Starting phenix.real_space_refine on Sat Aug 23 16:17:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp5_36468/08_2025/8jp5_36468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp5_36468/08_2025/8jp5_36468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jp5_36468/08_2025/8jp5_36468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp5_36468/08_2025/8jp5_36468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jp5_36468/08_2025/8jp5_36468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp5_36468/08_2025/8jp5_36468.map" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 sd= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 Zn 4 6.06 5 S 38 5.16 5 C 8460 2.51 5 N 2342 2.21 5 O 2630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13490 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 308} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 1 Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: E, F, G, H Time building chain proxies: 4.23, per 1000 atoms: 0.31 Number of scatterers: 13490 At special positions: 0 Unit cell: (120.516, 116.532, 127.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 16 19.99 S 38 16.00 O 2630 8.00 N 2342 7.00 C 8460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 825.2 milliseconds Enol-peptide restraints added in 1.4 microseconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 32.3% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 283 through 308 removed outlier: 3.706A pdb=" N GLU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 325 through 367 removed outlier: 4.068A pdb=" N VAL A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.680A pdb=" N ASN B 180 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 283 through 309 removed outlier: 3.897A pdb=" N GLU B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 365 removed outlier: 3.652A pdb=" N SER B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.623A pdb=" N VAL C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 70 through 80 removed outlier: 3.613A pdb=" N LEU C 74 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'D' and resid 42 through 47 removed outlier: 3.691A pdb=" N VAL D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 4.435A pdb=" N ILE D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 removed outlier: 3.644A pdb=" N GLN D 73 " --> pdb=" O PRO D 69 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 74 " --> pdb=" O GLN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 99 Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.695A pdb=" N ASP D 127 " --> pdb=" O GLY D 123 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'E' and resid 283 through 308 removed outlier: 3.705A pdb=" N GLU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 325 through 367 removed outlier: 4.068A pdb=" N VAL E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.679A pdb=" N ASN F 180 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP F 181 " --> pdb=" O HIS F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 181' Processing helix chain 'F' and resid 283 through 309 removed outlier: 3.897A pdb=" N GLU F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 365 removed outlier: 3.653A pdb=" N SER F 365 " --> pdb=" O ARG F 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 47 removed outlier: 3.624A pdb=" N VAL G 46 " --> pdb=" O ASP G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 56 Processing helix chain 'G' and resid 70 through 80 removed outlier: 3.614A pdb=" N LEU G 74 " --> pdb=" O GLN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 99 Processing helix chain 'G' and resid 113 through 129 Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'H' and resid 42 through 47 removed outlier: 3.691A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 56 removed outlier: 4.434A pdb=" N ILE H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 80 removed outlier: 3.644A pdb=" N GLN H 73 " --> pdb=" O PRO H 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU H 74 " --> pdb=" O GLN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 99 Processing helix chain 'H' and resid 113 through 129 removed outlier: 3.694A pdb=" N ASP H 127 " --> pdb=" O GLY H 123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 53 removed outlier: 4.638A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 11.037A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.515A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 83 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A 259 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG A 81 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 53 removed outlier: 4.638A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 11.037A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.515A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 261 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN A 103 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 212 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A 232 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 214 " --> pdb=" O CYS A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.912A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.912A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.542A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 10.640A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 12.045A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.822A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.542A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 10.640A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 12.045A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.822A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 261 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 212 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS B 232 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 214 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.947A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.947A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 123 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 43 through 53 removed outlier: 4.638A pdb=" N THR E 264 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS E 49 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 11.037A pdb=" N PHE E 262 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N SER E 51 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N LEU E 260 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N LYS E 53 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 14.515A pdb=" N ASP E 258 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA E 83 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL E 259 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG E 81 " --> pdb=" O VAL E 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 43 through 53 removed outlier: 4.638A pdb=" N THR E 264 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS E 49 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 11.037A pdb=" N PHE E 262 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N SER E 51 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N LEU E 260 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N LYS E 53 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 14.515A pdb=" N ASP E 258 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 261 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN E 103 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU E 212 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS E 232 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 214 " --> pdb=" O CYS E 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.912A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.912A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.542A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.640A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 12.045A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.823A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N HIS F 257 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.542A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.640A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 12.045A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.823A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER F 261 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU F 212 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS F 232 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL F 214 " --> pdb=" O CYS F 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.948A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.948A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU F 123 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1902 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: 2.11 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4618 1.35 - 1.46: 3071 1.46 - 1.58: 6027 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 13784 Sorted by residual: bond pdb=" N GLU A 283 " pdb=" CA GLU A 283 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.62e+00 bond pdb=" N GLU E 283 " pdb=" CA GLU E 283 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.56e+00 bond pdb=" N LEU H 56 " pdb=" CA LEU H 56 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.32e-02 5.74e+03 6.79e+00 bond pdb=" N LEU D 56 " pdb=" CA LEU D 56 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.32e-02 5.74e+03 6.36e+00 bond pdb=" N LEU H 74 " pdb=" CA LEU H 74 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.41e+00 ... (remaining 13779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18324 2.03 - 4.06: 255 4.06 - 6.09: 33 6.09 - 8.12: 4 8.12 - 10.15: 2 Bond angle restraints: 18618 Sorted by residual: angle pdb=" C ALA F 120 " pdb=" N ASP F 121 " pdb=" CA ASP F 121 " ideal model delta sigma weight residual 121.70 128.20 -6.50 1.80e+00 3.09e-01 1.30e+01 angle pdb=" C ALA B 120 " pdb=" N ASP B 121 " pdb=" CA ASP B 121 " ideal model delta sigma weight residual 121.70 128.11 -6.41 1.80e+00 3.09e-01 1.27e+01 angle pdb=" C ALA A 120 " pdb=" N ASP A 121 " pdb=" CA ASP A 121 " ideal model delta sigma weight residual 121.70 127.21 -5.51 1.80e+00 3.09e-01 9.36e+00 angle pdb=" C ALA E 120 " pdb=" N ASP E 121 " pdb=" CA ASP E 121 " ideal model delta sigma weight residual 121.70 127.13 -5.43 1.80e+00 3.09e-01 9.11e+00 angle pdb=" CA VAL D 100 " pdb=" CB VAL D 100 " pdb=" CG1 VAL D 100 " ideal model delta sigma weight residual 110.40 115.45 -5.05 1.70e+00 3.46e-01 8.84e+00 ... (remaining 18613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 6918 16.46 - 32.91: 935 32.91 - 49.37: 286 49.37 - 65.82: 83 65.82 - 82.28: 22 Dihedral angle restraints: 8244 sinusoidal: 3430 harmonic: 4814 Sorted by residual: dihedral pdb=" CA LEU E 356 " pdb=" C LEU E 356 " pdb=" N ASP E 357 " pdb=" CA ASP E 357 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LEU A 356 " pdb=" C LEU A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ILE A 355 " pdb=" C ILE A 355 " pdb=" N LEU A 356 " pdb=" CA LEU A 356 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 8241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1408 0.045 - 0.089: 364 0.089 - 0.134: 128 0.134 - 0.179: 12 0.179 - 0.223: 4 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CG LEU F 356 " pdb=" CB LEU F 356 " pdb=" CD1 LEU F 356 " pdb=" CD2 LEU F 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 356 " pdb=" CB LEU B 356 " pdb=" CD1 LEU B 356 " pdb=" CD2 LEU B 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LEU D 111 " pdb=" N LEU D 111 " pdb=" C LEU D 111 " pdb=" CB LEU D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 1913 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 356 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LEU A 356 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 356 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 357 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 356 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C LEU E 356 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU E 356 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP E 357 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 352 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C LEU E 352 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU E 352 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP E 353 " 0.012 2.00e-02 2.50e+03 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 30 2.20 - 2.87: 5059 2.87 - 3.55: 18487 3.55 - 4.22: 32111 4.22 - 4.90: 55388 Nonbonded interactions: 111075 Sorted by model distance: nonbonded pdb=" CE1 HIS D 51 " pdb="ZN ZN D 703 " model vdw 1.524 2.450 nonbonded pdb=" CE1 HIS H 51 " pdb="ZN ZN H 703 " model vdw 1.525 2.450 nonbonded pdb=" OD1 ASP G 129 " pdb=" OD1 ASP G 133 " model vdw 1.788 3.040 nonbonded pdb=" OD1 ASP C 129 " pdb=" OD1 ASP C 133 " model vdw 1.789 3.040 nonbonded pdb=" OD1 ASP E 157 " pdb=" OD2 ASP E 181 " model vdw 1.920 3.040 ... (remaining 111070 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 0.041 13788 Z= 0.136 Angle : 0.580 10.146 18626 Z= 0.323 Chirality : 0.046 0.223 1916 Planarity : 0.004 0.039 2508 Dihedral : 17.357 82.276 5136 Min Nonbonded Distance : 1.524 