Starting phenix.real_space_refine on Sun Nov 17 08:14:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp5_36468/11_2024/8jp5_36468.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp5_36468/11_2024/8jp5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp5_36468/11_2024/8jp5_36468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp5_36468/11_2024/8jp5_36468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp5_36468/11_2024/8jp5_36468.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp5_36468/11_2024/8jp5_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-5513/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: 7.82, per 1000 atoms: 0.58 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=2, 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 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: 3.18 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: 1.42 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: 4.01 Time building geometry restraints manager: 3.64 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: 6915 16.46 - 32.91: 934 32.91 - 49.37: 284 49.37 - 65.82: 83 65.82 - 82.28: 22 Dihedral angle restraints: 8238 sinusoidal: 3424 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 8235 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: 32 2.20 - 2.87: 5059 2.87 - 3.55: 18491 3.55 - 4.22: 32111 4.22 - 4.90: 55388 Nonbonded interactions: 111081 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 111076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'B' selection = (chain 'E' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 41 through 101 or resid 108 through 144 or resid 701 throu \ gh 703)) selection = chain 'D' selection = (chain 'G' and (resid 41 through 101 or resid 108 through 144 or resid 701 throu \ gh 703)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.390 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.920 ------------------------------------------------------------------------------- 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 13784 Z= 0.162 Angle : 0.580 10.146 18618 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 *********************** 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 : 1.416 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: 1.0670 time to fit residues: 351.9261 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 : 1.780 ------------------------------------------------------------------------------- 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: 8.9990 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: 1.5786 ------------------------------------------------------------------------------- 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 339 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 339 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13784 Z= 0.239 Angle : 0.584 9.838 18618 Z= 0.307 Chirality : 0.046 0.161 1916 Planarity : 0.004 0.039 2508 Dihedral : 6.549 59.653 1828 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.81 % Allowed : 22.48 % 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: 0.22 (0.21), residues: 1648 helix: 1.17 (0.24), residues: 482 sheet: 1.30 (0.29), residues: 338 loop : -1.00 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.004 0.001 HIS D 80 PHE 0.021 0.002 PHE A 262 TYR 0.023 0.002 TYR H 76 ARG 0.005 0.001 ARG B 350 *********************** 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 303 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 219 time to evaluate : 1.420 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: 0.8111 (tm-30) cc_final: 0.7522 (mt0) REVERT: A 294 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8327 (mp0) REVERT: A 329 ARG cc_start: 0.7328 (ttm110) cc_final: 0.6792 (ttp80) REVERT: A 344 GLU cc_start: 0.7868 (tp30) cc_final: 0.7607 (tp30) REVERT: B 105 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: B 330 GLU cc_start: 0.6743 (tp30) cc_final: 0.6191 (tp30) REVERT: B 336 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7493 (mm-30) REVERT: C 122 ASP cc_start: 0.6950 (m-30) cc_final: 0.6600 (m-30) REVERT: D 99 HIS cc_start: 0.6720 (OUTLIER) cc_final: 0.6472 (m-70) REVERT: E 191 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: E 294 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8348 (mp0) REVERT: E 329 ARG cc_start: 0.7344 (ttm110) cc_final: 0.6807 (ttp80) REVERT: E 344 GLU cc_start: 0.7935 (tp30) cc_final: 0.7638 (tp30) REVERT: F 78 ASP cc_start: 0.7541 (t0) cc_final: 0.7341 (t0) REVERT: F 105 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: F 179 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7539 (tp-100) REVERT: F 330 GLU cc_start: 0.6739 (tp30) cc_final: 0.6184 (tp30) REVERT: F 336 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7480 (mm-30) REVERT: F 352 