Starting phenix.real_space_refine on Thu Jul 31 07:45:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp5_36468/07_2025/8jp5_36468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp5_36468/07_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_36468/07_2025/8jp5_36468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp5_36468/07_2025/8jp5_36468.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp5_36468/07_2025/8jp5_36468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp5_36468/07_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-5711/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: 9.38, per 1000 atoms: 0.70 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: 3.41 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: 1.59 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: 4.24 Time building geometry restraints manager: 4.02 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: 0.720 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.730 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.020 ------------------------------------------------------------------------------- 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 : 1.392 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: 0.9701 time to fit residues: 320.0548 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 : 1.492 ------------------------------------------------------------------------------- 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 = 63)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129031 restraints weight = 16822.633| |-----------------------------------------------------------------------------| 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: 0.3395 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 1.467 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: 0.8358 (tm-30) cc_final: 0.7610 (mt0) REVERT: A 294 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8401 (mp0) REVERT: A 329 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7058 (ttp80) REVERT: A 344 GLU cc_start: 0.8164 (tp30) cc_final: 0.7774 (tp30) REVERT: B 78 ASP cc_start: 0.7937 (t0) cc_final: 0.7683 (t0) REVERT: B 105 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8212 (pt0) REVERT: B 177 ASP cc_start: 0.8034 (t0) cc_final: 0.7673 (t0) REVERT: B 330 GLU cc_start: 0.6697 (tp30) cc_final: 0.6124 (tp30) REVERT: B 336 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7364 (mm-30) REVERT: B 354 MET cc_start: 0.6791 (ttm) cc_final: 0.6578 (ptm) REVERT: C 122 ASP cc_start: 0.6879 (m-30) cc_final: 0.6387 (m-30) REVERT: C 144 SER cc_start: 0.7057 (OUTLIER) cc_final: 0.6851 (p) REVERT: D 99 HIS cc_start: 0.6847 (OUTLIER) cc_final: 0.6481 (m-70) REVERT: D 114 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6945 (tp30) REVERT: D 127 ASP cc_start: 0.7210 (p0) cc_final: 0.7006 (p0) REVERT: E 191 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7588 (mt0) REVERT: E 294 GLU cc_start: 0.8860 (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: 0.8207 (tp30) cc_final: 0.7819 (tp30) REVERT: F 78 ASP cc_start: 0.7942 (t0) cc_final: 0.7671 (t0) REVERT: F 105 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: F 179 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7853 (tp-100) REVERT: F 330 GLU cc_start: 0.6668 (tp30) cc_final: 0.6120 (tp30) REVERT: F 336 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7463 (mm-30) REVERT: F 352 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7248 (tt) REVERT: G 113 SER cc_start: 0.8514 (m) cc_final: 0.8103 (t) REVERT: G 122 ASP cc_start: 0.6851 (m-30) cc_final: 0.6403 (m-30) REVERT: H 99 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6505 (m-70) REVERT: H 114 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6940 (tp30) outliers start: 78 outliers final: 29 residues processed: 272 average time/residue: 1.0832 time to fit residues: 326.4914 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 : 1.435 ------------------------------------------------------------------------------- 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: 0.0670 chunk 90 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 87 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.191800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.130718 restraints weight = 16894.830| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.40 r_work: 0.3550 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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= 0.108 Angle : 0.536 7.702 18626 Z= 0.278 Chirality : 0.045 0.160 1916 Planarity : 0.003 0.045 2508 Dihedral : 5.641 56.198 1808 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.39 % Allowed : 23.72 % 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: 0.39 (0.21), residues: 1648 helix: 1.34 (0.24), residues: 486 sheet: 1.39 (0.29), residues: 336 loop : -0.91 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 126 HIS 0.005 0.001 HIS G 47 PHE 0.013 0.001 PHE A 296 TYR 0.022 0.001 TYR D 76 ARG 0.004 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 