Starting phenix.real_space_refine on Fri Jul 3 09:00:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp5_36468/07_2026/8jp5_36468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp5_36468/07_2026/8jp5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jp5_36468/07_2026/8jp5_36468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp5_36468/07_2026/8jp5_36468.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp5_36468/07_2026/8jp5_36468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp5_36468/07_2026/8jp5_36468.cif" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Restraints were copied for chains: E, F, G, H Time building chain proxies: 3.78, per 1000 atoms: 0.28 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: 0.99 Conformation dependent library (CDL) restraints added in 457.5 milliseconds 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: 0.27 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: 2.15 Time building geometry restraints manager: 1.31 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: 0.03 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.210 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 are 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/Z covalent geometry : bond 0.00250 / 0.14 (13784) covalent geometry : angle 0.57979 / 0.32 (18618) SS BOND : bond 0.00130 / 0.07 ( 4) SS BOND : angle 0.96226 / 0.55 ( 8) hydrogen bonds : bond 0.15735 / 10.84 ( 624) hydrogen bonds : angle 7.13383 / 4.91 ( 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 : 0.522 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: 0.6678 (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: 0.4386 time to fit residues: 144.5591 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 : 0.491 ------------------------------------------------------------------------------- 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: 5.9990 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: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 235 ASN A 339 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN B 217 ASN B 338 GLN ** 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 339 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN F 175 HIS F 210 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.188802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126519 restraints weight = 16909.630| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.41 r_work: 0.3500 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13788 Z= 0.191 Angle : 0.614 9.149 18626 Z= 0.324 Chirality : 0.047 0.166 1916 Planarity : 0.004 0.039 2508 Dihedral : 6.680 54.961 1828 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 6.09 % Allowed : 22.27 % 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 are not related in a simple way. whole: 0.13 (0.21), residues: 1648 helix: 1.09 (0.24), residues: 482 sheet: 1.28 (0.28), residues: 336 loop : -1.07 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 350 TYR 0.023 0.002 TYR D 76 PHE 0.024 0.002 PHE A 262 TRP 0.013 0.002 TRP F 126 HIS 0.004 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (13784) covalent geometry : angle 0.61357 / 0.32 (18618) SS BOND : bond 0.00182 / 0.11 ( 4) SS BOND : angle 1.22523 / 0.70 ( 8) hydrogen bonds : bond 0.04519 / 3.08 ( 624) hydrogen bonds : angle 4.83945 / 3.35 ( 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 308 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 220 time to evaluate : 0.486 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 57 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 88 SER cc_start: 0.8138 (m) cc_final: 0.7937 (p) REVERT: A 191 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7678 (mt0) REVERT: A 294 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8415 (mp0) REVERT: A 344 GLU cc_start: 0.8132 (tp30) cc_final: 0.7740 (tp30) REVERT: B 78 ASP cc_start: 0.7984 (t0) cc_final: 0.7717 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: B 177 ASP cc_start: 0.8050 (t0) cc_final: 0.7656 (t0) REVERT: B 330 GLU cc_start: 0.6726 (tp30) cc_final: 0.6177 (tp30) REVERT: B 336 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 354 MET cc_start: 0.6781 (ttm) cc_final: 0.6564 (ptm) REVERT: C 122 ASP cc_start: 0.6875 (m-30) cc_final: 0.6410 (m-30) REVERT: D 99 HIS cc_start: 0.6714 (OUTLIER) cc_final: 0.6337 (m-70) REVERT: D 114 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7069 (tp30) REVERT: D 127 ASP cc_start: 0.7250 (p0) cc_final: 0.7047 (p0) REVERT: E 57 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8740 (tt) REVERT: E 88 SER cc_start: 0.8151 (m) cc_final: 0.7946 (p) REVERT: E 191 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7664 (mt0) REVERT: E 294 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8419 (mp0) REVERT: E 344 GLU cc_start: 0.8191 (tp30) cc_final: 0.7782 (tp30) REVERT: F 78 ASP cc_start: 0.7984 (t0) cc_final: 0.7711 (t0) REVERT: F 105 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: F 173 GLN cc_start: 0.7900 (mm110) cc_final: 0.7543 (mm110) REVERT: F 177 ASP cc_start: 0.8035 (t0) cc_final: 0.7685 (t0) REVERT: F 179 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7903 (tp-100) REVERT: F 330 GLU cc_start: 0.6720 (tp30) cc_final: 0.6162 (tp30) REVERT: F 336 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7609 (mt-10) REVERT: F 352 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7436 (tt) REVERT: G 49 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8284 (tp-100) REVERT: G 113 SER cc_start: 0.8510 (m) cc_final: 0.8099 (t) REVERT: G 122 ASP cc_start: 0.6827 (m-30) cc_final: 0.6355 (m-30) REVERT: H 99 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.6350 (m-70) REVERT: H 114 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7071 (tp30) outliers start: 88 outliers final: 37 residues processed: 282 average time/residue: 0.4589 time to fit residues: 143.7564 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 221 THR 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 147 VAL Chi-restraints excluded: chain B residue 189 SER 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 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 99 HIS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 