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7525 (tt) REVERT: G 113 SER cc_start: 0.8627 (m) cc_final: 0.8249 (t) REVERT: G 122 ASP cc_start: 0.6918 (m-30) cc_final: 0.6584 (m-30) REVERT: H 99 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.6496 (m-70) outliers start: 84 outliers final: 31 residues processed: 275 average time/residue: 1.0810 time to fit residues: 330.2204 Evaluate side-chains 245 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 211 THR 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 45 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 0.0030 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- 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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 217 ASN B 338 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 119 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13784 Z= 0.316 Angle : 0.617 9.247 18618 Z= 0.324 Chirality : 0.048 0.176 1916 Planarity : 0.004 0.046 2508 Dihedral : 6.057 55.441 1807 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 6.78 % Allowed : 22.75 % Favored : 70.47 % 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: 1.20 (0.24), residues: 482 sheet: 1.14 (0.29), residues: 340 loop : -0.97 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 126 HIS 0.005 0.001 HIS H 55 PHE 0.025 0.002 PHE E 262 TYR 0.023 0.002 TYR H 76 ARG 0.003 0.000 ARG F 350 *********************** 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: 98 poor density : 206 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8431 (pt0) REVERT: A 191 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: A 294 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8347 (mp0) REVERT: A 329 ARG cc_start: 0.7437 (ttm110) cc_final: 0.6887 (ttp80) REVERT: A 344 GLU cc_start: 0.7957 (tp30) cc_final: 0.7686 (tp30) REVERT: A 350 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6674 (ptp90) REVERT: B 179 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7372 (tp-100) REVERT: B 224 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7818 (mptp) REVERT: B 330 GLU cc_start: 0.6772 (tp30) cc_final: 0.6254 (tp30) REVERT: B 336 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 352 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7635 (tt) REVERT: C 47 HIS cc_start: 0.7514 (m-70) cc_final: 0.6677 (m-70) REVERT: C 62 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8102 (mptp) REVERT: C 120 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7500 (mp) REVERT: C 122 ASP cc_start: 0.7071 (m-30) cc_final: 0.6694 (m-30) REVERT: D 70 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: D 99 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.6563 (m-70) REVERT: E 79 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: E 191 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: E 218 ASN cc_start: 0.8288 (m-40) cc_final: 0.8072 (m-40) REVERT: E 294 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8279 (mp0) REVERT: E 329 ARG cc_start: 0.7440 (ttm110) cc_final: 0.6891 (ttp80) REVERT: E 344 GLU cc_start: 0.7964 (tp30) cc_final: 0.7678 (tp30) REVERT: F 78 ASP cc_start: 0.7641 (t0) cc_final: 0.7432 (OUTLIER) REVERT: F 224 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7815 (mptp) REVERT: F 330 GLU cc_start: 0.6768 (tp30) cc_final: 0.6249 (tp30) REVERT: F 336 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7508 (mt-10) REVERT: F 352 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7619 (tt) REVERT: G 47 HIS cc_start: 0.7669 (m-70) cc_final: 0.6783 (m-70) REVERT: G 49 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8127 (tp-100) REVERT: G 62 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8141 (mptp) REVERT: G 113 SER cc_start: 0.8633 (m) cc_final: 0.8264 (t) REVERT: G 120 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7431 (mp) REVERT: G 122 ASP cc_start: 0.7032 (m-30) cc_final: 0.6650 (m-30) REVERT: H 67 MET cc_start: 0.7235 (mmt) cc_final: 0.6736 (tpt) REVERT: H 99 HIS cc_start: 0.6821 (OUTLIER) cc_final: 0.6577 (m-70) outliers start: 98 outliers final: 37 residues processed: 272 average time/residue: 1.1107 time to fit residues: 334.0200 Evaluate side-chains 243 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 VAL 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 352 LEU Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS 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 115 ASP Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 217 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 119 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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 G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13784 Z= 0.377 Angle : 0.661 10.279 18618 Z= 0.345 Chirality : 0.049 0.183 1916 Planarity : 0.004 0.050 2508 Dihedral : 5.753 58.064 1797 