624) hydrogen bonds : angle 4.35801 ( 1902) SS BOND : bond 0.00111 ( 4) SS BOND : angle 1.03933 ( 8) covalent geometry : bond 0.00232 (13784) covalent geometry : angle 0.53590 (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 304 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 226 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: A 215 MET cc_start: 0.8006 (mtm) cc_final: 0.7768 (mmm) REVERT: A 294 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8449 (mp0) REVERT: A 329 ARG cc_start: 0.7500 (ttm110) cc_final: 0.7073 (ttp80) REVERT: A 344 GLU cc_start: 0.8151 (tp30) cc_final: 0.7856 (tp30) REVERT: A 350 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6949 (ptp90) REVERT: B 78 ASP cc_start: 0.7923 (t0) cc_final: 0.7675 (t0) REVERT: B 105 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: B 177 ASP cc_start: 0.8009 (t0) cc_final: 0.7687 (t0) REVERT: B 202 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7420 (mtt-85) REVERT: B 224 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7678 (mptp) REVERT: B 226 ASP cc_start: 0.7398 (t70) cc_final: 0.6811 (t0) REVERT: B 264 THR cc_start: 0.8154 (m) cc_final: 0.7894 (m) REVERT: B 330 GLU cc_start: 0.6703 (tp30) cc_final: 0.6104 (tp30) REVERT: B 336 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7434 (mm-30) REVERT: B 352 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7258 (tt) REVERT: C 47 HIS cc_start: 0.7781 (m-70) cc_final: 0.6913 (m-70) REVERT: C 49 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8172 (tp-100) REVERT: C 120 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7365 (mp) REVERT: C 122 ASP cc_start: 0.6853 (m-30) cc_final: 0.6351 (m-30) REVERT: D 67 MET cc_start: 0.6932 (mmt) cc_final: 0.6582 (tpt) REVERT: D 99 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.6388 (m-70) REVERT: D 114 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6921 (tp30) REVERT: E 191 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: E 215 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7855 (mmm) REVERT: E 294 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8467 (mp0) REVERT: E 297 GLN cc_start: 0.7397 (mp10) cc_final: 0.6995 (mp10) REVERT: E 329 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7077 (ttp80) REVERT: E 344 GLU cc_start: 0.8186 (tp30) cc_final: 0.7920 (tp30) REVERT: F 78 ASP cc_start: 0.7950 (t0) cc_final: 0.7690 (t0) REVERT: F 105 GLU cc_start: 0.8435 (tt0) cc_final: 0.8179 (pt0) REVERT: F 202 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7420 (mtt-85) REVERT: F 224 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7706 (mptp) REVERT: F 264 THR cc_start: 0.8139 (m) cc_final: 0.7882 (m) REVERT: F 330 GLU cc_start: 0.6632 (tp30) cc_final: 0.6063 (tp30) REVERT: F 336 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7367 (mm-30) REVERT: F 352 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7230 (tt) REVERT: G 47 HIS cc_start: 0.7793 (m-70) cc_final: 0.6896 (m-70) REVERT: G 49 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8192 (tp-100) REVERT: G 62 LYS cc_start: 0.9154 (ttpp) cc_final: 0.8064 (mptp) REVERT: G 113 SER cc_start: 0.8548 (m) cc_final: 0.8138 (t) REVERT: G 120 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7301 (mp) REVERT: G 122 ASP cc_start: 0.6864 (m-30) cc_final: 0.6385 (m-30) REVERT: H 67 MET cc_start: 0.6934 (mmt) cc_final: 0.6419 (tpt) REVERT: H 99 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6420 (m-70) outliers start: 78 outliers final: 19 residues processed: 282 average time/residue: 1.0202 time to fit residues: 319.1779 Evaluate side-chains 241 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 59 VAL Chi-restraints excluded: chain D residue 99 HIS 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 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 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: 0.0870 chunk 145 optimal weight: 10.0000 chunk 105 optimal weight: 0.0050 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: 1.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.4178 ------------------------------------------------------------------------------- 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 217 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS C 80 HIS C 119 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 ASN F 338 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 HIS G 80 HIS G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.190211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.128133 restraints weight = 16741.733| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.40 r_work: 0.3516 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2335 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= 0.144 Angle : 0.572 9.190 18626 Z= 0.295 Chirality : 0.046 0.175 1916 Planarity : 0.004 0.046 2508 Dihedral : 5.217 59.577 1796 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.05 % Allowed : 25.03 % Favored : 69.92 % 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: 1.44 (0.24), residues: 