Starting phenix.real_space_refine on Thu May 15 14:31:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp5_36468/05_2025/8jp5_36468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp5_36468/05_2025/8jp5_36468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jp5_36468/05_2025/8jp5_36468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp5_36468/05_2025/8jp5_36468.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp5_36468/05_2025/8jp5_36468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp5_36468/05_2025/8jp5_36468.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13490 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 308} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 1 Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: H, F, E, G Time building chain proxies: 8.63, per 1000 atoms: 0.64 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: 3.04 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.86 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: 4.34 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4618 1.35 - 1.46: 3071 1.46 - 1.58: 6027 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 13784 Sorted by residual: bond pdb=" N GLU A 283 " pdb=" CA GLU A 283 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.62e+00 bond pdb=" N GLU E 283 " pdb=" CA GLU E 283 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.56e+00 bond pdb=" N LEU H 56 " pdb=" CA LEU H 56 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.32e-02 5.74e+03 6.79e+00 bond pdb=" N LEU D 56 " pdb=" CA LEU D 56 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.32e-02 5.74e+03 6.36e+00 bond pdb=" N LEU H 74 " pdb=" CA LEU H 74 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.41e+00 ... (remaining 13779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18324 2.03 - 4.06: 255 4.06 - 6.09: 33 6.09 - 8.12: 4 8.12 - 10.15: 2 Bond angle restraints: 18618 Sorted by residual: angle pdb=" C ALA F 120 " pdb=" N ASP F 121 " pdb=" CA ASP F 121 " ideal model delta sigma weight residual 121.70 128.20 -6.50 1.80e+00 3.09e-01 1.30e+01 angle pdb=" C ALA B 120 " pdb=" N ASP B 121 " pdb=" CA ASP B 121 " ideal model delta sigma weight residual 121.70 128.11 -6.41 1.80e+00 3.09e-01 1.27e+01 angle pdb=" C ALA A 120 " pdb=" N ASP A 121 " pdb=" CA ASP A 121 " ideal model delta sigma weight residual 121.70 127.21 -5.51 1.80e+00 3.09e-01 9.36e+00 angle pdb=" C ALA E 120 " pdb=" N ASP E 121 " pdb=" CA ASP E 121 " ideal model delta sigma weight residual 121.70 127.13 -5.43 1.80e+00 3.09e-01 9.11e+00 angle pdb=" CA VAL D 100 " pdb=" CB VAL D 100 " pdb=" CG1 VAL D 100 " ideal model delta sigma weight residual 110.40 115.45 -5.05 1.70e+00 3.46e-01 8.84e+00 ... (remaining 18613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 6918 16.46 - 32.91: 935 32.91 - 49.37: 286 49.37 - 65.82: 83 65.82 - 82.28: 22 Dihedral angle restraints: 8244 sinusoidal: 3430 harmonic: 4814 Sorted by residual: dihedral pdb=" CA LEU E 356 " pdb=" C LEU E 356 " pdb=" N ASP E 357 " pdb=" CA ASP E 357 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LEU A 356 " pdb=" C LEU A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ILE A 355 " pdb=" C ILE A 355 " pdb=" N LEU A 356 " pdb=" CA LEU A 356 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 8241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1408 0.045 - 0.089: 364 0.089 - 0.134: 128 0.134 - 0.179: 12 0.179 - 0.223: 4 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CG LEU F 356 " pdb=" CB LEU F 356 " pdb=" CD1 LEU F 356 " pdb=" CD2 LEU F 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 356 " pdb=" CB LEU B 356 " pdb=" CD1 LEU B 356 " pdb=" CD2 LEU B 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LEU D 111 " pdb=" N LEU D 111 " pdb=" C LEU D 111 " pdb=" CB LEU D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 1913 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 356 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LEU A 356 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 356 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 357 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 356 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C LEU E 356 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU E 356 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP E 357 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 352 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C LEU E 352 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU E 352 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP E 353 " 0.012 2.00e-02 2.50e+03 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 30 2.20 - 2.87: 5059 2.87 - 3.55: 18487 3.55 - 4.22: 32111 4.22 - 4.90: 55388 Nonbonded interactions: 111075 Sorted by model distance: nonbonded pdb=" CE1 HIS D 51 " pdb="ZN ZN D 703 " model vdw 1.524 2.450 nonbonded pdb=" CE1 HIS H 51 " pdb="ZN ZN H 703 " model vdw 1.525 2.450 nonbonded pdb=" OD1 ASP G 129 " pdb=" OD1 ASP G 133 " model vdw 1.788 3.040 nonbonded pdb=" OD1 ASP C 129 " pdb=" OD1 ASP C 133 " model vdw 1.789 3.040 nonbonded pdb=" OD1 ASP E 157 " pdb=" OD2 ASP E 181 " model vdw 1.920 3.040 ... (remaining 111070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.670 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.690 Find NCS groups from input model: 0.240 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13788 Z= 0.136 Angle : 0.580 10.146 18626 Z= 0.323 Chirality : 0.046 0.223 1916 Planarity : 0.004 0.039 2508 Dihedral : 17.357 82.276 5136 Min Nonbonded Distance : 1.524 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.35 % Allowed : 21.85 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (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 TRP 0.009 0.001 TRP E 126 HIS 0.005 0.001 HIS D 99 PHE 0.015 0.001 PHE B 296 TYR 0.010 0.001 TYR G 76 ARG 0.010 0.001 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.15735 ( 624) hydrogen bonds : angle 7.13383 ( 1902) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.96226 ( 8) covalent geometry : bond 0.00250 (13784) covalent geometry : angle 0.57979 (18618) *********************** 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 : 1.647 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: 0.7554 (t0) REVERT: B 330 GLU cc_start: 0.6678 (tp30) cc_final: 0.6087 (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: 0.7487 (tt) REVERT: B 354 MET cc_start: 0.6679 (ttm) cc_final: 0.6471 (ptm) REVERT: C 43 LYS cc_start: 0.7353 (tptt) cc_final: 0.6813 (mmtm) REVERT: C 49 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7947 (tp-100) REVERT: C 122 ASP cc_start: 0.6903 (m-30) cc_final: 0.6570 (m-30) REVERT: E 191 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7196 (mt0) REVERT: E 218 ASN cc_start: 0.7403 (m-40) cc_final: 0.6598 (OUTLIER) REVERT: E 329 ARG cc_start: 0.7197 (ttm110) cc_final: 0.6702 (ttp80) REVERT: F 78 ASP cc_start: 0.7549 (t0) cc_final: 0.7338 (t0) REVERT: F 330 GLU cc_start: 0.6665 (tp30) cc_final: 0.6082 (tp30) REVERT: F 336 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7414 (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: 0.9951 time to fit residues: 328.4871 Evaluate side-chains 234 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 138 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 175 HIS B 179 GLN B 210 ASN B 217 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 80 HIS C 119 ASN D 51 HIS E 178 HIS E 235 ASN ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN F 175 HIS F 179 GLN F 210 ASN F 217 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 80 HIS G 119 ASN H 51 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.190395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129021 restraints weight = 16822.629| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.40 r_work: 0.3530 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13788 Z= 0.137 Angle : 0.568 9.823 18626 Z= 0.297 Chirality : 0.045 0.156 1916 Planarity : 0.003 0.040 2508 Dihedral : 6.292 54.514 1828 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.39 % Allowed : 22.89 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1648 helix: 1.21 (0.24), residues: 482 sheet: 1.32 (0.28), residues: 338 loop : -0.98 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 126 HIS 0.004 0.001 HIS D 80 PHE 0.017 0.002 PHE A 262 TYR 0.023 0.002 TYR D 76 ARG 0.005 0.001 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 624) hydrogen bonds : angle 4.73409 ( 1902) SS BOND : bond 0.00125 ( 4) SS BOND : angle 1.03214 ( 8) covalent geometry : bond 0.00305 (13784) covalent geometry : angle 0.56797 (18618) *********************** 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 299 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 221 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7609 (mt0) REVERT: A 294 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8402 (mp0) REVERT: A 329 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7058 (ttp80) REVERT: A 344 GLU cc_start: 0.8167 (tp30) cc_final: 0.7775 (tp30) REVERT: B 78 ASP cc_start: 0.7936 (t0) cc_final: 0.7682 (t0) REVERT: B 105 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: B 177 ASP cc_start: 0.8040 (t0) cc_final: 0.7684 (t0) REVERT: B 330 GLU cc_start: 0.6696 (tp30) cc_final: 0.6130 (tp30) REVERT: B 336 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7359 (mm-30) REVERT: B 354 MET cc_start: 0.6789 (ttm) cc_final: 0.6576 (ptm) REVERT: C 122 ASP cc_start: 0.6879 (m-30) cc_final: 0.6387 (m-30) REVERT: C 144 SER cc_start: 0.7060 (OUTLIER) cc_final: 0.6854 (p) REVERT: D 99 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6482 (m-70) REVERT: D 114 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6949 (tp30) REVERT: D 127 ASP cc_start: 0.7205 (p0) cc_final: 0.7002 (p0) REVERT: E 191 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7587 (mt0) REVERT: E 294 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8426 (mp0) REVERT: E 329 ARG cc_start: 0.7593 (ttm110) cc_final: 0.7103 (ttp80) REVERT: E 344 GLU cc_start: 0.8209 (tp30) cc_final: 0.7818 (tp30) REVERT: F 78 ASP cc_start: 0.7942 (t0) cc_final: 0.7671 (t0) REVERT: F 105 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: F 179 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7833 (tp-100) REVERT: F 330 GLU cc_start: 0.6671 (tp30) cc_final: 0.6127 (tp30) REVERT: F 336 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7460 (mm-30) REVERT: F 352 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7247 (tt) REVERT: G 113 SER cc_start: 0.8514 (m) cc_final: 0.8104 (t) REVERT: G 122 ASP cc_start: 0.6853 (m-30) cc_final: 0.6405 (m-30) REVERT: H 99 HIS cc_start: 0.6876 (OUTLIER) cc_final: 0.6506 (m-70) REVERT: H 114 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6943 (tp30) outliers start: 78 outliers final: 29 residues processed: 272 average time/residue: 1.0501 time to fit residues: 316.9258 Evaluate side-chains 248 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 144 SER 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 230 CYS Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 GLN 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 55 HIS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 115 ASP 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 59 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 127 optimal weight: 0.0980 chunk 87 optimal weight: 0.0010 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 217 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 119 ASN E 178 HIS E 235 ASN E 338 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 217 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS G 119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.191355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129978 restraints weight = 16895.433| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.41 r_work: 0.3540 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13788 Z= 0.113 Angle : 0.541 7.816 18626 Z= 0.281 Chirality : 0.045 0.156 1916 Planarity : 0.003 0.045 2508 Dihedral : 5.681 55.926 1808 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.26 % Allowed : 23.86 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1648 