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.35 % Allowed : 21.85 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.21), residues: 1648 helix: 0.35 (0.23), residues: 478 sheet: 1.50 (0.29), residues: 328 loop : -1.11 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 360 TYR 0.010 0.001 TYR G 76 PHE 0.015 0.001 PHE B 296 TRP 0.009 0.001 TRP E 126 HIS 0.005 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00250 (13784) covalent geometry : angle 0.57979 (18618) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.96226 ( 8) hydrogen bonds : bond 0.15735 ( 624) hydrogen bonds : angle 7.13383 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7223 (mt0) REVERT: A 218 ASN cc_start: 0.7408 (m-40) cc_final: 0.6597 (OUTLIER) REVERT: A 329 ARG cc_start: 0.7059 (ttm110) cc_final: 0.6596 (ttp80) REVERT: B 78 ASP cc_start: 0.7563 (t0) cc_final: 0.7357 (t0) REVERT: B 177 ASP cc_start: 0.7804 (t0) cc_final: 0.7510 (t0) REVERT: B 330 GLU cc_start: 0.6678 (tp30) cc_final: 0.6099 (tp30) REVERT: B 336 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7433 (mt-10) REVERT: B 352 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7485 (tt) REVERT: B 354 MET cc_start: 0.6679 (ttm) cc_final: 0.6471 (ptm) REVERT: C 43 LYS cc_start: 0.7353 (tptt) cc_final: 0.6813 (mmtm) REVERT: C 49 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7947 (tp-100) REVERT: C 122 ASP cc_start: 0.6903 (m-30) cc_final: 0.6570 (m-30) REVERT: E 191 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7196 (mt0) REVERT: E 218 ASN cc_start: 0.7403 (m-40) cc_final: 0.6598 (OUTLIER) REVERT: E 329 ARG cc_start: 0.7197 (ttm110) cc_final: 0.6702 (ttp80) REVERT: F 78 ASP cc_start: 0.7549 (t0) cc_final: 0.7338 (t0) REVERT: F 177 ASP cc_start: 0.7749 (t0) cc_final: 0.7524 (t0) REVERT: F 330 GLU cc_start: 0.6665 (tp30) cc_final: 0.6081 (tp30) REVERT: F 336 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7413 (mt-10) REVERT: G 49 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8030 (tp-100) REVERT: G 122 ASP cc_start: 0.6892 (m-30) cc_final: 0.6597 (m-30) outliers start: 34 outliers final: 27 residues processed: 297 average time/residue: 0.5333 time to fit residues: 175.0433 Evaluate side-chains 237 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 131 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 175 HIS B 179 GLN B 210 ASN B 217 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 80 HIS C 119 ASN D 51 HIS E 178 HIS E 235 ASN ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN F 175 HIS F 210 ASN F 217 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 80 HIS G 119 ASN H 51 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.192314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131745 restraints weight = 16900.386| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.41 r_work: 0.3567 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13788 Z= 0.113 Angle : 0.549 9.416 18626 Z= 0.286 Chirality : 0.045 0.155 1916 Planarity : 0.003 0.040 2508 Dihedral : 6.117 54.307 1828 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.12 % Allowed : 23.24 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.21), residues: 1648 helix: 1.17 (0.24), residues: 486 sheet: 1.45 (0.28), residues: 336 loop : -1.03 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 350 TYR 0.022 0.001 TYR D 76 PHE 0.013 0.001 PHE E 296 TRP 0.011 0.001 TRP F 94 HIS 0.004 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00241 (13784) covalent geometry : angle 0.54856 (18618) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.96520 ( 8) hydrogen bonds : bond 0.04120 ( 624) hydrogen bonds : angle 4.68085 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: A 294 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8407 (mp0) REVERT: A 329 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7051 (ttp80) REVERT: A 344 GLU cc_start: 0.8113 (tp30) cc_final: 0.7733 (tp30) REVERT: B 78 ASP cc_start: 0.7937 (t0) cc_final: 0.7660 (t0) REVERT: B 105 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: B 177 ASP cc_start: 0.8002 (t0) cc_final: 0.7608 (t0) REVERT: B 226 ASP cc_start: 0.7602 (t70) cc_final: 0.6985 (t0) REVERT: B 264 THR cc_start: 0.8092 (m) cc_final: 0.7822 (m) REVERT: B 330 GLU cc_start: 0.6622 (tp30) cc_final: 0.6087 (tp30) REVERT: B 336 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7419 (mm-30) REVERT: B 354 MET cc_start: 0.6800 (ttm) cc_final: 0.6557 (ptm) REVERT: C 122 ASP cc_start: 0.6784 (m-30) cc_final: 0.6334 (m-30) REVERT: D 99 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6587 (m-70) REVERT: D 114 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6909 (tp30) REVERT: D 127 ASP cc_start: 0.7204 (p0) cc_final: 0.6992 (p0) REVERT: E 191 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: E 255 ASP cc_start: 0.8268 (m-30) cc_final: 0.8042 (m-30) REVERT: E 329 ARG cc_start: 0.7539 (ttm110) cc_final: 0.7066 (ttp80) REVERT: E 344 GLU cc_start: 0.8186 (tp30) cc_final: 0.7811 (tp30) REVERT: F 78 ASP cc_start: 0.7937 (t0) cc_final: 0.7646 (t0) REVERT: F 105 GLU cc_start: 0.8487 (tt0) cc_final: 0.8248 (pt0) REVERT: F 177 ASP cc_start: 0.8031 (t0) cc_final: 0.7675 (t0) REVERT: F 226 ASP cc_start: 0.7476 (t70) cc_final: 0.6897 (t0) REVERT: F 264 THR cc_start: 0.8118 (m) cc_final: 0.7864 (m) REVERT: F 330 GLU cc_start: 0.6583 (tp30) cc_final: 0.6041 (tp30) REVERT: F 336 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7419 (mm-30) REVERT: F 352 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7222 (tt) REVERT: G 113 SER cc_start: 0.8516 (m) cc_final: 0.8112 (t) REVERT: G 122 ASP cc_start: 0.6775 (m-30) cc_final: 0.6348 (m-30) REVERT: H 99 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6517 (m-70) outliers start: 74 outliers final: 25 residues processed: 275 average time/residue: 0.5101 time to fit residues: 155.7737 Evaluate side-chains 246 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 3 optimal weight: 0.3980 chunk 32 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 55 optimal weight: 0.0870 chunk 146 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 119 ASN D 70 GLN E 178 HIS E 235 ASN E 338 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS G 119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.192149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131241 restraints weight = 16945.412| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.41 r_work: 0.3557 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13788 Z= 0.110 Angle : 0.539 8.732 18626 Z= 0.278 Chirality : 0.045 0.167 1916 Planarity : 0.003 0.045 2508 Dihedral : 5.575 55.880 1806 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.77 % Allowed : 23.93 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1648 helix: 1.34 (0.24), residues: 486 sheet: 1.53 (0.29), residues: 324 loop : -0.97 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 350 TYR 0.022 0.002 TYR H 76 PHE 0.014 0.001 PHE A 262 TRP 0.009 0.001 TRP F 126 HIS 0.005 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00243 (13784) covalent geometry : angle 0.53839 (18618) SS BOND : bond 0.00098 ( 4) SS BOND : angle 1.05654 ( 8) hydrogen bonds : bond 0.03702 ( 624) hydrogen bonds : angle 4.34306 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: A 294 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8459 (mp0) REVERT: A 329 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7048 (ttp80) REVERT: A 344 GLU cc_start: 0.8148 (tp30) cc_final: 0.7869 (tp30) REVERT: B 78 ASP cc_start: 0.7933 (t0) cc_final: 0.7665 (t0) REVERT: B 105 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: B 177 ASP cc_start: 0.8013 (t0) cc_final: 0.7665 (t0) REVERT: B 202 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7421 (mtt-85) REVERT: B 264 THR cc_start: 0.8157 (m) cc_final: 0.7899 (m) REVERT: B 330 GLU cc_start: 0.6654 (tp30) cc_final: 0.6087 (tp30) REVERT: B 336 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7422 (mm-30) REVERT: B 352 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7225 (tt) REVERT: B 354 MET cc_start: 0.6774 (ttm) cc_final: 0.6541 (ptm) REVERT: C 47 HIS cc_start: 0.7750 (m-70) cc_final: 0.6909 (m-70) REVERT: C 62 LYS cc_start: 0.9167 (ttpp) cc_final: 0.7983 (mmtm) REVERT: C 120 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7361 (mp) REVERT: C 122 ASP cc_start: 0.6881 (m-30) cc_final: 0.6394 (m-30) REVERT: D 70 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: D 71 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7511 (mp0) REVERT: D 99 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6483 (m-70) REVERT: D 114 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6988 (tp30) REVERT: E 191 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: E 294 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8459 (mp0) REVERT: E 297 GLN cc_start: 0.7394 (mp10) cc_final: 0.7026 (mp10) REVERT: E 329 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7072 (ttp80) REVERT: E 344 GLU cc_start: 0.8161 (tp30) cc_final: 0.7858 (tp30) REVERT: F 78 ASP cc_start: 0.7969 (t0) cc_final: 0.7672 (t0) REVERT: F 105 GLU cc_start: 0.8439 (tt0) cc_final: 0.8199 (pt0) REVERT: F 173 GLN cc_start: 0.7772 (mm110) cc_final: 0.7464 (mm-40) REVERT: F 177 ASP cc_start: 0.8054 (t0) cc_final: 0.7701 (t0) REVERT: F 202 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7435 (mtt-85) REVERT: F 264 THR cc_start: 0.8138 (m) cc_final: 0.7879 (m) REVERT: F 330 GLU cc_start: 0.6630 (tp30) cc_final: 0.6078 (tp30) REVERT: F 336 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7452 (mm-30) REVERT: F 352 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7193 (tt) REVERT: G 47 HIS cc_start: 0.7779 (m-70) cc_final: 0.6851 (m-70) REVERT: G 49 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8172 (tp-100) REVERT: G 62 LYS cc_start: 0.9148 (ttpp) cc_final: 0.7944 (mmtm) REVERT: G 113 SER cc_start: 0.8509 (m) cc_final: 0.8156 (t) REVERT: G 120 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7245 (mp) REVERT: H 67 MET cc_start: 0.6969 (mmt) cc_final: 0.6185 (tpt) REVERT: H 99 HIS cc_start: 0.6765 (OUTLIER) cc_final: 0.6439 (m-70) outliers start: 69 outliers final: 22 residues processed: 264 average time/residue: 0.5375 time to fit residues: 156.7281 Evaluate side-chains 238 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 99 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 113 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 157 optimal weight: 0.1980 chunk 127 optimal weight: 9.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 338 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 119 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN E 338 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 ASN F 338 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 HIS G 80 HIS G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.188899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126004 restraints weight = 16982.080| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.42 r_work: 0.3490 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13788 Z= 0.182 Angle : 0.594 8.017 18626 Z= 0.310 Chirality : 0.047 0.167 1916 Planarity : 0.004 0.044 2508 Dihedral : 5.359 58.908 1796 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 6.09 % Allowed : 24.27 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.21), residues: 1648 helix: 1.42 (0.24), residues: 482 sheet: 0.94 (0.29), residues: 354 loop : -0.89 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 350 TYR 0.023 0.002 TYR H 76 PHE 0.025 0.002 PHE E 262 TRP 0.012 0.002 TRP F 126 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00423 (13784) covalent geometry : angle 0.59331 (18618) SS BOND : bond 0.00203 ( 4) SS BOND : angle 1.24540 ( 8) hydrogen bonds : bond 0.04004 ( 624) hydrogen bonds : angle 4.43423 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 207 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: A 191 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7664 (mt0) REVERT: A 294 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8440 (mp0) REVERT: A 329 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7175 (ttp80) REVERT: A 344 GLU cc_start: 0.8200 (tp30) cc_final: 0.7886 (tp30) REVERT: B 78 ASP cc_start: 0.7933 (t0) cc_final: 0.7679 (t0) REVERT: B 105 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: B 177 ASP cc_start: 0.8092 (t0) cc_final: 0.7734 (t0) REVERT: B 179 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7828 (tp-100) REVERT: B 224 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7716 (mptp) REVERT: B 330 GLU cc_start: 0.6737 (tp30) cc_final: 0.6212 (tp30) REVERT: B 336 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7496 (mm-30) REVERT: B 352 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7369 (tt) REVERT: B 354 MET cc_start: 0.6806 (ttm) cc_final: 0.6569 (ptm) REVERT: C 49 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8191 (tp-100) REVERT: C 120 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7339 (mp) REVERT: C 122 ASP cc_start: 0.6951 (m-30) cc_final: 0.6452 (m-30) REVERT: D 70 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: D 71 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7770 (mt-10) REVERT: D 99 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6465 (m-70) REVERT: E 79 