482 sheet: 1.38 (0.29), residues: 336 loop : -0.96 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.004 0.001 HIS G 47 PHE 0.019 0.002 PHE A 262 TYR 0.021 0.002 TYR H 76 ARG 0.004 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 624) hydrogen bonds : angle 4.32331 ( 1902) SS BOND : bond 0.00157 ( 4) SS BOND : angle 1.17613 ( 8) covalent geometry : bond 0.00332 (13784) covalent geometry : angle 0.57169 (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 276 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 203 time to evaluate : 1.593 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: 0.8392 (OUTLIER) cc_final: 0.7658 (mt0) REVERT: A 294 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8497 (mp0) REVERT: A 297 GLN cc_start: 0.7376 (mp10) cc_final: 0.6911 (mp10) REVERT: A 329 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7134 (ttp80) REVERT: A 344 GLU cc_start: 0.8177 (tp30) cc_final: 0.7870 (tp30) REVERT: A 350 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6873 (ptp90) REVERT: B 78 ASP cc_start: 0.7969 (t0) cc_final: 0.7706 (t0) REVERT: B 105 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: B 177 ASP cc_start: 0.8065 (t0) cc_final: 0.7756 (t0) REVERT: B 224 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7726 (mptp) REVERT: B 330 GLU cc_start: 0.6726 (tp30) cc_final: 0.6138 (tp30) REVERT: B 336 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7565 (mt-10) REVERT: B 352 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7331 (tt) REVERT: C 120 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7320 (mp) REVERT: C 122 ASP cc_start: 0.6908 (m-30) cc_final: 0.6416 (m-30) REVERT: D 70 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: D 71 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7674 (mp0) REVERT: D 99 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.6431 (m-70) REVERT: D 114 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6956 (tp30) REVERT: E 79 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8369 (pt0) REVERT: E 191 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: E 258 ASP cc_start: 0.8148 (m-30) cc_final: 0.7864 (m-30) REVERT: E 294 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8436 (mp0) REVERT: E 329 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7155 (ttp80) REVERT: E 344 GLU cc_start: 0.8173 (tp30) cc_final: 0.7888 (tp30) REVERT: F 78 ASP cc_start: 0.7972 (t0) cc_final: 0.7708 (t0) REVERT: F 105 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: F 179 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7457 (tp40) REVERT: F 224 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7714 (mptp) REVERT: F 330 GLU cc_start: 0.6747 (tp30) cc_final: 0.6133 (tp30) REVERT: F 336 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7481 (mm-30) REVERT: G 47 HIS cc_start: 0.7762 (m-70) cc_final: 0.6852 (m-70) REVERT: G 49 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8224 (tp-100) REVERT: G 113 SER cc_start: 0.8569 (m) cc_final: 0.8218 (t) REVERT: G 120 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7312 (mp) REVERT: G 122 ASP cc_start: 0.6853 (m-30) cc_final: 0.6360 (m-30) REVERT: H 70 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: H 99 HIS cc_start: 0.6799 (OUTLIER) cc_final: 0.6503 (m-70) outliers start: 73 outliers final: 29 residues processed: 253 average time/residue: 1.3417 time to fit residues: 376.9200 Evaluate side-chains 244 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 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 E residue 79 GLN Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 324 GLU 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 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 49 GLN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 99 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 115 optimal weight: 0.0270 chunk 141 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- 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 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.190858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129036 restraints weight = 16858.580| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.40 r_work: 0.3527 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13788 Z= 0.119 Angle : 0.560 9.939 18626 Z= 0.283 Chirality : 0.045 0.191 1916 Planarity : 0.003 0.049 2508 Dihedral : 5.099 59.396 1796 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.84 % Allowed : 25.73 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.21), residues: 1648 helix: 1.54 (0.24), residues: 484 sheet: 1.36 (0.29), residues: 336 loop : -0.90 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.003 0.001 HIS G 47 PHE 0.016 0.001 PHE A 262 TYR 0.024 0.002 TYR F 208 ARG 0.004 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 624) hydrogen bonds : angle 4.20888 ( 1902) SS BOND : bond 0.00123 ( 4) SS BOND : angle 1.06097 ( 8) covalent geometry : bond 0.00268 (13784) covalent geometry : angle 0.56015 (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 