221 THR 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 147 VAL Chi-restraints excluded: chain F residue 189 SER 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 49 GLN 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 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 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: 0.4980 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 359 GLN ** 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 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 49 GLN G 80 HIS G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.190085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127523 restraints weight = 17034.970| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.43 r_work: 0.3515 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2176 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= 0.143 Angle : 0.577 9.150 18626 Z= 0.300 Chirality : 0.046 0.166 1916 Planarity : 0.004 0.045 2508 Dihedral : 6.030 56.306 1810 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.05 % Allowed : 24.55 % Favored : 70.40 % 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 are not related in a simple way. whole: 0.25 (0.21), residues: 1648 helix: 1.26 (0.24), residues: 482 sheet: 1.17 (0.29), residues: 338 loop : -0.96 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.023 0.002 TYR H 76 PHE 0.018 0.002 PHE A 262 TRP 0.013 0.001 TRP F 126 HIS 0.006 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13784) covalent geometry : angle 0.57665 / 0.30 (18618) SS BOND : bond 0.00311 / 0.16 ( 4) SS BOND : angle 1.44743 / 0.87 ( 8) hydrogen bonds : bond 0.04076 / 2.76 ( 624) hydrogen bonds : angle 4.55879 / 3.17 ( 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 281 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8553 (pt0) REVERT: A 88 SER cc_start: 0.8128 (m) cc_final: 0.7920 (p) REVERT: A 191 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7644 (mt0) REVERT: A 215 MET cc_start: 0.8043 (mtm) cc_final: 0.7786 (mmm) REVERT: A 294 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8434 (mp0) REVERT: A 329 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6711 (mtp-110) REVERT: A 344 GLU cc_start: 0.8202 (tp30) cc_final: 0.7889 (tp30) REVERT: B 78 ASP cc_start: 0.7994 (t0) cc_final: 0.7733 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: B 177 ASP cc_start: 0.8045 (t0) cc_final: 0.7653 (t0) REVERT: B 224 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7738 (mptp) REVERT: B 330 GLU cc_start: 0.6759 (tp30) cc_final: 0.6174 (tp30) REVERT: B 336 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 352 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7438 (tt) REVERT: B 354 MET cc_start: 0.6815 (ttm) cc_final: 0.6589 (ptm) REVERT: C 47 HIS cc_start: 0.7723 (m-70) cc_final: 0.6794 (m-70) REVERT: C 62 LYS cc_start: 0.9206 (ttpp) cc_final: 0.8014 (mmtm) REVERT: C 114 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7319 (tp30) REVERT: C 120 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7398 (mp) REVERT: C 122 ASP cc_start: 0.6889 (m-30) cc_final: 0.6415 (m-30) REVERT: D 70 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: D 71 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7819 (pt0) REVERT: D 99 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.6434 (m-70) REVERT: D 112 MET cc_start: 0.6261 (mpp) cc_final: 0.5864 (OUTLIER) REVERT: E 79 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8533 (pt0) REVERT: E 88 SER cc_start: 0.8133 (m) cc_final: 0.7920 (p) REVERT: E 191 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7625 (mt0) REVERT: E 215 MET cc_start: 0.8045 (mtm) cc_final: 0.7791 (mmm) REVERT: E 294 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8423 (mp0) REVERT: E 297 GLN cc_start: 0.7445 (mp10) cc_final: 0.7028 (mp10) REVERT: E 329 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6702 (mtp-110) REVERT: E 344 GLU cc_start: 0.8235 (tp30) cc_final: 0.7938 (tp30) REVERT: F 78 ASP cc_start: 0.7997 (t0) cc_final: 0.7727 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: F 173 GLN cc_start: 0.7917 (mm110) cc_final: 0.7552 (mm110) REVERT: F 177 ASP cc_start: 0.8076 (t0) cc_final: 0.7696 (t0) REVERT: F 179 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7852 (tp-100) REVERT: F 224 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7673 (mptp) REVERT: F 330 GLU cc_start: 0.6741 (tp30) cc_final: 0.6148 (tp30) REVERT: F 336 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7573 (mt-10) REVERT: F 352 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7425 (tt) REVERT: G 49 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8176 (tp-100) REVERT: G 113 SER cc_start: 0.8510 (m) cc_final: 0.8082 (t) REVERT: G 120 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7388 (mp) REVERT: G 122 ASP cc_start: 0.6894 (m-30) cc_final: 0.6417 (m-30) REVERT: H 67 MET cc_start: 0.6964 (mmt) cc_final: 0.6464 (tpt) REVERT: H 99 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6447 (m-70) REVERT: H 112 MET cc_start: 0.6266 (mpp) cc_final: 0.5908 (OUTLIER) outliers start: 73 outliers final: 28 residues processed: 261 average time/residue: 0.5060 time to fit residues: 145.8491 Evaluate side-chains 236 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 329 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 118 ILE 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 55 HIS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU 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 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 329 ARG 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 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 G residue 49 GLN Chi-restraints excluded: chain G residue 55 HIS 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 59 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 157 optimal weight: 40.0000 chunk 127 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 80 HIS C 119 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN D 86 ASN 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 80 HIS G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN H 86 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.186640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123894 