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: E 191 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7646 (mt0) REVERT: E 294 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8442 (mp0) REVERT: E 297 GLN cc_start: 0.7470 (mt0) cc_final: 0.7267 (mp10) REVERT: E 329 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7172 (ttp80) REVERT: E 344 GLU cc_start: 0.8209 (tp30) cc_final: 0.7921 (tp30) REVERT: F 78 ASP cc_start: 0.7950 (t0) cc_final: 0.7668 (t0) REVERT: F 105 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8257 (pt0) REVERT: F 177 ASP cc_start: 0.8108 (t0) cc_final: 0.7759 (t0) REVERT: F 179 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7881 (tp-100) REVERT: F 224 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7644 (mptp) REVERT: F 330 GLU cc_start: 0.6762 (tp30) cc_final: 0.6208 (tp30) REVERT: F 336 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7492 (mm-30) REVERT: F 352 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7421 (tt) REVERT: G 47 HIS cc_start: 0.7800 (m-70) cc_final: 0.6849 (m-70) REVERT: G 49 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8236 (tp-100) REVERT: G 113 SER cc_start: 0.8529 (m) cc_final: 0.8153 (t) REVERT: G 120 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7353 (mp) REVERT: G 122 ASP cc_start: 0.6927 (m-30) cc_final: 0.6451 (m-30) REVERT: H 67 MET cc_start: 0.6899 (mmt) cc_final: 0.6355 (tpt) REVERT: H 99 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6478 (m-70) outliers start: 88 outliers final: 30 residues processed: 268 average time/residue: 0.5566 time to fit residues: 164.4559 Evaluate side-chains 246 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 99 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 153 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 109 optimal weight: 0.0050 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 0.0870 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.7976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN D 70 GLN D 75 HIS E 178 HIS E 235 ASN E 338 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS G 99 HIS H 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.190721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129036 restraints weight = 16889.799| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.40 r_work: 0.3528 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13788 Z= 0.114 Angle : 0.564 10.425 18626 Z= 0.283 Chirality : 0.045 0.153 1916 Planarity : 0.003 0.048 2508 Dihedral : 5.085 59.224 1796 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.05 % Allowed : 26.07 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.21), residues: 1648 helix: 1.54 (0.24), residues: 484 sheet: 1.33 (0.29), residues: 336 loop : -0.91 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 350 TYR 0.024 0.002 TYR F 208 PHE 0.015 0.001 PHE A 296 TRP 0.013 0.001 TRP F 126 HIS 0.005 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00254 (13784) covalent geometry : angle 0.56386 (18618) SS BOND : bond 0.00112 ( 4) SS BOND : angle 1.01734 ( 8) hydrogen bonds : bond 0.03460 ( 624) hydrogen bonds : angle 4.19108 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 197 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: A 191 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: A 294 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8428 (mp0) REVERT: A 329 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7136 (ttp80) REVERT: A 350 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6595 (ptp90) REVERT: B 78 ASP cc_start: 0.7911 (t0) cc_final: 0.7660 (t0) REVERT: B 105 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: B 177 ASP cc_start: 0.8100 (t0) cc_final: 0.7727 (t0) REVERT: B 179 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7673 (tp-100) REVERT: B 202 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7431 (mtt-85) REVERT: B 224 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7595 (mptp) REVERT: B 330 GLU cc_start: 0.6733 (tp30) cc_final: 0.6132 (tp30) REVERT: B 336 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 352 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7355 (tt) REVERT: C 47 HIS cc_start: 0.7752 (m-70) cc_final: 0.6830 (m-70) REVERT: C 116 GLU cc_start: 0.8071 (tp30) cc_final: 0.7855 (tp30) REVERT: C 120 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7344 (mp) REVERT: C 122 ASP cc_start: 0.6900 (m-30) cc_final: 0.6413 (m-30) REVERT: D 67 MET cc_start: 0.6842 (mmt) cc_final: 0.6250 (tpt) REVERT: D 70 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: D 71 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7831 (mt-10) REVERT: D 99 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.6608 (m-70) REVERT: E 191 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7635 (mt0) REVERT: E 294 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8422 (mp0) REVERT: E 329 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7144 (ttp80) REVERT: E 344 GLU cc_start: 0.8130 (tp30) cc_final: 0.7879 (tp30) REVERT: E 350 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6718 (ptp90) REVERT: F 78 ASP cc_start: 0.7922 (t0) cc_final: 0.7654 (t0) REVERT: F 105 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: F 177 ASP cc_start: 0.8108 (t0) cc_final: 0.7731 (t0) REVERT: F 179 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7714 (tp-100) REVERT: F 202 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7443 (mtt-85) REVERT: F 224 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7593 (mptp) REVERT: F 330 GLU cc_start: 0.6733 (tp30) cc_final: 0.6128 (tp30) REVERT: F 336 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7600 (mt-10) REVERT: F 352 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7359 (tt) REVERT: G 47 HIS cc_start: 0.7740 (m-70) cc_final: 0.6822 (m-70) REVERT: G 113 SER cc_start: 0.8545 (m) cc_final: 0.8228 (t) REVERT: G 120 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7341 (mp) REVERT: G 122 ASP cc_start: 0.6882 (m-30) cc_final: 0.6386 (m-30) REVERT: H 67 MET cc_start: 0.7018 (mmt) cc_final: 0.6194 (tpt) REVERT: H 70 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: H 71 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7647 (mt-10) REVERT: H 79 MET cc_start: 0.7886 (ppp) cc_final: 0.7683 (ppp) outliers start: 73 outliers final: 32 residues processed: 250 average time/residue: 0.5676 time to fit residues: 156.3644 Evaluate side-chains 246 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 139 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN E 338 GLN E 347 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.186190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.123353 