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 201 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: A 191 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: A 294 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8447 (mp0) REVERT: A 329 ARG cc_start: 0.7571 (ttm110) cc_final: 0.7087 (ttp80) REVERT: A 350 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6770 (ptp90) REVERT: B 78 ASP cc_start: 0.7955 (t0) cc_final: 0.7690 (t0) REVERT: B 105 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8107 (pt0) REVERT: B 177 ASP cc_start: 0.8060 (t0) cc_final: 0.7722 (t0) REVERT: B 202 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7418 (mtt-85) REVERT: B 224 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7610 (mptp) REVERT: B 330 GLU cc_start: 0.6695 (tp30) cc_final: 0.6082 (tp30) REVERT: B 336 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 47 HIS cc_start: 0.7762 (m-70) cc_final: 0.6835 (m-70) REVERT: C 115 ASP cc_start: 0.7109 (p0) cc_final: 0.6788 (m-30) REVERT: C 120 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7355 (mp) REVERT: C 122 ASP cc_start: 0.6913 (m-30) cc_final: 0.6406 (m-30) REVERT: D 70 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: D 71 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7927 (mt-10) REVERT: E 79 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8548 (pt0) REVERT: E 191 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: E 294 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8401 (mp0) REVERT: E 329 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7107 (ttp80) REVERT: E 344 GLU cc_start: 0.8113 (tp30) cc_final: 0.7854 (tp30) REVERT: F 78 ASP cc_start: 0.7980 (t0) cc_final: 0.7709 (t0) REVERT: F 105 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: F 179 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7432 (tp40) REVERT: F 202 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7411 (mtt-85) REVERT: F 224 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7667 (mptp) REVERT: F 330 GLU cc_start: 0.6680 (tp30) cc_final: 0.6048 (tp30) REVERT: F 336 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7596 (mt-10) REVERT: G 43 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6630 (tptt) REVERT: G 47 HIS cc_start: 0.7757 (m-70) cc_final: 0.6841 (m-70) REVERT: G 113 SER cc_start: 0.8551 (m) cc_final: 0.8220 (t) REVERT: G 120 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7314 (mp) REVERT: G 122 ASP cc_start: 0.6857 (m-30) cc_final: 0.6396 (m-30) outliers start: 70 outliers final: 29 residues processed: 251 average time/residue: 1.2184 time to fit residues: 339.4097 Evaluate side-chains 244 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 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 72 LEU 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 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 191 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE 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 43 LYS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 135 optimal weight: 0.7980 chunk 151 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.3180 ------------------------------------------------------------------------------- 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 162 ASN B 179 GLN B 217 ASN B 338 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 217 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.190187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127624 restraints weight = 17145.793| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.42 r_work: 0.3513 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13788 Z= 0.137 Angle : 0.573 9.168 18626 Z= 0.293 Chirality : 0.046 0.176 1916 Planarity : 0.003 0.049 2508 Dihedral : 4.841 59.869 1792 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.12 % Allowed : 26.07 % 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: 0.49 (0.21), residues: 1648 helix: 1.64 (0.24), residues: 482 sheet: 1.27 (0.29), residues: 338 loop : -0.91 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.008 0.001 HIS H 99 PHE 0.018 0.002 PHE E 262 TYR 0.028 0.002 TYR F 208 ARG 0.005 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 624) hydrogen bonds : angle 4.20568 ( 1902) SS BOND : bond 0.00163 ( 4) SS BOND : angle 1.11084 ( 8) covalent geometry : bond 0.00315 (13784) covalent geometry : angle 0.57254 (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 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 197 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: A 191 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: A 218 ASN cc_start: 0.8092 (m-40) cc_final: 0.7884 (m-40) REVERT: A 294 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8495 (mp0) REVERT: A 344 GLU cc_start: 0.8212 (tp30) cc_final: 0.7689 (tp30) REVERT: A 350 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6620 (ptp90) REVERT: B 78 ASP cc_start: 0.7984 (t0) cc_final: 0.7714 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: B 177 ASP cc_start: 