restraints weight = 17000.611| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.42 r_work: 0.3466 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13788 Z= 0.268 Angle : 0.671 9.642 18626 Z= 0.351 Chirality : 0.050 0.184 1916 Planarity : 0.004 0.051 2508 Dihedral : 5.955 57.369 1800 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.50 % Allowed : 24.07 % Favored : 69.43 % 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 are not related in a simple way. whole: 0.07 (0.21), residues: 1648 helix: 1.17 (0.24), residues: 482 sheet: 1.19 (0.30), residues: 314 loop : -1.10 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 350 TYR 0.023 0.002 TYR D 76 PHE 0.027 0.003 PHE E 262 TRP 0.013 0.002 TRP F 126 HIS 0.004 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 (13784) covalent geometry : angle 0.67017 / 0.35 (18618) SS BOND : bond 0.00318 / 0.19 ( 4) SS BOND : angle 1.60533 / 0.94 ( 8) hydrogen bonds : bond 0.04529 / 3.06 ( 624) hydrogen bonds : angle 4.76467 / 3.31 ( 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 294 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 200 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: A 88 SER cc_start: 0.8111 (m) cc_final: 0.7865 (p) REVERT: A 191 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: A 294 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8450 (mp0) REVERT: A 329 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7065 (mtp-110) REVERT: A 344 GLU cc_start: 0.8244 (tp30) cc_final: 0.7876 (tp30) REVERT: B 78 ASP cc_start: 0.8069 (t0) cc_final: 0.7824 (OUTLIER) REVERT: B 177 ASP cc_start: 0.8188 (t0) cc_final: 0.7826 (t0) REVERT: B 179 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7839 (tp-100) REVERT: B 224 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7641 (mptp) REVERT: B 330 GLU cc_start: 0.6770 (tp30) cc_final: 0.6260 (tp30) REVERT: B 352 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7315 (tt) REVERT: B 354 MET cc_start: 0.6853 (ttm) cc_final: 0.6624 (ptm) REVERT: C 62 LYS cc_start: 0.9184 (ttpp) cc_final: 0.8363 (mptp) REVERT: C 120 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7495 (mp) REVERT: C 122 ASP cc_start: 0.7071 (m-30) cc_final: 0.6462 (m-30) REVERT: D 70 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: D 71 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7579 (mp0) REVERT: D 99 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.6370 (m-70) REVERT: D 112 MET cc_start: 0.6423 (mpp) cc_final: 0.6187 (mpp) REVERT: E 79 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: E 88 SER cc_start: 0.8107 (m) cc_final: 0.7855 (p) REVERT: E 191 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: E 294 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8458 (mp0) REVERT: E 329 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7068 (mtp-110) REVERT: E 344 GLU cc_start: 0.8242 (tp30) cc_final: 0.7878 (tp30) REVERT: F 78 ASP cc_start: 0.8076 (t0) cc_final: 0.7818 (OUTLIER) REVERT: F 177 ASP cc_start: 0.8193 (t0) cc_final: 0.7902 (t0) REVERT: F 179 GLN cc_start: 0.8347 (tp-100) cc_final: 0.7773 (tp-100) REVERT: F 224 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7566 (mptp) REVERT: F 330 GLU cc_start: 0.6783 (tp30) cc_final: 0.6265 (tp30) REVERT: F 352 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7574 (tt) REVERT: G 49 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8153 (tp-100) REVERT: G 62 LYS cc_start: 0.9155 (ttpp) cc_final: 0.8312 (mptp) REVERT: G 113 SER cc_start: 0.8523 (m) cc_final: 0.8173 (t) REVERT: G 120 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7458 (mp) REVERT: G 122 ASP cc_start: 0.7062 (m-30) cc_final: 0.6466 (m-30) REVERT: H 70 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: H 71 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7798 (pt0) REVERT: H 99 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6341 (m-70) REVERT: H 112 MET cc_start: 0.6272 (mpp) cc_final: 0.5925 (OUTLIER) outliers start: 94 outliers final: 46 residues processed: 262 average time/residue: 0.4840 time to fit residues: 140.0397 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 329 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 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU 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 99 HIS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 329 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 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET 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 114 GLU Chi-restraints excluded: chain G residue 115 ASP 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 99 HIS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 153 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 80 HIS C 119 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.191275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129473 restraints weight = 16946.042| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.41 r_work: 0.3540 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13788 Z= 0.108 Angle : 0.559 9.258 18626 Z= 0.285 Chirality : 0.045 0.159 1916 Planarity : 0.004 0.049 2508 Dihedral : 5.357 59.359 1798 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.67 % Allowed : 25.38 % Favored : 68.95 % 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 are not related in a simple way. whole: 0.36 (0.21), residues: 1648 helix: 1.40 (0.24), residues: 484 sheet: 1.20 (0.29), residues: 320 loop : -0.87 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 350 TYR 0.024 0.002 TYR B 208 PHE 0.018 0.001 PHE A 296 TRP 0.014 0.001 TRP F 126 HIS 0.005 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (13784) covalent geometry : angle 0.55872 / 0.28 (18618) SS BOND : bond 0.00179 / 0.11 ( 4) SS BOND : angle 1.16179 / 0.64 ( 8) hydrogen bonds : bond 0.03529 / 2.38 ( 624) hydrogen bonds : angle 4.30106 / 3.00 ( 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 281 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 199 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8572 (pt0) REVERT: A 88 SER cc_start: 0.8156 (m) cc_final: 0.7924 (p) REVERT: A 215 