restraints weight = 17166.090| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.42 r_work: 0.3457 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13788 Z= 0.270 Angle : 0.685 8.980 18626 Z= 0.355 Chirality : 0.050 0.185 1916 Planarity : 0.004 0.048 2508 Dihedral : 5.487 57.846 1794 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.71 % Allowed : 24.83 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.21), residues: 1648 helix: 1.40 (0.24), residues: 482 sheet: 1.14 (0.29), residues: 328 loop : -1.07 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 350 TYR 0.028 0.003 TYR F 208 PHE 0.031 0.003 PHE E 262 TRP 0.011 0.002 TRP F 126 HIS 0.010 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00638 (13784) covalent geometry : angle 0.68404 (18618) SS BOND : bond 0.00326 ( 4) SS BOND : angle 1.48491 ( 8) hydrogen bonds : bond 0.04379 ( 624) hydrogen bonds : angle 4.64401 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 198 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8390 (pt0) REVERT: A 191 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: A 216 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 294 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8496 (mp0) REVERT: A 297 GLN cc_start: 0.7513 (mt0) cc_final: 0.7264 (mp10) REVERT: A 344 GLU cc_start: 0.8188 (tp30) cc_final: 0.7661 (tp30) REVERT: A 350 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6652 (ptp90) REVERT: B 78 ASP cc_start: 0.8067 (t0) cc_final: 0.7835 (OUTLIER) REVERT: B 177 ASP cc_start: 0.8240 (t0) cc_final: 0.7891 (t0) REVERT: B 179 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7793 (tp-100) REVERT: B 224 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7607 (mptp) REVERT: B 330 GLU cc_start: 0.6777 (tp30) cc_final: 0.6126 (tp30) REVERT: B 352 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7506 (tt) REVERT: C 49 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8257 (tp-100) REVERT: C 120 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7411 (mp) REVERT: C 122 ASP cc_start: 0.7096 (m-30) cc_final: 0.6541 (m-30) REVERT: D 67 MET cc_start: 0.6981 (mmt) cc_final: 0.6359 (tpt) REVERT: D 70 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: E 79 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8403 (pt0) REVERT: E 191 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: E 216 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8434 (mm) REVERT: E 294 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8502 (mp0) REVERT: E 297 GLN cc_start: 0.7326 (mp10) cc_final: 0.6854 (mp10) REVERT: E 344 GLU cc_start: 0.8222 (tp30) cc_final: 0.7987 (tp30) REVERT: E 350 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6599 (ptp90) REVERT: F 78 ASP cc_start: 0.8088 (t0) cc_final: 0.7847 (OUTLIER) REVERT: F 177 ASP cc_start: 0.8221 (t0) cc_final: 0.7892 (t0) REVERT: F 179 GLN cc_start: 0.8322 (tp-100) cc_final: 0.7704 (tp-100) REVERT: F 224 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7598 (mptp) REVERT: F 330 GLU cc_start: 0.6765 (tp30) cc_final: 0.6125 (tp30) REVERT: F 352 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7503 (tt) REVERT: G 49 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8266 (tp-100) REVERT: G 113 SER cc_start: 0.8583 (m) cc_final: 0.8246 (t) REVERT: G 120 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7379 (mp) REVERT: G 122 ASP cc_start: 0.7098 (m-30) cc_final: 0.6577 (m-30) REVERT: H 67 MET cc_start: 0.6953 (mmt) cc_final: 0.6290 (tpt) REVERT: H 70 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: H 71 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7613 (pt0) outliers start: 97 outliers final: 42 residues processed: 264 average time/residue: 0.5168 time to fit residues: 150.3393 Evaluate side-chains 244 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN E 338 GLN E 359 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS H 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.189383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.128214 restraints weight = 17012.173| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.38 r_work: 0.3523 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13788 Z= 0.118 Angle : 0.582 9.685 18626 Z= 0.295 Chirality : 0.046 0.205 1916 Planarity : 0.004 0.049 2508 Dihedral : 4.889 57.941 1792 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.70 % Allowed : 26.90 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1648 helix: 1.47 (0.24), residues: 486 sheet: 1.12 (0.29), residues: 340 loop : -0.88 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 350 TYR 0.030 0.002 TYR B 208 PHE 0.018 0.001 PHE E 296 TRP 0.015 0.001 TRP B 126 HIS 0.010 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00265 (13784) covalent geometry : angle 0.58172 (18618) SS BOND : bond 0.00127 ( 4) SS BOND : angle 1.11363 ( 8) hydrogen bonds : bond 0.03464 ( 624) hydrogen bonds : angle 4.24445 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 195 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: A 294 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8415 (mp0) REVERT: A 329 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6904 (mtp-110) REVERT: A 344 GLU cc_start: 0.8116 (tp30) cc_final: 0.7577 (tp30) REVERT: A 350 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6788 (ptp90) REVERT: B 78 ASP cc_start: 0.7999 (t0) cc_final: 0.7757 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8404 (tt0) cc_final: 0.8107 (pt0) REVERT: B 177 ASP cc_start: 0.8164 (t0) cc_final: 0.7799 (t0) REVERT: B 179 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7834 (tp-100) REVERT: B 224 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7570 (mptp) REVERT: B 330 GLU cc_start: 0.6738 (tp30) cc_final: 0.6174 (tp30) REVERT: B 352 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7466 (tt) REVERT: C 47 HIS cc_start: 0.7797 (m-70) cc_final: 0.6888 (m-70) REVERT: C 116 GLU cc_start: 0.8125 (tp30) cc_final: 0.7882 (tp30) REVERT: C 120 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7407 (mp) REVERT: C 122 ASP cc_start: 0.6966 (m-30) cc_final: 0.6426 (m-30) REVERT: D 67 MET cc_start: 0.6728 (mmt) cc_final: 0.6244 (tpt) REVERT: D 79 MET cc_start: 0.7887 (ppp) cc_final: 0.7661 (ppp) REVERT: E 79 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: E 191 GLN cc_start: 0.8493 (tm-30) cc_final: 0.7732 (mt0) REVERT: E 294 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8433 (mp0) REVERT: E 329 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6901 (mtp-110) REVERT: E 350 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6831 (ptp90) REVERT: F 78 ASP