0.8091 (t0) cc_final: 0.7775 (t0) REVERT: B 202 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7455 (mtt-85) REVERT: B 224 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7641 (mptp) REVERT: B 330 GLU cc_start: 0.6731 (tp30) cc_final: 0.6154 (tp30) REVERT: B 336 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 47 HIS cc_start: 0.7740 (m-70) cc_final: 0.6842 (m-70) REVERT: C 120 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7360 (mp) REVERT: C 122 ASP cc_start: 0.6934 (m-30) cc_final: 0.6433 (m-30) REVERT: D 67 MET cc_start: 0.6974 (mmt) cc_final: 0.6332 (tpt) REVERT: D 70 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: E 79 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: E 191 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: E 258 ASP cc_start: 0.8186 (m-30) cc_final: 0.7936 (m-30) REVERT: E 294 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8462 (mp0) REVERT: E 344 GLU cc_start: 0.8100 (tp30) cc_final: 0.7886 (tp30) REVERT: F 78 ASP cc_start: 0.7991 (t0) cc_final: 0.7721 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: F 179 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7578 (tp40) REVERT: F 202 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7435 (mtt-85) REVERT: F 224 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7658 (mptp) REVERT: F 330 GLU cc_start: 0.6697 (tp30) cc_final: 0.6081 (tp30) REVERT: F 336 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7658 (mt-10) REVERT: G 113 SER cc_start: 0.8556 (m) cc_final: 0.8233 (t) REVERT: G 120 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7315 (mp) REVERT: G 122 ASP cc_start: 0.6939 (m-30) cc_final: 0.6442 (m-30) outliers start: 74 outliers final: 38 residues processed: 247 average time/residue: 1.1514 time to fit residues: 315.2542 Evaluate side-chains 243 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 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 355 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 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 D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 324 GLU 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 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 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 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: 2.9990 chunk 8 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124473 restraints weight = 17110.500| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.43 r_work: 0.3472 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13788 Z= 0.215 Angle : 0.641 9.977 18626 Z= 0.331 Chirality : 0.049 0.209 1916 Planarity : 0.004 0.045 2508 Dihedral : 5.177 59.842 1792 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.26 % Allowed : 26.00 % Favored : 68.74 % 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: 0.29 (0.21), residues: 1648 helix: 1.46 (0.24), residues: 482 sheet: 1.15 (0.29), residues: 328 loop : -0.99 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 126 HIS 0.008 0.001 HIS H 99 PHE 0.027 0.002 PHE E 262 TYR 0.030 0.002 TYR F 208 ARG 0.007 0.001 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 624) hydrogen bonds : angle 4.53874 ( 1902) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.31681 ( 8) covalent geometry : bond 0.00506 (13784) covalent geometry : angle 0.64010 (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 274 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 198 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8403 (pt0) REVERT: A 191 GLN cc_start: 0.8593 (tm-30) cc_final: 0.7797 (mt0) REVERT: A 294 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8458 (mp0) REVERT: A 329 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7088 (mtp-110) REVERT: A 344 GLU cc_start: 0.8162 (tp30) cc_final: 0.7941 (tp30) REVERT: B 78 ASP cc_start: 0.8003 (t0) cc_final: 0.7764 (OUTLIER) REVERT: B 177 ASP cc_start: 0.8178 (t0) cc_final: 0.7877 (t0) REVERT: B 179 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7849 (tp-100) REVERT: B 224 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7645 (mptp) REVERT: B 330 GLU cc_start: 0.6792 (tp30) cc_final: 0.6137 (tp30) REVERT: B 336 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 116 GLU cc_start: 0.8165 (tp30) cc_final: 0.7927 (tp30) REVERT: C 120 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7398 (mp) REVERT: C 122 ASP cc_start: 0.7064 (m-30) cc_final: 0.6510 (m-30) REVERT: D 67 MET cc_start: 0.7043 (mmt) cc_final: 0.6689 (mmt) REVERT: D 70 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: E 79 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8580 (pt0) REVERT: E 191 GLN cc_start: 0.8577 (tm-30) cc_final: 0.7790 (mt0) REVERT: E 294 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8473 (mp0) REVERT: E 297 GLN cc_start: 0.7308 (mp10) cc_final: 0.6997 (mp-120) REVERT: E 329 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7149 (mtp-110) REVERT: E 344 GLU cc_start: 0.8198 (tp30) cc_final: 0.7952 (tp30) REVERT: F 78 ASP cc_start: 0.8022 (t0) cc_final: 