helix: 1.33 (0.24), residues: 486 sheet: 1.38 (0.29), residues: 336 loop : -0.92 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.005 0.001 HIS H 55 PHE 0.014 0.001 PHE A 296 TYR 0.022 0.001 TYR D 76 ARG 0.003 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 624) hydrogen bonds : angle 4.39106 ( 1902) SS BOND : bond 0.00118 ( 4) SS BOND : angle 1.05622 ( 8) covalent geometry : bond 0.00245 (13784) covalent geometry : angle 0.54036 (18618) *********************** 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 301 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 225 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8632 (pt0) REVERT: A 191 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: A 215 MET cc_start: 0.8015 (mtm) cc_final: 0.7769 (mmm) REVERT: A 294 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8435 (mp0) REVERT: A 329 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7084 (ttp80) REVERT: A 344 GLU cc_start: 0.8170 (tp30) cc_final: 0.7864 (tp30) REVERT: A 350 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6954 (ptp90) REVERT: B 78 ASP cc_start: 0.7933 (t0) cc_final: 0.7688 (t0) REVERT: B 105 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: B 177 ASP cc_start: 0.8024 (t0) cc_final: 0.7701 (t0) REVERT: B 202 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7448 (mtt-85) REVERT: B 224 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7713 (mptp) REVERT: B 226 ASP cc_start: 0.7472 (t70) cc_final: 0.6851 (t0) REVERT: B 264 THR cc_start: 0.8165 (m) cc_final: 0.7900 (m) REVERT: B 330 GLU cc_start: 0.6721 (tp30) cc_final: 0.6127 (tp30) REVERT: B 336 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7450 (mm-30) REVERT: B 352 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7263 (tt) REVERT: C 47 HIS cc_start: 0.7811 (m-70) cc_final: 0.6934 (m-70) REVERT: C 49 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8206 (tp-100) REVERT: C 62 LYS cc_start: 0.9181 (ttpp) cc_final: 0.8105 (mptp) REVERT: C 120 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7369 (mp) REVERT: C 122 ASP cc_start: 0.6869 (m-30) cc_final: 0.6364 (m-30) REVERT: D 67 MET cc_start: 0.6862 (mmt) cc_final: 0.6555 (tpt) REVERT: D 99 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6425 (m-70) REVERT: D 114 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6969 (tp30) REVERT: E 79 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8633 (pt0) REVERT: E 191 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: E 215 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7845 (mmm) REVERT: E 294 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8444 (mp0) REVERT: E 297 GLN cc_start: 0.7400 (mp10) cc_final: 0.7007 (mp10) REVERT: E 329 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7108 (ttp80) REVERT: E 344 GLU cc_start: 0.8199 (tp30) cc_final: 0.7926 (tp30) REVERT: F 78 ASP cc_start: 0.7946 (t0) cc_final: 0.7685 (t0) REVERT: F 105 GLU cc_start: 0.8429 (tt0) cc_final: 0.8170 (pt0) REVERT: F 202 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7414 (mtt-85) REVERT: F 224 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7701 (mptp) REVERT: F 264 THR cc_start: 0.8145 (m) cc_final: 0.7882 (m) REVERT: F 330 GLU cc_start: 0.6657 (tp30) cc_final: 0.6082 (tp30) REVERT: F 336 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7402 (mm-30) REVERT: F 352 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7251 (tt) REVERT: G 47 HIS cc_start: 0.7793 (m-70) cc_final: 0.6885 (m-70) REVERT: G 49 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8177 (tp-100) REVERT: G 62 LYS cc_start: 0.9159 (ttpp) cc_final: 0.8085 (mptp) REVERT: G 113 SER cc_start: 0.8573 (m) cc_final: 0.8132 (t) REVERT: G 120 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7304 (mp) REVERT: G 122 ASP cc_start: 0.6882 (m-30) cc_final: 0.6396 (m-30) REVERT: H 67 MET cc_start: 0.6923 (mmt) cc_final: 0.6588 (tpt) REVERT: H 99 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6426 (m-70) outliers start: 76 outliers final: 23 residues processed: 279 average time/residue: 1.0082 time to fit residues: 312.4111 Evaluate side-chains 246 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 49 GLN 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 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 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 45 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 99 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 338 GLN ** 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 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 179 GLN F 217 ASN F 338 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.188383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.125632 restraints weight = 16820.568| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.40 r_work: 0.3484 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13788 Z= 0.194 Angle : 0.613 9.662 18626 Z= 0.319 Chirality : 0.048 0.180 1916 Planarity : 0.004 0.045 2508 Dihedral : 5.629 57.958 1800 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 6.29 % Allowed : 23.86 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1648 helix: 1.36 (0.24), residues: 482 sheet: 0.89 (0.29), residues: 354 loop : -0.89 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 126 HIS 0.003 0.001 HIS G 75 PHE 0.024 0.002 PHE A 262 TYR 0.021 0.002 TYR H 76 ARG 0.005 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 624) hydrogen bonds : angle 4.50659 ( 1902) SS BOND : bond 0.00207 ( 4) SS BOND : angle 1.31478 ( 8) covalent geometry : bond 0.00455 (13784) covalent geometry : angle 0.61235 (18618) *********************** 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 296 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 205 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8650 (pt0) REVERT: A 191 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: A 258 ASP cc_start: 0.8197 (m-30) cc_final: 0.7922 (m-30) REVERT: A 294 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8489 (mp0) REVERT: A 297 GLN cc_start: 0.7452 (mp10) cc_final: 0.6985 (mp10) REVERT: A 344 GLU cc_start: 0.8219 (tp30) cc_final: 0.7912 (tp30) REVERT: A 350 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6832 (ptp90) REVERT: B 78 ASP cc_start: 0.7989 (t0) cc_final: 0.7738 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: B 177 ASP cc_start: 0.8114 (t0) cc_final: 0.7797 (t0) REVERT: B 179 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7864 (tp-100) REVERT: B 224 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7649 (mptp) REVERT: B 330 GLU cc_start: 0.6738 (tp30) cc_final: 0.6189 (tp30) REVERT: B 336 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7698 (mt-10) REVERT: B 352 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7414 (tt) REVERT: C 49 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8215 (tp-100) REVERT: C 120 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7353 (mp) REVERT: C 122 ASP cc_start: 0.6974 (m-30) cc_final: 0.6477 (m-30) REVERT: D 70 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: D 99 HIS cc_start: 0.6716 (OUTLIER) cc_final: 0.6425 (m-70) REVERT: D 114 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7019 (tp30) REVERT: E 79 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8704 (pt0) REVERT: E 191 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: E 216 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8421 (mm) REVERT: E 294 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8455 (mp0) REVERT: E 329 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7178 (ttp80) REVERT: E 344 GLU cc_start: 0.8207 (tp30) cc_final: 0.7874 (tp30) REVERT: F 78 ASP cc_start: 0.8012 (t0) cc_final: 0.7757 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: F 224 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7634 (mptp) REVERT: F 330 GLU cc_start: 0.6771 (tp30) cc_final: 0.6214 (tp30) REVERT: F 336 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7648 (mt-10) REVERT: F 352 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7417 (tt) REVERT: G 49 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8269 (tp-100) REVERT: G 113 SER cc_start: 0.8558 (m) cc_final: 0.8198 (t) REVERT: G 114 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: G 120 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7374 (mp) REVERT: G 122 ASP cc_start: 0.6956 (m-30) cc_final: 0.6474 (m-30) REVERT: H 70 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: H 99 HIS cc_start: 0.6720 (OUTLIER) cc_final: 0.6393 (m-70) outliers start: 91 outliers final: 34 residues processed: 262 average time/residue: 1.0513 time to fit residues: 305.4589 Evaluate side-chains 248 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 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 B residue 355 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 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 E residue 79 GLN Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain 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 F residue 355 ILE Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 55 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 115 optimal weight: 0.3980 chunk 141 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN ** D 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 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 HIS G 80 HIS G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN H 75 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.191319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129728 restraints weight = 16889.711| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.39 r_work: 0.3539 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13788 Z= 0.106 Angle : 0.555 9.943 18626 Z= 0.281 Chirality : 0.045 0.151 1916 Planarity : 0.003 0.049 2508 Dihedral : 5.047 54.426 1796 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.19 % Allowed : 25.10 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1648 helix: 1.54 (0.24), residues: 484 sheet: 1.26 (0.29), residues: 338 loop : -0.87 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 126 HIS 0.004 0.001 HIS G 47 PHE 0.017 0.001 PHE A 296 TYR 0.024 0.002 TYR F 208 ARG 0.007 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 624) hydrogen bonds : angle 4.20697 ( 1902) SS BOND : bond 0.00141 ( 4) SS BOND : angle 1.08219 ( 8) covalent geometry : bond 0.00232 (13784) covalent geometry : angle 0.55491 (18618) *********************** 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 276 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 201 time to evaluate : 1.630 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: 0.8843 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: A 191 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: A 215 MET cc_start: 0.7950 (mtm) cc_final: 0.7682 (mmm) REVERT: A 258 ASP cc_start: 0.8166 (m-30) cc_final: 0.7853 (m-30) REVERT: A 294 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8436 (mp0) REVERT: A 329 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6987 (mtp-110) REVERT: A 350 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6786 (ptp90) REVERT: B 78 ASP cc_start: 0.7950 (t0) cc_final: 0.7691 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: B 177 ASP cc_start: 0.8083 (t0) cc_final: 0.7769 (t0) REVERT: B 179 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7654 (tp-100) REVERT: B 224 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7710 (mptp) REVERT: B 264 THR cc_start: 0.8122 (m) cc_final: 0.7854 (m) REVERT: B 330 GLU cc_start: 0.6682 (tp30) cc_final: 0.6053 (tp30) REVERT: B 336 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7606 (mt-10) REVERT: C 47 HIS cc_start: 0.7765 (m-70) cc_final: 0.6799 (m-70) REVERT: C 87 LEU cc_start: 0.8754 (mp) cc_final: 0.8543 (mm) REVERT: C 120 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7342 (mp) REVERT: C 122 ASP cc_start: 0.6903 (m-30) cc_final: 0.6413 (m-30) REVERT: D 67 MET cc_start: 0.7005 (mmt) cc_final: 0.6342 (tpt) REVERT: D 70 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: D 71 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7869 (mp0) REVERT: D 114 