cc_start: 0.8005 (t0) cc_final: 0.7750 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8416 (tt0) cc_final: 0.8101 (pt0) REVERT: F 177 ASP cc_start: 0.8164 (t0) cc_final: 0.7801 (t0) REVERT: F 179 GLN cc_start: 0.8322 (tp-100) cc_final: 0.7945 (tp-100) REVERT: F 224 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7641 (mptp) REVERT: F 330 GLU cc_start: 0.6722 (tp30) cc_final: 0.6168 (tp30) REVERT: F 352 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7452 (tt) REVERT: G 113 SER cc_start: 0.8575 (m) cc_final: 0.8236 (t) REVERT: G 120 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7357 (mp) REVERT: G 122 ASP cc_start: 0.6974 (m-30) cc_final: 0.6503 (m-30) REVERT: H 67 MET cc_start: 0.6933 (mmt) cc_final: 0.6322 (tpt) REVERT: H 70 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: H 79 MET cc_start: 0.7828 (ppp) cc_final: 0.7607 (ppp) outliers start: 68 outliers final: 39 residues processed: 245 average time/residue: 0.4667 time to fit residues: 127.0396 Evaluate side-chains 237 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 43 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS H 70 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.188628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127613 restraints weight = 16968.243| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.36 r_work: 0.3512 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13788 Z= 0.137 Angle : 0.591 9.165 18626 Z= 0.301 Chirality : 0.046 0.245 1916 Planarity : 0.004 0.050 2508 Dihedral : 4.864 57.042 1792 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.36 % Allowed : 27.46 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.21), residues: 1648 helix: 1.55 (0.24), residues: 484 sheet: 1.09 (0.29), residues: 340 loop : -0.90 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 350 TYR 0.030 0.002 TYR B 208 PHE 0.017 0.002 PHE A 262 TRP 0.012 0.001 TRP F 126 HIS 0.008 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00319 (13784) covalent geometry : angle 0.59024 (18618) SS BOND : bond 0.00192 ( 4) SS BOND : angle 1.16694 ( 8) hydrogen bonds : bond 0.03520 ( 624) hydrogen bonds : angle 4.26246 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 193 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 79 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: A 294 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8484 (mp0) REVERT: A 329 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6847 (mtp-110) REVERT: A 344 GLU cc_start: 0.8108 (tp30) cc_final: 0.7578 (tp30) REVERT: A 350 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6784 (ptp90) REVERT: A 354 MET cc_start: 0.6987 (ppp) cc_final: 0.6764 (pp-130) REVERT: B 78 ASP cc_start: 0.7974 (t0) cc_final: 0.7725 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8374 (tt0) cc_final: 0.8094 (pt0) REVERT: B 177 ASP cc_start: 0.8172 (t0) cc_final: 0.7820 (t0) REVERT: B 179 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7882 (tp-100) REVERT: B 224 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7684 (mptp) REVERT: B 330 GLU cc_start: 0.6766 (tp30) cc_final: 0.6202 (tp30) REVERT: B 352 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7473 (tt) REVERT: C 120 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7408 (mp) REVERT: C 122 ASP cc_start: 0.7060 (m-30) cc_final: 0.6542 (m-30) REVERT: D 67 MET cc_start: 0.6941 (mmt) cc_final: 0.6297 (tpt) REVERT: D 70 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: D 71 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7530 (pt0) REVERT: E 57 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8695 (tt) REVERT: E 79 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: E 191 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7750 (mt0) REVERT: E 294 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8431 (mp0) REVERT: E 329 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.6906 (mtp-110) REVERT: E 344 GLU cc_start: 0.8156 (tp30) cc_final: 0.7652 (tp30) REVERT: E 350 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6811 (ptp90) REVERT: F 78 ASP cc_start: 0.8008 (t0) cc_final: 0.7749 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8376 (tt0) cc_final: 0.8082 (pt0) REVERT: F 177 ASP cc_start: 0.8174 (t0) cc_final: 0.7836 (t0) REVERT: F 179 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7948 (tp-100) REVERT: F 224 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7705 (mptp) REVERT: F 330 GLU cc_start: 0.6769 (tp30) cc_final: 0.6209 (tp30) REVERT: G 113 SER cc_start: 0.8621 (m) cc_final: 0.8295 (t) REVERT: G 120 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7361 (mp) REVERT: G 122 ASP cc_start: 0.7031 (m-30) cc_final: 0.6518 (m-30) REVERT: H 67 MET cc_start: 0.6852 (mmt) cc_final: 0.6166 (tpt) REVERT: H 70 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: H 127 ASP cc_start: 0.7673 (p0) cc_final: 0.7215 (t70) outliers start: 63 outliers final: 37 residues processed: 238 average time/residue: 0.4636 time to fit residues: 122.4875 Evaluate side-chains 238 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 151 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 127 optimal weight: 0.0040 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN E 235 ASN E 338 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.187419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124984 restraints weight = 17318.547| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.42 r_work: 0.3479 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13788 Z= 0.204 Angle : 0.640 9.467 18626 Z= 0.329 Chirality : 0.048 0.261 1916 Planarity : 0.004 0.048 2508 Dihedral : 5.116 57.848 1792 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.29 % Allowed : 27.66 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.21), residues: 1648 helix: 1.49 (0.24), residues: 480 sheet: 0.97 (0.29), residues: 340 loop : -0.90 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 350 TYR 0.031 0.002 TYR F 208 PHE 0.025 0.002 PHE E 262 TRP 0.012 0.002 TRP F 126 HIS 0.008 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00482 (13784) covalent geometry : angle 0.63966 (18618) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.25493 ( 8) hydrogen bonds : bond 0.03903 ( 624) hydrogen bonds : angle 4.49382 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: A 294 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8445 (mp0) REVERT: A 329 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6946 (mtp-110) REVERT: A 344 GLU cc_start: 0.8001 (tp30) cc_final: 0.7741 (tp30) REVERT: A 350 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6767 (ptp90) REVERT: B 78 ASP