0.7779 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8103 (pt0) REVERT: F 224 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7640 (mptp) REVERT: F 330 GLU cc_start: 0.6781 (tp30) cc_final: 0.6134 (tp30) REVERT: G 49 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8265 (tp-100) REVERT: G 113 SER cc_start: 0.8581 (m) cc_final: 0.8240 (t) REVERT: G 120 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7377 (mp) REVERT: G 122 ASP cc_start: 0.7094 (m-30) cc_final: 0.6573 (m-30) outliers start: 76 outliers final: 37 residues processed: 249 average time/residue: 1.1231 time to fit residues: 308.6033 Evaluate side-chains 237 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain 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 179 GLN 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 52 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 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 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 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 49 GLN Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** 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 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.189451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127864 restraints weight = 17005.381| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.38 r_work: 0.3514 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2801 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= 0.129 Angle : 0.585 9.405 18626 Z= 0.297 Chirality : 0.046 0.223 1916 Planarity : 0.003 0.048 2508 Dihedral : 4.871 57.397 1792 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.36 % Allowed : 26.69 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.24), residues: 484 sheet: 1.10 (0.29), residues: 338 loop : -0.93 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 126 HIS 0.008 0.001 HIS H 99 PHE 0.019 0.001 PHE E 296 TYR 0.030 0.002 TYR F 208 ARG 0.010 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 624) hydrogen bonds : angle 4.29776 ( 1902) SS BOND : bond 0.00137 ( 4) SS BOND : angle 1.04222 ( 8) covalent geometry : bond 0.00295 (13784) covalent geometry : angle 0.58499 (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 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 1.327 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: 0.8794 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: A 191 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7758 (mt0) REVERT: A 294 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8487 (mp0) REVERT: A 297 GLN cc_start: 0.7401 (mp10) cc_final: 0.6968 (mp-120) REVERT: A 329 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7063 (mtp-110) REVERT: A 344 GLU cc_start: 0.8091 (tp30) cc_final: 0.7584 (tp30) REVERT: B 78 ASP cc_start: 0.7992 (t0) cc_final: 0.7739 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8406 (tt0) cc_final: 0.8063 (pt0) REVERT: B 177 ASP cc_start: 0.8136 (t0) cc_final: 0.7775 (t0) REVERT: B 224 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7610 (mptp) REVERT: B 330 GLU cc_start: 0.6727 (tp30) cc_final: 0.6115 (tp30) REVERT: B 336 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7698 (mt-10) REVERT: C 116 GLU cc_start: 0.8154 (tp30) cc_final: 0.7908 (tp30) REVERT: C 120 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7369 (mp) REVERT: C 122 ASP cc_start: 0.7042 (m-30) cc_final: 0.6517 (m-30) REVERT: D 67 MET cc_start: 0.6920 (mmt) cc_final: 0.6108 (tpt) REVERT: D 70 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: E 79 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8535 (pt0) REVERT: E 191 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7738 (mt0) REVERT: E 294 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8415 (mp0) REVERT: E 329 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7029 (mtp-110) REVERT: F 78 ASP cc_start: 0.7986 (t0) cc_final: 0.7727 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: F 179 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: F 202 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7509 (mtt-85) REVERT: F 224 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7566 (mptp) REVERT: F 330 GLU cc_start: 0.6766 (tp30) cc_final: 0.6161 (tp30) REVERT: G 47 HIS cc_start: 0.7788 (m-70) cc_final: 0.6862 (m-70) REVERT: G 113 SER cc_start: 0.8574 (m) cc_final: 0.8237 (t) REVERT: G 120 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7324 (mp) REVERT: G 122 ASP cc_start: 0.7039 (m-30) cc_final: 0.6532 (m-30) REVERT: H 67 MET cc_start: 0.6691 (mmt) cc_final: 0.6359 (mmt) outliers start: 63 outliers final: 38 residues processed: 243 average time/residue: 1.0169 time to fit residues: 274.8089 Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain 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 329 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 72 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 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: 0.0070 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 