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7825 (mmm) REVERT: A 294 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8465 (mp0) REVERT: A 329 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6823 (mtp-110) REVERT: A 344 GLU cc_start: 0.8123 (tp30) cc_final: 0.7799 (tp30) REVERT: A 350 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6622 (ptp90) REVERT: B 78 ASP cc_start: 0.7984 (t0) cc_final: 0.7736 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8414 (tt0) cc_final: 0.8114 (pt0) REVERT: B 177 ASP cc_start: 0.8088 (t0) cc_final: 0.7729 (t0) REVERT: B 179 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7773 (tp-100) REVERT: B 224 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7534 (mptp) REVERT: B 330 GLU cc_start: 0.6693 (tp30) cc_final: 0.6094 (tp30) REVERT: C 47 HIS cc_start: 0.7472 (m-70) cc_final: 0.6732 (m-70) REVERT: C 116 GLU cc_start: 0.8163 (tp30) cc_final: 0.7952 (tp30) REVERT: C 120 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7421 (mp) REVERT: C 122 ASP cc_start: 0.6930 (m-30) cc_final: 0.6370 (m-30) REVERT: D 67 MET cc_start: 0.6947 (mmt) cc_final: 0.6217 (tpt) REVERT: D 70 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: D 99 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.6372 (m-70) REVERT: D 112 MET cc_start: 0.6344 (mpp) cc_final: 0.6100 (mpp) REVERT: E 79 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: E 88 SER cc_start: 0.8143 (m) cc_final: 0.7909 (p) REVERT: E 191 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7649 (mt0) REVERT: E 215 MET cc_start: 0.8049 (mtm) cc_final: 0.7826 (mmm) REVERT: E 294 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8429 (mp0) REVERT: E 329 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6710 (mtp-110) REVERT: F 78 ASP cc_start: 0.7984 (t0) cc_final: 0.7734 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8419 (tt0) cc_final: 0.8114 (pt0) REVERT: F 177 ASP cc_start: 0.8146 (t0) cc_final: 0.7773 (t0) REVERT: F 179 GLN cc_start: 0.8281 (tp-100) cc_final: 0.7944 (tp-100) REVERT: F 224 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7564 (mptp) REVERT: F 330 GLU cc_start: 0.6688 (tp30) cc_final: 0.6091 (tp30) REVERT: F 352 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7507 (tt) REVERT: G 49 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8205 (tp-100) REVERT: G 113 SER cc_start: 0.8593 (m) cc_final: 0.8304 (t) REVERT: G 120 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7407 (mp) REVERT: G 122 ASP cc_start: 0.6930 (m-30) cc_final: 0.6386 (m-30) REVERT: H 67 MET cc_start: 0.6978 (mmt) cc_final: 0.6285 (tpt) REVERT: H 70 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: H 99 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6421 (m-70) outliers start: 82 outliers final: 35 residues processed: 259 average time/residue: 0.4606 time to fit residues: 132.7078 Evaluate side-chains 239 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 ILE 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 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 355 ILE 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 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 75 HIS Chi-restraints excluded: chain D residue 99 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 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 F residue 106 VAL 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 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 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 75 HIS Chi-restraints excluded: chain H residue 99 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 139 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** 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 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** H 55 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 = 0.4283 r_free = 0.4283 target = 0.186342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123572 restraints weight = 17080.034| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.42 r_work: 0.3462 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2993 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= 0.272 Angle : 0.682 9.423 18626 Z= 0.356 Chirality : 0.050 0.185 1916 Planarity : 0.004 0.050 2508 Dihedral : 5.782 58.604 1796 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 6.64 % Allowed : 24.55 % Favored : 68.81 % 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 are not related in a simple way. whole: 0.07 (0.21), residues: 1648 helix: 1.31 (0.24), residues: 482 sheet: 0.97 (0.29), residues: 328 loop : -1.13 (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 B 208 PHE 0.028 0.003 PHE A 262 TRP 0.012 0.002 TRP B 67 HIS 0.006 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.27 (13784) covalent geometry : angle 0.68166 / 0.36 (18618) SS BOND : bond 0.00407 / 0.24 ( 4) SS BOND : angle 1.60500 / 0.94 ( 8) hydrogen bonds : bond 0.04447 / 3.02 ( 624) hydrogen bonds : angle 4.77174 / 3.31 ( 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 298 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 202 time to evaluate : 0.575 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: 0.8879 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: A 294 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8478 (mp0) REVERT: A 329 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7128 (mtp-110) REVERT: A 344 GLU cc_start: 0.8198 (tp30) cc_final: 0.7917 (tp30) REVERT: A 350 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6548 (ptp90) REVERT: B 78 ASP cc_start: 0.8020 (t0) cc_final: 0.7812 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8395 (tt0) cc_final: 0.8033 (pt0) REVERT: B 177 ASP cc_start: 0.8196 (t0) cc_final: 0.7875 (t0) REVERT: B 179 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7879 (tp-100) REVERT: B 224 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7479 (mptp) REVERT: B 330 GLU cc_start: 0.6794 (tp30) cc_final: 0.6146 (tp30) REVERT: C 116 GLU cc_start: 0.8188 (tp30) cc_final: 0.7963 (tp30) REVERT: C 120 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7499 (mp) REVERT: C 122 ASP cc_start: 0.7137 (m-30) cc_final: 0.6528 (m-30) REVERT: D 67 MET cc_start: 0.6786 (mmt) cc_final: 0.6013 (tpt) REVERT: D 70 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: D 71 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7551 (pt0) REVERT: D 99 HIS cc_start: 0.6688 (OUTLIER) cc_final: 0.6285 (m-70) REVERT: E 79 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: E 191 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: E 294 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8505 (mp0) REVERT: E 329 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7082 (mtp-110) REVERT: E 344 GLU cc_start: 0.8195 (tp30) cc_final: 0.7738 (tp30) REVERT: E 350 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6581 (ptp90) REVERT: F 78 ASP cc_start: 0.8072 (t0) cc_final: 0.7827 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8421 (tt0) cc_final: 0.8092 (pt0) REVERT: F 177 ASP cc_start: 0.8260 (t0) cc_final: 0.7973 (t0) REVERT: F 179 GLN cc_start: 0.8402 (tp-100) cc_final: 0.7873 (tp-100) REVERT: F 224 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7513 (mptp) REVERT: F 307 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.6114 (t80) REVERT: F 330 GLU cc_start: 0.6793 (tp30) cc_final: 0.6145 (tp30) REVERT: F 352 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7554 (tt) REVERT: G 49 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8259 (tp-100) REVERT: G 113 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8253 (t) REVERT: G 120 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7465 (mp) REVERT: G 122 ASP cc_start: 0.7128 (m-30) cc_final: 0.6518 (m-30) REVERT: G 137 ASP cc_start: 0.7031 (m-30) cc_final: 0.6762 (m-30) REVERT: H 99 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.6322 (m-70) outliers start: 96 outliers final: 47 residues processed: 264 average time/residue: 0.4839 time to fit residues: 141.6133 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 : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 221 THR 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 326 VAL Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 118 ILE 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 253 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU 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 99 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 79 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 118 ILE 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 307 PHE 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 113 SER Chi-restraints excluded: chain G residue 114 GLU 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 75 HIS Chi-restraints excluded: chain H residue 99 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** 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 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 119 ASN ** H 55 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 = 0.4311 r_free = 0.4311 target = 0.189238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127331 restraints weight = 16902.804| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.41 r_work: 0.3515 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13788 Z= 0.131 Angle : 0.595 9.749 18626 Z= 0.303 Chirality : 0.046 0.211 1916 Planarity : 0.004 0.047 2508 Dihedral : 5.377 59.469 1796 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.05 % Allowed : 26.42 % Favored : 68.53 % 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 are not related in a simple way. whole: 0.24 (0.21), residues: 1648 helix: 1.49 (0.24), residues: 482 sheet: 1.05 (0.29), residues: 326 loop : -1.03 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 350 TYR 0.029 0.002 TYR F 208 PHE 0.022 0.002 PHE E 307 TRP 0.014 0.001 TRP F 126 HIS 0.008 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13784) covalent geometry : angle 0.59466 / 0.30 (18618) SS BOND : bond 0.00163 / 0.09 ( 4) SS BOND : angle 1.16459 / 0.68 ( 8) hydrogen bonds : bond 0.03631 / 2.45 ( 624) hydrogen bonds : angle 4.41028 / 3.07 ( 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 264 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: A 88 SER cc_start: 0.8103 (m) cc_final: 0.7836 (p) REVERT: A 294 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8423 (mp0) REVERT: A 329 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.6850 (mtp-110) REVERT: A 350 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6684 (ptp90) REVERT: B 105 GLU cc_start: 0.8367 (tt0) cc_final: 0.8067 (pt0) REVERT: B 177 ASP cc_start: 0.8174 (t0) cc_final: 0.7805 (t0) REVERT: B 179 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7978 (tp-100) REVERT: B 202 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7572 (mtt-85) REVERT: B 224 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7489 (mptp) REVERT: B 330 GLU cc_start: 0.6768 (tp30) cc_final: 0.6039 (tp30) REVERT: C 47 HIS cc_start: 0.7229 (m-70) cc_final: 0.6350 (m-70) REVERT: C 114 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: C 116 GLU cc_start: 0.8104 (tp30) cc_final: 0.7893 (tp30) REVERT: C 120 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7440 (mp) REVERT: C 122 ASP cc_start: 0.7032 (m-30) cc_final: 0.6426 (m-30) REVERT: D 67 MET cc_start: 0.6828 (mmt) cc_final: 0.6190 (tpt) REVERT: D 70 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: D 71 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7523 (pt0) REVERT: D 99 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.6442 (m-70) REVERT: E 79 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: E 88 SER cc_start: 0.8091 (m) cc_final: 0.7824 (p) REVERT: E 191 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7629 (OUTLIER) REVERT: E 215 MET cc_start: 0.7976 (mtm) cc_final: 0.7739 (mmm) REVERT: E 294 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8503 (mp0) REVERT: E 329 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6803 (mtp-110) REVERT: E 344 GLU cc_start: 0.8128 (tp30) cc_final: 0.7711 (tp30) REVERT: E 350 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6745 (ptp90) REVERT: F 78 ASP cc_start: 0.7904 (t0) cc_final: 0.7655 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8378 (tt0) cc_final: 0.8081 (pt0) REVERT: F 177 ASP cc_start: 0.8192 (t0) cc_final: 0.7875 (t0) REVERT: F 179 GLN cc_start: 0.8379 (tp-100) cc_final: 0.8081 (tp-100) REVERT: F 202 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7552 (mtt-85) REVERT: F 224 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7494 (mptp) REVERT: F 307 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.6174 (t80) REVERT: F 330 GLU cc_start: 0.6756 (tp30) cc_final: 0.6179 (tp30) REVERT: F 352 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7520 (tt) REVERT: G 49 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8063 (tp-100) REVERT: G 113 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8272 (t) REVERT: G 114 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: G 120 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7447 (mp) REVERT: G 122 ASP cc_start: 0.7039 (m-30) cc_final: 0.6445 (m-30) REVERT: H 67 MET cc_start: 0.6712 (mmt) cc_final: 0.5885 (tpt) outliers start: 73 outliers final: 34 residues processed: 245 average time/residue: 0.4891 time to fit residues: 132.5925 Evaluate side-chains 241 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 93 VAL 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 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU 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 99 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 326 VAL 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 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 307 PHE 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 113 SER Chi-restraints excluded: chain G residue 114 GLU 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 75 HIS Chi-restraints excluded: chain H residue 100 VAL 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: 0.9980 chunk 90 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN E 297 GLN E 359 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.189654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127733 restraints weight = 16883.307| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.41 r_work: 0.3521 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13788 Z= 0.129 Angle : 0.593 9.089 18626 Z= 0.303 Chirality : 0.046 0.245 1916 Planarity : 0.004 0.049 2508 Dihedral : 5.118 58.819 1794 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.70 % Allowed : 26.69 % Favored : 68.60 % 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 are not related in a simple way. whole: 0.34 (0.21), residues: 1648 helix: 1.54 (0.24), residues: 482 sheet: 1.05 (0.28), residues: 334 loop : -0.94 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 350 TYR 0.029 0.002 TYR B 208 PHE 0.016 0.001 PHE A 296 TRP 0.013 0.001 TRP F 126 HIS 0.010 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13784) covalent geometry : angle 0.59286 / 0.30 (18618) SS BOND : bond 0.00167 / 0.09 ( 4) SS BOND : angle 1.12122 / 0.64 ( 8) hydrogen bonds : bond 0.03528 / 2.38 ( 624) hydrogen bonds : angle 4.33832 / 3.03 ( 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: 68 poor density : 188 time to evaluate : 0.462 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 57 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8685 (tt) REVERT: A 79 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8564 (pt0) REVERT: A 88 SER cc_start: 0.8094 (m) cc_final: 0.7823 (p) REVERT: A 294 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8388 (mp0) REVERT: A 329 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6795 (mtp-110) REVERT: A 344 GLU cc_start: 0.8265 (tp30) cc_final: 0.7791 (tp30) REVERT: A 350 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6718 (ptp90) REVERT: B 78 ASP cc_start: 0.8054 (t0) cc_final: 0.7806 (t0) REVERT: B 105 GLU cc_start: 0.8369 (tt0) cc_final: 0.8063 (pt0) REVERT: B 177 ASP cc_start: 0.8171 (t0) cc_final: 0.7805 (t0) REVERT: B 179 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7980 (tp-100) REVERT: B 202 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7587 (mtt-85) REVERT: B 224 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7503 (mptp) REVERT: B 330 GLU cc_start: 0.6756 (tp30) cc_final: 0.6179 (tp30) REVERT: C 47 HIS cc_start: 0.7243 (m-70) cc_final: 0.6560 (m-70) REVERT: C 114 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: C 120 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7416 (mp) REVERT: C 122 ASP cc_start: 0.7014 (m-30) cc_final: 0.6412 (m-30) REVERT: D 67 MET cc_start: 0.6893 (mmt) cc_final: 0.6219 (tpt) REVERT: D 70 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: E 57 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8688 (tt) REVERT: E 79 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8573 (pt0) REVERT: E 88 SER cc_start: 0.8092 (m) cc_final: 0.7820 (p) REVERT: E 191 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: E 215 MET cc_start: 0.8003 (mtm) cc_final: 0.7791 (mmm) REVERT: E 294 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8530 (mp0) REVERT: E 307 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6714 (t80) REVERT: E 329 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6786 (mtp-110) REVERT: E 344 GLU cc_start: 0.8114 (tp30) cc_final: 0.7692 (tp30) REVERT: E 350 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6743 (ptp90) REVERT: E 359 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: F 78 ASP cc_start: 0.7936 (t0) cc_final: 0.7676 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8372 (tt0) cc_final: 0.8068 (pt0) REVERT: F 177 ASP cc_start: 0.8172 (t0) cc_final: 0.7894 (t0) REVERT: F 179 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8075 (tp-100) REVERT: F 202 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7505 (mtt-85) REVERT: F 224 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7502 (mptp) REVERT: F 307 PHE cc_start: 0.6378 (OUTLIER) cc_final: 0.6174 (t80) REVERT: F 330 GLU cc_start: 0.6735 (tp30) cc_final: 0.6162 (tp30) REVERT: F 352 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7478 (tt) REVERT: G 47 HIS cc_start: 0.7181 (m-70) cc_final: 0.6445 (m-70) REVERT: G 49 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8239 (tp-100) REVERT: G 62 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8401 (mptp) REVERT: G 113 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8339 (t) REVERT: G 114 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: G 120 