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6870 (tt0) REVERT: E 79 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8620 (pt0) REVERT: E 191 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7599 (mt0) REVERT: E 294 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8417 (mp0) REVERT: E 329 ARG cc_start: 0.7571 (ttm110) cc_final: 0.7092 (ttp80) REVERT: F 78 ASP cc_start: 0.7989 (t0) cc_final: 0.7723 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: F 179 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7382 (tp40) REVERT: F 224 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7672 (mptp) REVERT: F 330 GLU cc_start: 0.6654 (tp30) cc_final: 0.6028 (tp30) REVERT: F 336 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7554 (mt-10) REVERT: G 47 HIS cc_start: 0.7768 (m-70) cc_final: 0.6862 (m-70) REVERT: G 113 SER cc_start: 0.8579 (m) cc_final: 0.8234 (t) REVERT: G 114 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: G 120 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7315 (mp) REVERT: G 122 ASP cc_start: 0.6872 (m-30) cc_final: 0.6371 (m-30) REVERT: H 67 MET cc_start: 0.6981 (mmt) cc_final: 0.6336 (tpt) REVERT: H 70 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: H 71 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7902 (mp0) outliers start: 75 outliers final: 32 residues processed: 254 average time/residue: 1.0419 time to fit residues: 294.3570 Evaluate side-chains 247 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 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 72 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 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 100 VAL 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 324 GLU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 GLN 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 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 151 optimal weight: 0.0170 chunk 14 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.188951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125883 restraints weight = 17216.621| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.44 r_work: 0.3491 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13788 Z= 0.171 Angle : 0.602 8.783 18626 Z= 0.310 Chirality : 0.047 0.178 1916 Planarity : 0.004 0.047 2508 Dihedral : 4.944 58.088 1792 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.60 % Allowed : 25.52 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1648 helix: 1.51 (0.24), residues: 486 sheet: 1.14 (0.29), residues: 340 loop : -0.90 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 67 HIS 0.010 0.001 HIS H 99 PHE 0.023 0.002 PHE A 262 TYR 0.028 0.002 TYR F 208 ARG 0.008 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 624) hydrogen bonds : angle 4.35499 ( 1902) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.23999 ( 8) covalent geometry : bond 0.00398 (13784) covalent geometry : angle 0.60124 (18618) *********************** 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 287 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 206 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8630 (pt0) REVERT: A 191 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7695 (mt0) REVERT: A 294 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8452 (mp0) REVERT: A 329 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7095 (mtp-110) REVERT: A 344 GLU cc_start: 0.8250 (tp30) cc_final: 0.7716 (tp30) REVERT: A 350 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6633 (ptp90) REVERT: B 78 ASP cc_start: 0.7983 (t0) cc_final: 0.7742 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: B 177 ASP cc_start: 0.8151 (t0) cc_final: 0.7846 (t0) REVERT: B 179 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7755 (tp-100) REVERT: B 202 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7531 (mtt-85) REVERT: B 224 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7556 (mptp) REVERT: B 330 GLU cc_start: 0.6747 (tp30) cc_final: 0.6161 (tp30) REVERT: B 336 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 120 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7405 (mp) REVERT: C 122 ASP cc_start: 0.7054 (m-30) cc_final: 0.6536 (m-30) REVERT: D 67 MET cc_start: 0.6909 (mmt) cc_final: 0.6224 (tpt) REVERT: D 70 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: D 114 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7045 (tt0) REVERT: E 79 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8634 (pt0) REVERT: E 191 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7754 (mt0) REVERT: E 294 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8449 (mp0) REVERT: E 344 GLU cc_start: 0.8147 (tp30) cc_final: 0.7648 (tp30) REVERT: F 78 ASP cc_start: 0.8013 (t0) cc_final: 0.7765 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: F 202 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7520 (mtt-85) REVERT: F 224 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7564 (mptp) REVERT: F 330 GLU cc_start: 0.6738 (tp30) cc_final: 0.6164 (tp30) REVERT: F 336 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7696 (mt-10) REVERT: G 113 SER cc_start: 0.8593 (m) cc_final: 0.8264 (t) REVERT: G 120 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7343 (mp) REVERT: G 122 ASP cc_start: 0.7012 (m-30) cc_final: 0.6518 (m-30) REVERT: H 67 MET cc_start: 0.6889 (mmt) cc_final: 0.6250 (tpt) REVERT: H 70 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7676 (tm-30) outliers start: 81 outliers final: 36 residues processed: 261 average time/residue: 1.1179 time to fit residues: 322.8516 Evaluate side-chains 250 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 202 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 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 355 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 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 100 VAL Chi-restraints excluded: chain E residue 79 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 324 GLU Chi-restraints excluded: chain F residue 105 GLU 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 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125036 restraints weight = 17099.372| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.39 r_work: 0.3479 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13788 Z= 0.199 Angle : 0.629 10.541 18626 Z= 0.322 Chirality : 0.048 0.201 1916 Planarity : 0.004 0.045 2508 Dihedral : 5.100 58.219 1792 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.53 % Allowed : 25.