41 optimal weight: 0.0670 chunk 91 optimal weight: 0.0770 chunk 111 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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** ** 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 ** 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 = 0.4327 r_free = 0.4327 target = 0.191117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129234 restraints weight = 16947.218| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.41 r_work: 0.3535 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13788 Z= 0.108 Angle : 0.581 9.707 18626 Z= 0.293 Chirality : 0.046 0.257 1916 Planarity : 0.004 0.053 2508 Dihedral : 4.715 55.458 1792 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.94 % Allowed : 27.59 % 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: 0.49 (0.21), residues: 1648 helix: 1.69 (0.24), residues: 482 sheet: 1.13 (0.29), residues: 338 loop : -0.88 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 126 HIS 0.007 0.001 HIS F 178 PHE 0.019 0.001 PHE A 296 TYR 0.031 0.002 TYR B 208 ARG 0.011 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 624) hydrogen bonds : angle 4.19608 ( 1902) SS BOND : bond 0.00106 ( 4) SS BOND : angle 1.01275 ( 8) covalent geometry : bond 0.00241 (13784) covalent geometry : angle 0.58045 (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 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 199 time to evaluate : 1.543 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: 0.8736 (OUTLIER) cc_final: 0.8514 (pt0) REVERT: A 191 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7654 (mt0) REVERT: A 294 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8447 (mp0) REVERT: A 344 GLU cc_start: 0.8034 (tp30) cc_final: 0.7636 (tp30) REVERT: B 56 HIS cc_start: 0.7791 (m-70) cc_final: 0.7586 (m-70) REVERT: B 78 ASP cc_start: 0.7964 (t0) cc_final: 0.7708 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8412 (tt0) cc_final: 0.8120 (pt0) REVERT: B 177 ASP cc_start: 0.8160 (t0) cc_final: 0.7816 (t0) REVERT: B 202 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7502 (mtt-85) REVERT: B 224 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7596 (mptp) REVERT: B 330 GLU cc_start: 0.6693 (tp30) cc_final: 0.6083 (tp30) REVERT: B 336 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7673 (mt-10) REVERT: B 350 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7126 (mpp80) REVERT: C 47 HIS cc_start: 0.7758 (m-70) cc_final: 0.6883 (m-70) REVERT: C 49 GLN cc_start: 0.8642 (tp40) cc_final: 0.8262 (tp-100) REVERT: C 120 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7274 (mp) REVERT: C 122 ASP cc_start: 0.7016 (m-30) cc_final: 0.6500 (m-30) REVERT: D 67 MET cc_start: 0.6835 (mmt) cc_final: 0.6066 (tpt) REVERT: D 70 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: E 79 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: E 191 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7643 (mt0) REVERT: E 294 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8417 (mp0) REVERT: F 78 ASP cc_start: 0.7972 (t0) cc_final: 0.7707 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8431 (tt0) cc_final: 0.8091 (pt0) REVERT: F 179 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7485 (tp40) REVERT: F 202 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7496 (mtt-85) REVERT: F 224 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7598 (mptp) REVERT: F 330 GLU cc_start: 0.6726 (tp30) cc_final: 0.6128 (tp30) REVERT: F 350 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7353 (mtm180) REVERT: G 113 SER cc_start: 0.8591 (m) cc_final: 0.8255 (t) REVERT: G 120 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7325 (mp) REVERT: G 122 ASP cc_start: 0.7009 (m-30) cc_final: 0.6500 (m-30) REVERT: H 67 MET cc_start: 0.6682 (mmt) cc_final: 0.6258 (tpt) outliers start: 57 outliers final: 37 residues processed: 244 average time/residue: 1.0725 time to fit residues: 289.9987 Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain 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 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 230 CYS Chi-restraints excluded: chain E residue 307 PHE 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 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 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 134 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 179 GLN ** B 359 GLN ** 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.188838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126035 restraints weight = 17046.029| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.43 r_work: 0.3492 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13788 Z= 0.175 Angle : 0.627 9.682 18626 Z= 0.320 Chirality : 0.048 0.270 1916 Planarity : 0.004 0.046 2508 Dihedral : 4.964 56.722 1792 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.67 % Allowed : 28.08 % 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: 0.38 (0.21), residues: 1648 helix: 1.61 (0.24), residues: 482 sheet: 1.05 (0.28), residues: 340 loop : -0.94 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 67 HIS 0.007 0.001 HIS D 99 PHE 0.022 0.002 PHE E 262 TYR 0.031 0.002 TYR B 208 ARG 0.011 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 624) hydrogen bonds : angle 4.38992 ( 1902) SS BOND : bond 0.00232 ( 4) SS BOND : angle 1.18481 ( 8) covalent geometry : bond 0.00411 (13784) covalent geometry : angle 0.62715 (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 247 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 1.517 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: 0.8859 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: A 191 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: A 294 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8476 (mp0) REVERT: A 297 GLN cc_start: 0.7370 (mp10) cc_final: 0.6974 (mp-120) REVERT: A 329 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7107 (mtp-110) REVERT: A 344 GLU cc_start: 0.8045 (tp30) cc_final: 0.7691 (tp30) REVERT: B 56 HIS cc_start: 0.7807 (m-70) cc_final: 0.7606 (m-70) REVERT: B 78 ASP cc_start: 0.7980 (t0) cc_final: 0.7729 (OUTLIER) REVERT: B 105 GLU cc_start: 0.8402 (tt0) cc_final: 0.8110 (pt0) REVERT: B 177 ASP cc_start: 0.8177 (t0) cc_final: 0.7823 (t0) REVERT: B 179 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7617 (tp40) REVERT: B 202 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7557 (mtt-85) REVERT: B 224 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7534 (mptp) REVERT: B 330 GLU cc_start: 0.6730 (tp30) cc_final: 0.6187 (tp30) REVERT: B 336 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7696 (mt-10) REVERT: C 120 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7239 (mp) REVERT: C 122 ASP cc_start: 0.7146 (m-30) cc_final: 0.6553 (m-30) REVERT: D 67 MET cc_start: 0.6796 (mmt) cc_final: 0.6059 (tpt) REVERT: D 70 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: E 79 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: E 191 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7775 (mt0) REVERT: E 258 ASP cc_start: 0.8183 (m-30) cc_final: 0.7893 (m-30) REVERT: E 294 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8430 (mp0) REVERT: E 329 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7103 (mtp-110) REVERT: F 78 ASP cc_start: 0.7990 (t0) cc_final: 0.7760 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8422 (tt0) cc_final: 0.8080 (pt0) REVERT: F 179 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7401 (tp40) REVERT: F 202 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7536 (mtt-85) REVERT: F 224 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7552 (mptp) REVERT: F 330 GLU cc_start: 0.6786 (tp30) cc_final: 0.6183 (tp30) REVERT: F 350 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7345 (mtm180) REVERT: G 113 SER cc_start: 0.8615 (m) cc_final: 0.8285 (t) REVERT: G 120 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7330 (mp) REVERT: G 122 ASP cc_start: 0.7038 (m-30) cc_final: 0.6481 (m-30) REVERT: H 67 MET cc_start: 0.6668 (mmt) cc_final: 0.6266 (tpt) outliers start: 53 outliers final: 33 residues processed: 232 average time/residue: 1.5602 time to fit residues: 404.3437 Evaluate side-chains 237 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 2.082 ------------------------------------------------------------------------------- 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 B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain 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 230 CYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 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 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: 5.9990 chunk 124 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 179 GLN ** B 359 GLN ** 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 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.188654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125989 restraints weight = 17140.230| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.43 r_work: 0.3494 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 13788 Z= 0.243 Angle : 0.988 59.200 18626 Z= 0.587 Chirality : 0.053 0.977 1916 Planarity : 0.006 0.155 2508 Dihedral : 4.967 56.702 1792 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.87 % Allowed : 28.22 % Favored : 67.91 % Cbeta Deviations : 0.13 % 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: 0.34 (0.21), residues: 1648 helix: 1.61 (0.24), residues: 482 sheet: 1.03 (0.29), residues: 328 loop : -0.97 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 67 HIS 0.006 0.001 HIS D 99 PHE 0.022 0.002 PHE E 262 TYR 0.028 0.002 TYR B 208 ARG 0.008 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 624) hydrogen bonds : angle 4.39464 ( 1902) SS BOND : bond 0.00163 ( 4) SS BOND : angle 1.20873 ( 8) covalent geometry : bond 0.00539 (13784) covalent geometry : angle 0.98813 (18618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15419.56 seconds wall clock time: 272 minutes 56.54 seconds (16376.54 seconds total)