS D 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17505 Z= 0.212 Angle : 0.639 10.622 23815 Z= 0.318 Chirality : 0.047 0.292 2800 Planarity : 0.004 0.035 2890 Dihedral : 6.474 55.218 2740 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.57 % Allowed : 19.68 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.23 (0.19), residues: 2040 helix: 3.29 (0.17), residues: 825 sheet: 1.54 (0.24), residues: 470 loop : -0.77 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 494 HIS 0.004 0.001 HIS B 131 PHE 0.011 0.001 PHE E 312 TYR 0.013 0.001 TYR C 72 ARG 0.002 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 223 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8542 (mpp) REVERT: A 227 VAL cc_start: 0.8234 (m) cc_final: 0.7972 (m) REVERT: A 288 MET cc_start: 0.7802 (mmm) cc_final: 0.7228 (mmm) REVERT: A 291 MET cc_start: 0.7247 (mtp) cc_final: 0.6876 (mtp) REVERT: A 346 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6789 (ptpt) REVERT: A 493 ASP cc_start: 0.7651 (m-30) cc_final: 0.7319 (m-30) REVERT: A 516 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7048 (mp) REVERT: B 40 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8737 (pttm) REVERT: B 148 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8840 (tp) REVERT: B 203 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 291 MET cc_start: 0.7188 (mtp) cc_final: 0.6818 (mtp) REVERT: B 349 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7939 (ptmm) REVERT: B 493 ASP cc_start: 0.7704 (m-30) cc_final: 0.7390 (m-30) REVERT: C 40 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8775 (pttm) REVERT: C 47 ARG cc_start: 0.7991 (mpp-170) cc_final: 0.7474 (mtm180) REVERT: C 203 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7765 (mp) REVERT: C 227 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7819 (m) REVERT: C 288 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7491 (mmm) REVERT: C 291 MET cc_start: 0.7169 (mtp) cc_final: 0.6770 (mtp) REVERT: C 292 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6503 (mt) REVERT: C 493 ASP cc_start: 0.7628 (m-30) cc_final: 0.7340 (m-30) REVERT: C 513 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: D 36 GLU cc_start: 0.7808 (tt0) cc_final: 0.7453 (mt-10) REVERT: D 40 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8725 (pttm) REVERT: D 146 GLU cc_start: 0.8367 (tt0) cc_final: 0.8120 (tt0) REVERT: D 203 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7964 (mp) REVERT: D 288 MET cc_start: 0.7866 (mtm) cc_final: 0.7570 (mmm) REVERT: D 291 MET cc_start: 0.6966 (mtp) cc_final: 0.6746 (mtp) REVERT: D 383 MET cc_start: 0.2398 (OUTLIER) cc_final: 0.1391 (mmt) REVERT: E 23 ASP cc_start: 0.7582 (p0) cc_final: 0.7209 (p0) REVERT: E 47 ARG cc_start: 0.8040 (mpp-170) cc_final: 0.7692 (mpp-170) REVERT: E 102 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8485 (mpp) REVERT: E 146 GLU cc_start: 0.8397 (tt0) cc_final: 0.8166 (tt0) REVERT: E 203 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8099 (mp) REVERT: E 227 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7963 (m) REVERT: E 291 MET cc_start: 0.6966 (mtp) cc_final: 0.6643 (mtp) REVERT: E 292 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6349 (mt) REVERT: E 493 ASP cc_start: 0.7751 (m-30) cc_final: 0.7478 (m-30) outliers start: 67 outliers final: 29 residues processed: 264 average time/residue: 1.1359 time to fit residues: 337.6641 Evaluate side-chains 265 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 217 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 166 optimal weight: 0.0980 chunk 174 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17505 Z= 0.206 Angle : 0.638 9.757 23815 Z= 0.317 Chirality : 0.047 0.308 2800 Planarity : 0.004 0.036 2890 Dihedral : 6.507 55.309 2740 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.31 % Allowed : 19.89 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 2.24 (0.18), residues: 2040 helix: 3.28 (0.17), residues: 825 sheet: 1.55 (0.24), residues: 470 loop : -0.76 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 494 HIS 0.004 0.001 HIS B 131 PHE 0.012 0.001 PHE B 312 TYR 0.015 0.001 TYR E 229 ARG 0.002 0.000 ARG E 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 221 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7772 (mmm) cc_final: 0.7207 (mmm) REVERT: A 291 MET cc_start: 0.7189 (mtp) cc_final: 0.6809 (mtp) REVERT: A 346 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6889 (ptpt) REVERT: A 493 ASP cc_start: 0.7626 (m-30) cc_final: 0.7283 (m-30) REVERT: A 516 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7046 (mp) REVERT: B 40 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8732 (pttm) REVERT: B 148 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8840 (tp) REVERT: B 203 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 291 MET cc_start: 0.7131 (mtp) cc_final: 0.6767 (mtp) REVERT: B 349 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7951 (ptmm) REVERT: B 493 ASP cc_start: 0.7698 (m-30) cc_final: 0.7382 (m-30) REVERT: C 40 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8790 (pttm) REVERT: C 47 ARG cc_start: 0.8004 (mpp-170) cc_final: 0.7476 (mtm180) REVERT: C 146 GLU cc_start: 0.8342 (tt0) cc_final: 0.8139 (tt0) REVERT: C 203 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7782 (mp) REVERT: C 227 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7858 (m) REVERT: C 288 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7506 (mmm) REVERT: C 291 MET cc_start: 0.7161 (mtp) cc_final: 0.6767 (mtp) REVERT: C 292 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6558 (mt) REVERT: C 513 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: D 36 GLU cc_start: 0.7802 (tt0) cc_final: 0.7452 (mt-10) REVERT: D 40 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8709 (pttm) REVERT: D 146 GLU cc_start: 0.8361 (tt0) cc_final: 0.8117 (tt0) REVERT: D 203 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7961 (mp) REVERT: D 247 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8313 (mp) REVERT: D 288 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7587 (mmm) REVERT: D 291 MET cc_start: 0.7116 (mtp) cc_final: 0.6841 (mtp) REVERT: E 47 ARG cc_start: 0.7993 (mpp-170) cc_final: 0.7657 (mpp-170) REVERT: E 102 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8483 (mpp) REVERT: E 146 GLU cc_start: 0.8393 (tt0) cc_final: 0.8161 (tt0) REVERT: E 203 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8087 (mp) REVERT: E 227 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7977 (m) REVERT: E 291 MET cc_start: 0.7020 (mtp) cc_final: 0.6683 (mtp) REVERT: E 292 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6390 (mt) REVERT: E 493 ASP cc_start: 0.7737 (m-30) cc_final: 0.7453 (m-30) outliers start: 62 outliers final: 30 residues processed: 254 average time/residue: 1.1810 time to fit residues: 336.7067 Evaluate side-chains 262 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 213 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS C 271 HIS D 37 ASN E 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17505 Z= 0.182 Angle : 0.620 9.872 23815 Z= 0.307 Chirality : 0.047 0.287 2800 Planarity : 0.004 0.036 2890 Dihedral : 6.484 55.576 2740 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.88 % Allowed : 20.11 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 2.28 (0.19), residues: 2040 helix: 3.35 (0.17), residues: 825 sheet: 1.74 (0.25), residues: 425 loop : -0.74 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 494 HIS 0.003 0.001 HIS B 271 PHE 0.010 0.001 PHE E 312 TYR 0.014 0.001 TYR E 229 ARG 0.001 0.000 ARG A 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 221 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8253 (m) cc_final: 0.8023 (m) REVERT: A 288 MET cc_start: 0.7741 (mmm) cc_final: 0.7234 (mmm) REVERT: A 291 MET cc_start: 0.7178 (mtp) cc_final: 0.6787 (mtp) REVERT: A 346 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6910 (ptpt) REVERT: A 516 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.7027 (mp) REVERT: B 40 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8727 (pttm) REVERT: B 102 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8492 (mpp) REVERT: B 148 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8837 (tp) REVERT: B 203 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8079 (mp) REVERT: B 291 MET cc_start: 0.7148 (mtp) cc_final: 0.6774 (mtp) REVERT: B 349 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7943 (ptmm) REVERT: B 493 ASP cc_start: 0.7658 (m-30) cc_final: 0.7334 (m-30) REVERT: C 40 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8781 (pttm) REVERT: C 47 ARG cc_start: 0.7953 (mpp-170) cc_final: 0.7439 (mtm180) REVERT: C 146 GLU cc_start: 0.8343 (tt0) cc_final: 0.8132 (tt0) REVERT: C 203 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7788 (mp) REVERT: C 227 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7859 (m) REVERT: C 288 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7462 (mmm) REVERT: C 291 MET cc_start: 0.7123 (mtp) cc_final: 0.6695 (mtp) REVERT: C 292 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6604 (mt) REVERT: C 493 ASP cc_start: 0.7617 (m-30) cc_final: 0.7340 (m-30) REVERT: C 513 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: D 36 GLU cc_start: 0.7792 (tt0) cc_final: 0.7457 (mt-10) REVERT: D 40 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8704 (pttm) REVERT: D 146 GLU cc_start: 0.8357 (tt0) cc_final: 0.8109 (tt0) REVERT: D 203 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 247 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8316 (mp) REVERT: D 288 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7588 (mmm) REVERT: D 291 MET cc_start: 0.7090 (mtp) cc_final: 0.6822 (mtp) REVERT: E 47 ARG cc_start: 0.8027 (mpp-170) cc_final: 0.7669 (mpp-170) REVERT: E 102 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8482 (mpp) REVERT: E 146 GLU cc_start: 0.8381 (tt0) cc_final: 0.8148 (tt0) REVERT: E 203 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8092 (mp) REVERT: E 227 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7975 (m) REVERT: E 291 MET cc_start: 0.7095 (mtp) cc_final: 0.6754 (mtp) REVERT: E 292 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6364 (mt) REVERT: E 493 ASP cc_start: 0.7731 (m-30) cc_final: 0.7423 (m-30) outliers start: 54 outliers final: 25 residues processed: 250 average time/residue: 1.1420 time to fit residues: 322.0457 Evaluate side-chains 259 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 45 optimal weight: 0.0370 chunk 162 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 0.3980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS D 37 ASN E 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104398 restraints weight = 17612.889| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.90 r_work: 0.2927 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17505 Z= 0.139 Angle : 0.566 9.835 23815 Z= 0.279 Chirality : 0.045 0.289 2800 Planarity : 0.004 0.034 2890 Dihedral : 6.377 56.448 2740 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.76 % Allowed : 21.23 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 2.42 (0.19), residues: 2040 helix: 3.57 (0.17), residues: 825 sheet: 1.73 (0.26), residues: 420 loop : -0.71 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 83 HIS 0.003 0.000 HIS B 271 PHE 0.009 0.001 PHE B 312 TYR 0.012 0.001 TYR D 72 ARG 0.001 0.000 ARG A 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6476.08 seconds wall clock time: 114 minutes 2.44 seconds (6842.44 seconds total)