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7440 (mp) REVERT: G 122 ASP cc_start: 0.7014 (m-30) cc_final: 0.6414 (m-30) REVERT: H 67 MET cc_start: 0.6781 (mmt) cc_final: 0.6054 (tpt) REVERT: H 70 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7626 (tm-30) outliers start: 68 outliers final: 33 residues processed: 240 average time/residue: 0.4882 time to fit residues: 129.7362 Evaluate side-chains 241 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 326 VAL 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 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 114 GLU Chi-restraints excluded: chain C residue 120 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 100 VAL 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 93 VAL Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain E residue 359 GLN 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 224 LYS Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 307 PHE 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 113 SER Chi-restraints excluded: chain G residue 114 GLU 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 100 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 151 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** 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 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.189232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127356 restraints weight = 17106.985| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.41 r_work: 0.3514 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13788 Z= 0.141 Angle : 0.600 8.634 18626 Z= 0.307 Chirality : 0.047 0.272 1916 Planarity : 0.004 0.053 2508 Dihedral : 4.976 58.831 1792 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.77 % Allowed : 26.76 % 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 are not related in a simple way. whole: 0.38 (0.21), residues: 1648 helix: 1.63 (0.24), residues: 480 sheet: 1.05 (0.28), residues: 334 loop : -0.94 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 350 TYR 0.030 0.002 TYR F 208 PHE 0.016 0.001 PHE A 262 TRP 0.012 0.001 TRP E 126 HIS 0.008 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13784) covalent geometry : angle 0.59932 / 0.31 (18618) SS BOND : bond 0.00172 / 0.10 ( 4) SS BOND : angle 1.09843 / 0.63 ( 8) hydrogen bonds : bond 0.03547 / 2.40 ( 624) hydrogen bonds : angle 4.36844 / 3.05 ( 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 257 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 188 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8697 (tt) REVERT: A 79 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: A 294 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8439 (mp0) REVERT: A 329 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6812 (mtp-110) REVERT: A 350 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6761 (ptp90) REVERT: B 78 ASP cc_start: 0.7920 (t0) cc_final: 0.7664 (t0) REVERT: B 105 GLU cc_start: 0.8379 (tt0) cc_final: 0.8074 (pt0) REVERT: B 177 ASP cc_start: 0.8184 (t0) cc_final: 0.7834 (t0) REVERT: B 179 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7983 (tp-100) REVERT: B 202 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7570 (mtt-85) REVERT: B 224 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7483 (mptp) REVERT: B 330 GLU cc_start: 0.6749 (tp30) cc_final: 0.6162 (tp30) REVERT: C 120 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7346 (mp) REVERT: C 122 ASP cc_start: 0.7044 (m-30) cc_final: 0.6438 (m-30) REVERT: D 52 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8737 (mp) REVERT: D 67 MET cc_start: 0.6795 (mmt) cc_final: 0.6159 (tpt) REVERT: D 70 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: E 57 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8698 (tt) REVERT: E 79 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: E 191 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: E 215 MET cc_start: 0.8054 (mtm) cc_final: 0.7817 (mmm) REVERT: E 294 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8528 (mp0) REVERT: E 307 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6665 (t80) REVERT: E 329 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6811 (mtp-110) REVERT: E 344 GLU cc_start: 0.7922 (tp30) cc_final: 0.7532 (tp30) REVERT: E 350 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6762 (ptp90) REVERT: F 78 ASP cc_start: 0.7944 (t0) cc_final: 0.7688 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8381 (tt0) cc_final: 0.8078 (pt0) REVERT: F 177 ASP cc_start: 0.8210 (t0) cc_final: 0.7872 (t0) REVERT: F 179 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8090 (tp-100) REVERT: F 202 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7568 (mtt-85) REVERT: F 224 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7499 (mptp) REVERT: F 330 GLU cc_start: 0.6731 (tp30) cc_final: 0.6149 (tp30) REVERT: F 352 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7488 (tt) REVERT: G 113 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8360 (t) REVERT: G 114 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: G 120 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7388 (mp) REVERT: G 122 ASP cc_start: 0.7044 (m-30) cc_final: 0.6446 (m-30) REVERT: H 67 MET cc_start: 0.6760 (mmt) cc_final: 0.6058 (tpt) REVERT: H 70 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7611 (tm-30) outliers start: 69 outliers final: 38 residues processed: 240 average time/residue: 0.5164 time to fit residues: 137.3123 Evaluate side-chains 244 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL 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 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 114 GLU 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 100 VAL 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 93 VAL Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 326 VAL 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 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 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 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 GLU 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 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 145 optimal weight: 