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.71 % Allowed : 24.27 % Favored : 69.02 % 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: 0.07 (0.21), residues: 1648 helix: 1.15 (0.23), residues: 482 sheet: 1.08 (0.30), residues: 318 loop : -1.05 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 126 HIS 0.004 0.001 HIS E 56 PHE 0.027 0.002 PHE A 262 TYR 0.023 0.002 TYR H 76 ARG 0.004 0.000 ARG F 350 *********************** 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 297 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 200 time to evaluate : 1.519 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 79 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: A 191 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7658 (mt0) REVERT: A 294 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8356 (mp0) REVERT: A 297 GLN cc_start: 0.7385 (mp10) cc_final: 0.6991 (mp10) REVERT: A 344 GLU cc_start: 0.7942 (tp30) cc_final: 0.7674 (tp30) REVERT: A 350 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6596 (ptp90) REVERT: B 105 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: B 224 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7700 (mptp) REVERT: B 330 GLU cc_start: 0.6770 (tp30) cc_final: 0.6283 (tp30) REVERT: B 352 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7713 (tt) REVERT: C 120 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7585 (mp) REVERT: C 122 ASP cc_start: 0.7189 (m-30) cc_final: 0.6705 (m-30) REVERT: D 70 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: D 99 HIS cc_start: 0.6762 (OUTLIER) cc_final: 0.6548 (m-70) REVERT: E 79 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8449 (pt0) REVERT: E 191 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: E 294 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8385 (mp0) REVERT: E 297 GLN cc_start: 0.7282 (mp10) cc_final: 0.6842 (mp10) REVERT: E 344 GLU cc_start: 0.7962 (tp30) cc_final: 0.7687 (tp30) REVERT: F 78 ASP cc_start: 0.7627 (t0) cc_final: 0.7413 (OUTLIER) REVERT: F 105 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: F 179 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7587 (tp-100) REVERT: F 224 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7694 (mptp) REVERT: F 330 GLU cc_start: 0.6796 (tp30) cc_final: 0.6293 (tp30) REVERT: F 352 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7678 (tt) REVERT: G 49 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8127 (tp-100) REVERT: G 113 SER cc_start: 0.8641 (m) cc_final: 0.8294 (t) REVERT: G 120 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7567 (mp) REVERT: G 122 ASP cc_start: 0.7127 (m-30) cc_final: 0.6652 (m-30) REVERT: H 70 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7611 (tm-30) outliers start: 97 outliers final: 42 residues processed: 259 average time/residue: 1.1566 time to fit residues: 331.0118 Evaluate side-chains 249 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 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 354 MET Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.8980 chunk 89 optimal weight: 0.0000 chunk 2 optimal weight: 0.5980 chunk 118 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 119 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13784 Z= 0.161 Angle : 0.572 10.306 18618 Z= 0.291 Chirality : 0.045 0.160 1916 Planarity : 0.003 0.048 2508 Dihedral : 5.069 57.292 1795 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.88 % Allowed : 25.10 % Favored : 69.02 % 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: 0.37 (0.21), residues: 1648 helix: 1.42 (0.24), residues: 484 sheet: 1.10 (0.28), residues: 338 loop : -0.86 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 126 HIS 0.011 0.001 HIS H 99 PHE 0.016 0.001 PHE A 296 TYR 0.025 0.002 TYR B 208 ARG 0.004 0.000 ARG F 350 *********************** 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 286 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 201 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 79 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8668 (pt0) REVERT: A 191 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7535 (mt0) REVERT: A 215 MET cc_start: 0.7939 (mtm) cc_final: 0.7656 (mmm) REVERT: A 294 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8391 (mp0) REVERT: A 297 GLN cc_start: 0.7345 (mp10) cc_final: 0.7033 (mp10) REVERT: A 329 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6486 (mtp-110) REVERT: A 350 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6487 (ptp90) REVERT: B 105 GLU cc_start: 0.8047 (pt0) cc_final: 0.7782 (pt0) REVERT: B 179 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7255 (tp40) REVERT: B 202 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7412 (mtt-85) REVERT: B 224 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7650 (mptp) REVERT: B 330 GLU cc_start: 0.6756 (tp30) cc_final: 0.6157 (tp30) REVERT: B 336 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7521 (mt-10) REVERT: B 352 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7647 (tt) REVERT: C 47 HIS cc_start: 0.6992 (m-70) cc_final: 0.6231 (m-70) REVERT: C 114 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: C 120 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7434 (mp) REVERT: C 122 ASP cc_start: 0.7034 (m-30) cc_final: 0.6589 (m-30) REVERT: D 70 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: E 79 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8672 (pt0) REVERT: E 191 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7734 (mt0) REVERT: E 294 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8361 (mp0) REVERT: E 297 GLN cc_start: 0.7277 (mp10) cc_final: 0.6934 (mp10) REVERT: E 329 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6764 (mtp-110) REVERT: F 105 GLU cc_start: 0.8065 (pt0) cc_final: 0.7797 (pt0) REVERT: F 202 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7406 (mtt-85) REVERT: F 224 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7645 (mptp) REVERT: F 330 GLU cc_start: 0.6763 (tp30) cc_final: 0.6162 (tp30) REVERT: F 352 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7650 (tt) REVERT: G 113 SER cc_start: 0.8683 (m) cc_final: 0.8356 (t) REVERT: G 120 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7460 (mp) REVERT: G 122 ASP cc_start: 0.7027 (m-30) cc_final: 0.6592 (m-30) outliers start: 85 outliers final: 30 residues processed: 260 average time/residue: 1.0989 time to fit residues: 315.7627 Evaluate side-chains 239 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 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 352 LEU Chi-restraints excluded: chain B residue 354 MET 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 114 GLU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain F residue 78 ASP 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 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** C 80 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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 G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13784 Z= 0.310 Angle : 0.632 9.559 18618 Z= 0.327 Chirality : 0.048 0.180 1916 Planarity : 0.004 0.047 2508 Dihedral : 5.081 59.593 1791 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 6.43 % Allowed : 24.83 % 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: 0.28 (0.21), residues: 1648 helix: 1.54 (0.24), residues: 476 sheet: 1.05 (0.29), residues: 328 loop : -1.00 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 126 HIS 0.009 0.001 HIS D 99 PHE 0.023 0.002 PHE A 262 TYR 0.028 0.002 TYR B 208 ARG 0.005 0.000 ARG F 350 *********************** 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 296 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 203 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8429 (pt0) REVERT: A 191 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7658 (mt0) REVERT: A 294 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8389 (mp0) REVERT: A 329 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6398 (mtp-110) REVERT: A 344 GLU cc_start: 0.8026 (tp30) cc_final: 0.7504 (tp30) REVERT: A 350 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6425 (ptp90) REVERT: B 105 GLU cc_start: 0.8067 (pt0) cc_final: 0.7788 (pt0) REVERT: B 204 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8417 (mtmt) REVERT: B 224 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7661 (mptp) REVERT: B 330 GLU cc_start: 0.6799 (tp30) cc_final: 0.6240 (tp30) REVERT: C 47 HIS cc_start: 0.7043 (m-70) cc_final: 0.6246 (m-70) REVERT: C 120 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7471 (mp) REVERT: C 122 ASP cc_start: 0.7179 (m-30) cc_final: 0.6737 (m-30) REVERT: D 70 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: E 79 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8429 (pt0) REVERT: E 191 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: E 294 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8419 (mp0) REVERT: E 297 GLN cc_start: 0.7325 (mt0) cc_final: 0.7037 (mp10) REVERT: E 329 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6820 (mtp-110) REVERT: E 344 GLU cc_start: 0.7972 (tp30) cc_final: 0.7511 (tp30) REVERT: E 350 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6466 (ptp90) REVERT: F 105 GLU cc_start: 0.8065 (pt0) cc_final: 0.7787 (pt0) REVERT: F 204 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8428 (mtmt) REVERT: F 224 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7729 (mptp) REVERT: F 330 GLU cc_start: 0.6826 (tp30) cc_final: 0.6249 (tp30) REVERT: F 352 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7641 (tt) REVERT: G 113 SER cc_start: 0.8669 (m) cc_final: 