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1648 helix: 1.50 (0.24), residues: 482 sheet: 1.12 (0.29), residues: 328 loop : -0.99 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 126 HIS 0.009 0.001 HIS H 99 PHE 0.024 0.002 PHE A 262 TYR 0.030 0.002 TYR B 208 ARG 0.010 0.001 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 624) hydrogen bonds : angle 4.47233 ( 1902) SS BOND : bond 0.00238 ( 4) SS BOND : angle 1.21692 ( 8) covalent geometry : bond 0.00468 (13784) covalent geometry : angle 0.62837 (18618) *********************** 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 280 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 1.462 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: A 294 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8438 (mp0) REVERT: A 329 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7054 (mtp-110) REVERT: A 350 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6617 (ptp90) REVERT: B 78 ASP cc_start: 0.8059 (t0) cc_final: 0.7808 (OUTLIER) REVERT: B 177 ASP cc_start: 0.8182 (t0) cc_final: 0.7893 (t0) REVERT: B 179 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7861 (tp-100) REVERT: B 224 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7643 (mptp) REVERT: B 330 GLU cc_start: 0.6784 (tp30) cc_final: 0.6216 (tp30) REVERT: C 120 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7421 (mp) REVERT: C 122 ASP cc_start: 0.7070 (m-30) cc_final: 0.6516 (m-30) REVERT: D 67 MET cc_start: 0.6795 (mmt) cc_final: 0.6269 (tpt) REVERT: D 70 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: D 114 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7028 (tp30) REVERT: E 79 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8637 (pt0) REVERT: E 191 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7764 (mt0) REVERT: E 294 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8450 (mp0) REVERT: E 329 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7101 (mtp-110) REVERT: E 344 GLU cc_start: 0.8161 (tp30) cc_final: 0.7646 (tp30) REVERT: E 350 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6759 (ptp90) REVERT: F 78 ASP cc_start: 0.8074 (t0) cc_final: 0.7822 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: F 224 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7586 (mptp) REVERT: F 330 GLU cc_start: 0.6773 (tp30) cc_final: 0.6216 (tp30) REVERT: F 336 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7713 (mt-10) REVERT: G 113 SER cc_start: 0.8605 (m) cc_final: 0.8272 (t) REVERT: G 120 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7392 (mp) REVERT: G 122 ASP cc_start: 0.7040 (m-30) cc_final: 0.6471 (m-30) REVERT: H 67 MET cc_start: 0.6825 (mmt) cc_final: 0.6274 (tpt) REVERT: H 70 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7750 (tm-30) outliers start: 80 outliers final: 41 residues processed: 249 average time/residue: 1.0718 time to fit residues: 294.8336 Evaluate side-chains 247 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 191 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 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 355 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 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 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 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 253 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS 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 75 HIS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 191 GLN A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.187863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126280 restraints weight = 17069.838| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.36 r_work: 0.3492 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13788 Z= 0.162 Angle : 0.605 9.807 18626 Z= 0.309 Chirality : 0.047 0.230 1916 Planarity : 0.004 0.046 2508 Dihedral : 4.980 56.848 1792 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.33 % Allowed : 26.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1648 helix: 1.60 (0.24), residues: 480 sheet: 1.03 (0.29), residues: 328 loop : -0.99 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 126 HIS 0.008 0.001 HIS H 99 PHE 0.020 0.002 PHE A 262 TYR 0.030 0.002 TYR B 208 ARG 0.010 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 624) hydrogen bonds : angle 4.40341 ( 1902) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.13481 ( 8) covalent geometry : bond 0.00378 (13784) covalent geometry : angle 0.60495 (18618) *********************** 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 275 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 198 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: A 216 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 294 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8482 (mp0) REVERT: A 329 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7058 (mtp-110) REVERT: A 347 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: A 350 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6691 (ptp90) REVERT: B 78 ASP cc_start: 0.8009 (t0) cc_final: 0.7758 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8373 (tt0) cc_final: 0.8043 (pt0) REVERT: B 177 ASP cc_start: 0.8191 (t0) cc_final: 0.7880 (t0) REVERT: B 179 GLN cc_start: 0.8318 (tp-100) cc_final: 0.7943 (tp-100) REVERT: B 202 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7558 (mtt-85) REVERT: B 224 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7569 (mptp) REVERT: B 330 GLU cc_start: 0.6798 (tp30) cc_final: 0.6217 (tp30) REVERT: C 116 GLU cc_start: 0.8216 (tp30) cc_final: 0.7992 (tp30) REVERT: C 120 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7414 (mp) REVERT: C 122 ASP cc_start: 0.7050 (m-30) cc_final: 0.6489 (m-30) REVERT: D 67 MET cc_start: 0.6834 (mmt) cc_final: 0.6149 (tpt) REVERT: D 70 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: E 79 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8625 (pt0) REVERT: E 191 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7741 (mt0) REVERT: E 294 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8479 (mp0) REVERT: E 329 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7114 (mtp-110) REVERT: E 344 GLU cc_start: 0.8144 (tp30) cc_final: 0.7628 (tp30) REVERT: E 350 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6800 (ptp90) REVERT: F 78 ASP cc_start: 0.8028 (t0) cc_final: 0.7772 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: F 179 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: F 202 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7576 (mtt-85) REVERT: F 224 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7519 (mptp) REVERT: F 330 GLU cc_start: 0.6716 (tp30) cc_final: 0.6169 (tp30) REVERT: G 113 SER cc_start: 0.8606 (m) cc_final: 0.8285 (t) REVERT: G 120 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7379 (mp) REVERT: G 122 ASP cc_start: 0.7015 (m-30) cc_final: 0.6455 (m-30) REVERT: H 67 MET cc_start: 0.6839 (mmt) cc_final: 0.6151 (tpt) REVERT: H 70 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7897 (tm-30) outliers start: 77 outliers final: 42 residues processed: 248 average time/residue: 1.0187 time to fit residues: 280.0350 Evaluate side-chains 252 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 ILE 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 A residue 347 GLN Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 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 253 LEU Chi-restraints excluded: chain B residue 268 THR 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 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 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 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 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 179 GLN 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 253 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 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 75 HIS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 32 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 chunk 91 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.189996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128018 restraints weight = 17019.069| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.40 r_work: 0.3519 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2907 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= 0.120 Angle : 0.591 9.738 18626 Z= 0.301 Chirality : 0.046 0.261 1916 Planarity : 0.004 0.047 2508 Dihedral : 4.780 54.694 1792 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.22 % Allowed : 27.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1648 helix: 1.74 (0.24), residues: 472 sheet: 1.03 (0.29), residues: 340 loop : -0.85 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 126 HIS 0.007 0.001 HIS D 99 PHE 0.020 0.001 PHE A 296 TYR 0.030 0.002 TYR B 208 ARG 0.011 0.001 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 624) hydrogen bonds : angle 4.28369 ( 1902) SS BOND : bond 0.00191 ( 4) SS BOND : angle 0.94589 ( 8) covalent geometry : bond 0.00271 (13784) covalent geometry : angle 0.59130 (18618) *********************** 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: 61 poor density : 196 time to evaluate : 1.407 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 191 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7741 (mt0) REVERT: A 294 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8446 (mp0) REVERT: A 329 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6996 (mtp-110) REVERT: A 350 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6661 (ptp90) REVERT: B 78 ASP cc_start: 0.7988 (t0) cc_final: 0.7752 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8367 (tt0) cc_final: 0.8049 (pt0) REVERT: B 177 ASP cc_start: 0.8174 (t0) cc_final: 0.7858 (t0) REVERT: B 179 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7929 (tp-100) REVERT: B 202 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7497 (mtt-85) REVERT: B 224 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7590 (mptp) REVERT: B 330 GLU cc_start: 0.6766 (tp30) cc_final: 0.6169 (tp30) REVERT: B 350 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7446 (mtm180) REVERT: C 116 GLU cc_start: 0.8202 (tp30) cc_final: 0.7982 (tp30) REVERT: C 120 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7311 (mp) REVERT: C 122 ASP cc_start: 0.6997 (m-30) cc_final: 0.6452 (m-30) REVERT: D 67 MET cc_start: 0.6765 (mmt) cc_final: 0.6266 (tpt) REVERT: E 79 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8574 (pt0) REVERT: E 191 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7737 (mt0) REVERT: E 294 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8451 (mp0) REVERT: E 297 GLN cc_start: 0.7195 (mp10) cc_final: 0.6828 (mp-120) REVERT: E 329 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7009 (mtp-110) REVERT: E 344 GLU cc_start: 0.8112 (tp30) cc_final: 0.7660 (tp30) REVERT: E 350 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6836 (ptp90) REVERT: F 78 ASP cc_start: 0.7996 (t0) cc_final: 0.7750 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: F 179 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7369 (tp40) REVERT: F 202 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7515 (mtt-85) REVERT: F 224 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7568 (mptp) REVERT: F 330 GLU cc_start: 0.6748 (tp30) cc_final: 0.6159 (tp30) REVERT: G 47 HIS cc_start: 0.7574 (m-70) cc_final: 0.6565 (m-70) REVERT: G 113 SER cc_start: 0.8609 (m) cc_final: 0.8344 (t) REVERT: G 114 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: G 120 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7399 (mp) REVERT: G 122 ASP cc_start: 0.6999 (m-30) cc_final: 0.6444 (m-30) REVERT: H 67 MET cc_start: 0.6691 (mmt) cc_final: 0.6100 (tpt) REVERT: H 70 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: H 127 ASP cc_start: 0.7700 (p0) cc_final: 0.7241 (t70) outliers start: 61 outliers final: 35 residues processed: 242 average time/residue: 1.0028 time to fit residues: 269.5873 Evaluate side-chains 242 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 237 ILE Chi-restraints excluded: chain B residue 268 THR 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 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain 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 105 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 GLN 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 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 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 75 HIS Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN H 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.187299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124725 restraints weight = 17117.329| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.43 r_work: 0.3476 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13788 Z= 0.207 Angle : 0.652 9.314 18626 Z= 0.335 Chirality : 0.049 0.268 1916 Planarity : 0.004 0.053 2508 Dihedral : 5.085 56.393 1792 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.94 % Allowed : 27.80 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1648 helix: 1.57 (0.24), residues: 476 sheet: 0.88 (0.29), residues: 340 loop : -0.96 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 126 HIS 0.007 0.001 HIS D 99 PHE 0.025 0.002 PHE E 262 TYR 0.032 0.002 TYR B 208 ARG 0.011 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 624) hydrogen bonds : angle 4.54072 ( 1902) SS BOND : bond 0.00261 ( 4) SS BOND : angle 1.24780 ( 8) covalent geometry : bond 0.00489 (13784) covalent geometry : angle 0.65130 (18618) ********************** 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 253 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: A 294 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8472 (mp0) REVERT: A 329 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7125 (mtp-110) REVERT: B 78 ASP cc_start: 0.8069 (t0) cc_final: 0.7825 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8407 (tt0) cc_final: 0.8053 (pt0) REVERT: B 177 ASP cc_start: 0.8221 (t0) cc_final: 0.7920 (t0) REVERT: B 179 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8025 (tp-100) REVERT: B 224 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7637 (mptp) REVERT: B 330 GLU cc_start: 0.6789 (tp30) cc_final: 0.6233 (tp30) REVERT: C 120 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7347 (mp) REVERT: C 122 ASP cc_start: 0.7141 (m-30) cc_final: 0.6578 (m-30) REVERT: D 67 MET cc_start: 0.6865 (mmt) cc_final: 0.6132 (tpt) REVERT: E 79 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: E 191 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7789 (mt0) REVERT: E 294 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8458 (mp0) REVERT: E 329 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7142 (mtp-110) REVERT: E 344 GLU cc_start: 0.8026 (tp30) cc_final: 0.7613 (tp30) REVERT: E 350 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6806 (ptp90) REVERT: F 78 ASP cc_start: 0.8088 (t0) cc_final: 0.7836 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: F 179 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7327 (tp40) REVERT: F 202 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7553 (mtt-85) REVERT: F 224 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7598 (mptp) REVERT: F 330 GLU cc_start: 0.6781 (tp30) cc_final: 0.6222 (tp30) REVERT: G 47 HIS cc_start: 0.7517 (m-70) cc_final: 0.6587 (m-70) REVERT: G 113 SER cc_start: 0.8620 (m) cc_final: 0.8353 (t) REVERT: G 120 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7401 (mp) REVERT: G 122 ASP cc_start: 0.7080 (m-30) cc_final: 0.6498 (m-30) REVERT: H 67 MET cc_start: 0.6674 (mmt) cc_final: 0.6185 (tpt) REVERT: H 71 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7536 (pm20) REVERT: H 127 ASP cc_start: 0.7680 (p0) cc_final: 0.7214 (t70) outliers start: 57 outliers final: 37 residues processed: 238 average time/residue: 1.0419 time to fit residues: 277.1469 Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 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 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 237 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 355 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 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain 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 105 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 GLN 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 237 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 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 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.188981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.126637 restraints weight = 17175.205| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.43 r_work: 0.3503 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3030 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= 0.144 Angle : 0.622 9.272 18626 Z= 0.316 Chirality : 0.047 0.252 1916 Planarity : 0.004 0.055 2508 Dihedral : 4.896 54.990 1792 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.67 % Allowed : 28.28 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1648 helix: 1.67 (0.24), residues: 472 sheet: 0.92 (0.29), residues: 340 loop : -0.85 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 126 HIS 0.007 0.001 HIS D 99 PHE 0.022 0.002 PHE A 296 TYR 0.031 0.002 TYR B 208 ARG 0.013 0.001 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 624) hydrogen bonds : angle 4.39728 ( 1902) SS BOND : bond 0.00126 ( 4) SS BOND : angle 1.04577 ( 8) covalent geometry : bond 0.00333 (13784) covalent geometry : angle 0.62175 (18618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13669.69 seconds wall clock time: 235 minutes 5.27 seconds (14105.27 seconds total)