10.0000 chunk 123 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 0.3980 chunk 125 optimal weight: 0.0370 chunk 106 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN ** F 359 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.189052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127082 restraints weight = 16966.206| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.40 r_work: 0.3511 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3133 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= 0.151 Angle : 0.617 9.381 18626 Z= 0.315 Chirality : 0.047 0.268 1916 Planarity : 0.004 0.056 2508 Dihedral : 5.006 58.988 1792 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.36 % Allowed : 27.11 % Favored : 68.53 % 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 are not related in a simple way. whole: 0.33 (0.21), residues: 1648 helix: 1.57 (0.24), residues: 480 sheet: 1.02 (0.28), residues: 334 loop : -0.96 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 350 TYR 0.031 0.002 TYR F 208 PHE 0.021 0.002 PHE F 307 TRP 0.012 0.001 TRP E 126 HIS 0.007 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (13784) covalent geometry : angle 0.61628 / 0.31 (18618) SS BOND : bond 0.00191 / 0.11 ( 4) SS BOND : angle 1.11813 / 0.65 ( 8) hydrogen bonds : bond 0.03610 / 2.44 ( 624) hydrogen bonds : angle 4.42717 / 3.09 ( 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 250 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 0.506 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: 0.8883 (OUTLIER) cc_final: 0.8527 (pt0) REVERT: A 294 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8499 (mp0) REVERT: A 329 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6804 (mtp-110) REVERT: B 78 ASP cc_start: 0.7943 (t0) cc_final: 0.7685 (t0) REVERT: B 105 GLU cc_start: 0.8382 (tt0) cc_final: 0.8072 (pt0) REVERT: B 177 ASP cc_start: 0.8188 (t0) cc_final: 0.7830 (t0) REVERT: B 179 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8023 (tp-100) REVERT: B 202 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7568 (mtt-85) REVERT: B 224 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7486 (mptp) REVERT: B 330 GLU cc_start: 0.6754 (tp30) cc_final: 0.6194 (tp30) REVERT: C 120 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7342 (mp) REVERT: C 122 ASP cc_start: 0.7191 (m-30) cc_final: 0.6597 (m-30) REVERT: D 52 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8737 (mp) REVERT: D 67 MET cc_start: 0.6856 (mmt) cc_final: 0.6210 (tpt) REVERT: E 79 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8535 (pt0) REVERT: E 191 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: E 215 MET cc_start: 0.8013 (mtm) cc_final: 0.7770 (mmm) REVERT: E 294 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8525 (mp0) REVERT: E 307 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6709 (t80) REVERT: E 329 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6798 (mtp-110) REVERT: E 344 GLU cc_start: 0.7907 (tp30) cc_final: 0.7543 (tp30) REVERT: E 350 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6786 (ptp90) REVERT: F 78 ASP cc_start: 0.7877 (t0) cc_final: 0.7630 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8376 (tt0) cc_final: 0.8067 (pt0) REVERT: F 177 ASP cc_start: 0.8223 (t0) cc_final: 0.7915 (t0) REVERT: F 179 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8113 (tp-100) REVERT: F 202 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7559 (mtt-85) REVERT: F 224 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7492 (mptp) REVERT: F 330 GLU cc_start: 0.6734 (tp30) cc_final: 0.6176 (tp30) REVERT: F 352 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7484 (tt) REVERT: G 47 HIS cc_start: 0.7145 (m-70) cc_final: 0.6558 (m-70) REVERT: G 113 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8357 (t) REVERT: G 114 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: G 120 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7382 (mp) REVERT: G 122 ASP cc_start: 0.7051 (m-30) cc_final: 0.6449 (m-30) REVERT: H 67 MET cc_start: 0.6719 (mmt) cc_final: 0.6063 (tpt) outliers start: 63 outliers final: 36 residues processed: 232 average time/residue: 0.4392 time to fit residues: 113.0368 Evaluate side-chains 238 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain B residue 93 VAL 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 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 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 100 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 326 VAL 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 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 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 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 GLU 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 Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 75 optimal weight: 0.0770 chunk 139 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 235 ASN A 297 GLN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.188446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127289 restraints weight = 17048.032| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.38 r_work: 0.3512 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13788 Z= 0.149 Angle : 0.613 9.867 18626 Z= 0.312 Chirality : 0.047 0.275 1916 Planarity : 0.004 0.056 2508 Dihedral : 4.981 59.541 1792 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.87 % Allowed : 27.80 % Favored : 68.33 % 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 are not related in a simple way. whole: 0.30 (0.21), residues: 1648 helix: 1.55 (0.24), residues: 480 sheet: 0.96 (0.28), residues: 336 loop : -0.97 (0.22), residues: 832 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 0.018 0.002 PHE A 262 TRP 0.013 0.001 TRP E 126 HIS 0.006 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (13784) covalent geometry : angle 0.61223 / 0.31 (18618) SS BOND : bond 0.00186 / 0.11 ( 4) SS BOND : angle 1.09768 / 0.64 ( 8) hydrogen bonds : bond 0.03548 / 2.40 ( 624) hydrogen bonds : angle 4.42150 / 3.08 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6246.52 seconds wall clock time: 106 minutes 39.83 seconds (6399.83 seconds total)