0.8362 (t) REVERT: G 120 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7544 (mp) REVERT: G 122 ASP cc_start: 0.7130 (m-30) cc_final: 0.6661 (m-30) outliers start: 93 outliers final: 36 residues processed: 262 average time/residue: 1.1098 time to fit residues: 320.8642 Evaluate side-chains 250 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 204 LYS 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 354 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 179 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 178 HIS E 235 ASN E 338 GLN E 347 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 G 119 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13784 Z= 0.211 Angle : 0.605 10.298 18618 Z= 0.309 Chirality : 0.046 0.260 1916 Planarity : 0.004 0.045 2508 Dihedral : 4.930 58.721 1791 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.63 % Allowed : 26.69 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1648 helix: 1.54 (0.24), residues: 478 sheet: 1.10 (0.29), residues: 326 loop : -0.97 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 126 HIS 0.008 0.001 HIS D 99 PHE 0.017 0.002 PHE A 296 TYR 0.029 0.002 TYR B 208 ARG 0.006 0.000 ARG F 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 197 time to evaluate : 1.626 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: 0.8974 (OUTLIER) cc_final: 0.8585 (pt0) REVERT: A 191 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: A 215 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7755 (mmm) REVERT: A 294 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8385 (mp0) REVERT: A 307 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7169 (t80) REVERT: A 329 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6732 (mtp-110) REVERT: B 202 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7485 (mtt-85) REVERT: B 224 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7632 (mptp) REVERT: B 330 GLU cc_start: 0.6792 (tp30) cc_final: 0.6191 (tp30) REVERT: C 47 HIS cc_start: 0.6951 (m-70) cc_final: 0.6277 (m-70) REVERT: C 62 LYS cc_start: 0.8916 (ttpp) cc_final: 0.8410 (mptp) REVERT: C 120 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7459 (mp) REVERT: C 122 ASP cc_start: 0.7160 (m-30) cc_final: 0.6704 (m-30) REVERT: E 79 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8590 (pt0) REVERT: E 191 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: E 294 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8396 (mp0) REVERT: E 329 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6790 (mtp-110) REVERT: E 344 GLU cc_start: 0.7940 (tp30) cc_final: 0.7494 (tp30) REVERT: E 350 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6551 (ptp90) REVERT: F 105 GLU cc_start: 0.8013 (pt0) cc_final: 0.7813 (pt0) REVERT: F 202 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7480 (mtt-85) REVERT: F 224 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7648 (mptp) REVERT: F 330 GLU cc_start: 0.6835 (tp30) cc_final: 0.6229 (tp30) REVERT: F 352 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7595 (tt) REVERT: G 113 SER cc_start: 0.8704 (m) cc_final: 0.8397 (t) REVERT: G 120 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7511 (mp) REVERT: G 122 ASP cc_start: 0.7093 (m-30) cc_final: 0.6625 (m-30) REVERT: H 67 MET cc_start: 0.7156 (mmt) cc_final: 0.6823 (mmt) outliers start: 67 outliers final: 30 residues processed: 238 average time/residue: 1.1346 time to fit residues: 297.8636 Evaluate side-chains 239 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 215 MET 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 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 354 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 179 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13784 Z= 0.187 Angle : 0.593 10.009 18618 Z= 0.304 Chirality : 0.046 0.271 1916 Planarity : 0.004 0.046 2508 Dihedral : 4.816 59.829 1791 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.91 % Allowed : 26.83 % 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: 0.40 (0.21), residues: 1648 helix: 1.63 (0.24), residues: 474 sheet: 1.02 (0.28), residues: 338 loop : -0.89 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 126 HIS 0.007 0.001 HIS D 99 PHE 0.019 0.001 PHE A 296 TYR 0.030 0.002 TYR B 208 ARG 0.010 0.000 ARG B 350 *********************** 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 272 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 1.463 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: 0.8946 (OUTLIER) cc_final: 0.8701 (pt0) REVERT: A 191 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: A 294 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8381 (mp0) REVERT: A 329 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6714 (mtp-110) REVERT: A 344 GLU cc_start: 0.7968 (tp30) cc_final: 0.7731 (tp30) REVERT: B 105 