cc_start: 0.7994 (t0) cc_final: 0.7750 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8361 (tt0) cc_final: 0.8132 (pt0) REVERT: B 177 ASP cc_start: 0.8212 (t0) cc_final: 0.7847 (t0) REVERT: B 179 GLN cc_start: 0.8345 (tp-100) cc_final: 0.7982 (tp-100) REVERT: B 224 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7621 (mptp) REVERT: B 330 GLU cc_start: 0.6837 (tp30) cc_final: 0.6132 (tp30) REVERT: C 120 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7438 (mp) REVERT: C 122 ASP cc_start: 0.7083 (m-30) cc_final: 0.6501 (m-30) REVERT: D 67 MET cc_start: 0.6799 (mmt) cc_final: 0.6136 (tpt) REVERT: E 79 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: E 191 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: E 294 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8432 (mp0) REVERT: E 329 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6952 (mtp-110) REVERT: E 350 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6703 (ptp90) REVERT: F 78 ASP cc_start: 0.8010 (t0) cc_final: 0.7759 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8393 (tt0) cc_final: 0.8077 (pt0) REVERT: F 177 ASP cc_start: 0.8205 (t0) cc_final: 0.7876 (t0) REVERT: F 179 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8052 (tp-100) REVERT: F 224 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7619 (mptp) REVERT: F 330 GLU cc_start: 0.6839 (tp30) cc_final: 0.6134 (tp30) REVERT: G 113 SER cc_start: 0.8623 (m) cc_final: 0.8283 (t) REVERT: G 120 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7397 (mp) REVERT: G 122 ASP cc_start: 0.7045 (m-30) cc_final: 0.6479 (m-30) REVERT: H 67 MET cc_start: 0.6747 (mmt) cc_final: 0.6068 (tpt) REVERT: H 70 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: H 127 ASP cc_start: 0.7686 (p0) cc_final: 0.7215 (t70) outliers start: 62 outliers final: 34 residues processed: 237 average time/residue: 0.5115 time to fit residues: 133.4034 Evaluate side-chains 233 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 145 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN E 338 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.189235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127506 restraints weight = 17066.359| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.40 r_work: 0.3513 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13788 Z= 0.133 Angle : 0.606 9.895 18626 Z= 0.308 Chirality : 0.047 0.250 1916 Planarity : 0.004 0.049 2508 Dihedral : 4.891 55.685 1792 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.53 % Allowed : 28.84 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1648 helix: 1.51 (0.24), residues: 478 sheet: 1.01 (0.28), residues: 340 loop : -0.84 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 350 TYR 0.031 0.002 TYR B 208 PHE 0.021 0.001 PHE A 296 TRP 0.014 0.001 TRP F 126 HIS 0.008 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00307 (13784) covalent geometry : angle 0.60543 (18618) SS BOND : bond 0.00206 ( 4) SS BOND : angle 1.09553 ( 8) hydrogen bonds : bond 0.03514 ( 624) hydrogen bonds : angle 4.33933 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8425 (pt0) REVERT: A 294 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8451 (mp0) REVERT: A 344 GLU cc_start: 0.7925 (tp30) cc_final: 0.7534 (tp30) REVERT: A 350 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6802 (ptp90) REVERT: B 78 ASP cc_start: 0.7977 (t0) cc_final: 0.7730 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8373 (tt0) cc_final: 0.8078 (pt0) REVERT: B 177 ASP cc_start: 0.8188 (t0) cc_final: 0.7833 (t0) REVERT: B 179 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7966 (tp-100) REVERT: B 202 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7502 (mtt-85) REVERT: B 224 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7605 (mptp) REVERT: B 330 GLU cc_start: 0.6777 (tp30) cc_final: 0.6188 (tp30) REVERT: B 350 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7494 (mtm180) REVERT: C 47 HIS cc_start: 0.7522 (m-70) cc_final: 0.6533 (m-70) REVERT: C 49 GLN cc_start: 0.8674 (tp40) cc_final: 0.8291 (tp-100) REVERT: C 120 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7383 (mp) REVERT: C 122 ASP cc_start: 0.7009 (m-30) cc_final: 0.6455 (m-30) REVERT: D 67 MET cc_start: 0.6853 (mmt) cc_final: 0.6545 (tpt) REVERT: E 79 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: E 294 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8420 (mp0) REVERT: F 78 ASP cc_start: 0.7996 (t0) cc_final: 0.7744 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8385 (tt0) cc_final: 0.8093 (pt0) REVERT: F 177 ASP cc_start: 0.8191 (t0) cc_final: 0.7835 (t0) REVERT: F 179 GLN cc_start: 0.8323 (tp-100) cc_final: 0.8017 (tp-100) REVERT: F 224 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7695 (mptp) REVERT: F 330 GLU cc_start: 0.6768 (tp30) cc_final: 0.6196 (tp30) REVERT: G 47 HIS cc_start: 0.7786 (m-70) cc_final: 0.6889 (m-70) REVERT: G 49 GLN cc_start: 0.8692 (tp40) cc_final: 0.8304 (tp-100) REVERT: G 113 SER cc_start: 0.8618 (m) cc_final: 0.8341 (t) REVERT: G 120 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7377 (mp) REVERT: G 122 ASP cc_start: 0.6984 (m-30) cc_final: 0.6437 (m-30) REVERT: H 67 MET cc_start: 0.6790 (mmt) cc_final: 0.6114 (tpt) REVERT: H 127 ASP cc_start: 0.7622 (p0) cc_final: 0.7154 (t70) outliers start: 51 outliers final: 36 residues processed: 232 average time/residue: 0.4883 time to fit residues: 125.1191 Evaluate side-chains 237 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 75 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.189427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127672 restraints weight = 17237.523| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.41 r_work: 0.3515 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13788 Z= 0.135 Angle : 0.601 9.433 18626 Z= 0.308 Chirality : 0.046 0.248 1916 Planarity : 0.004 0.048 2508 Dihedral : 4.828 54.618 1792 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.25 % Allowed : 29.32 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1648 helix: 1.52 (0.24), residues: 476 sheet: 0.98 (0.28), residues: 340 loop : -0.82 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 350 TYR 0.030 0.002 TYR B 208 PHE 0.022 0.002 PHE A 296 TRP 0.013 0.001 TRP F 126 HIS 0.007 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00312 (13784) covalent geometry : angle 0.60021 (18618) SS BOND : bond 0.00183 ( 4) SS BOND : angle 1.12758 ( 8) hydrogen bonds : bond 0.03459 ( 624) hydrogen bonds : angle 4.32514 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6726.07 seconds wall clock time: 114 minutes 45.33 seconds (6885.33 seconds total)