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7800 (pt0) REVERT: B 179 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7273 (tp40) REVERT: B 202 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7459 (mtt-85) REVERT: B 224 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7692 (mptp) REVERT: B 330 GLU cc_start: 0.6746 (tp30) cc_final: 0.6152 (tp30) REVERT: C 47 HIS cc_start: 0.6841 (m-70) cc_final: 0.6206 (m-70) REVERT: C 114 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: C 120 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7458 (mp) REVERT: C 122 ASP cc_start: 0.7211 (m-30) cc_final: 0.6756 (m-30) REVERT: E 79 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8713 (pt0) REVERT: E 191 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7717 (mt0) REVERT: E 294 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8364 (mp0) REVERT: E 329 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6750 (mtp-110) REVERT: E 344 GLU cc_start: 0.7896 (tp30) cc_final: 0.7479 (tp30) REVERT: E 350 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6604 (ptp90) REVERT: F 105 GLU cc_start: 0.7963 (pt0) cc_final: 0.7711 (pt0) REVERT: F 179 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7096 (tp40) REVERT: F 202 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7448 (mtt-85) REVERT: F 224 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7666 (mptp) REVERT: F 330 GLU cc_start: 0.6752 (tp30) cc_final: 0.6145 (tp30) REVERT: F 352 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7529 (tt) REVERT: G 47 HIS cc_start: 0.7340 (m-70) cc_final: 0.6578 (m-70) REVERT: G 113 SER cc_start: 0.8691 (m) cc_final: 0.8490 (t) REVERT: G 120 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7397 (mp) REVERT: G 122 ASP cc_start: 0.7088 (m-30) cc_final: 0.6625 (m-30) REVERT: H 67 MET cc_start: 0.7100 (mmt) cc_final: 0.6655 (tpt) REVERT: H 70 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7722 (tm-30) outliers start: 71 outliers final: 31 residues processed: 252 average time/residue: 1.1599 time to fit residues: 325.1079 Evaluate side-chains 241 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 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 354 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 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 268 THR Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 133 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN E 338 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 13784 Z= 0.543 Angle : 0.756 9.498 18618 Z= 0.396 Chirality : 0.053 0.310 1916 Planarity : 0.005 0.049 2508 Dihedral : 5.482 55.074 1791 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.91 % Allowed : 27.39 % Favored : 67.70 % 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: -0.16 (0.21), residues: 1648 helix: 1.15 (0.23), residues: 480 sheet: 0.73 (0.29), residues: 320 loop : -1.21 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 67 HIS 0.008 0.001 HIS H 99 PHE 0.033 0.003 PHE E 262 TYR 0.032 0.003 TYR F 208 ARG 0.010 0.001 ARG B 350 *********************** 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 266 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 195 time to evaluate : 1.775 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 79 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: A 191 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: A 294 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8385 (mp0) REVERT: A 307 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 105 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: B 179 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7680 (tp-100) REVERT: B 204 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8483 (mtmt) REVERT: B 224 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7686 (mptp) REVERT: C 62 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8426 (mptt) REVERT: C 120 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7546 (mp) REVERT: E 79 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: E 191 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: E 294 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8373 (mp0) REVERT: E 329 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6754 (mtp-110) REVERT: E 344 GLU cc_start: 0.7908 (tp30) cc_final: 0.7449 (tp30) REVERT: E 350 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6380 (ptp90) REVERT: F 105 GLU cc_start: 0.8027 (pt0) cc_final: 0.7774 (pt0) REVERT: F 179 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7729 (tp-100) REVERT: F 204 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8477 (mtmt) REVERT: F 224 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7681 (mptp) REVERT: F 352 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7543 (tt) REVERT: G 113 SER cc_start: 0.8717 (m) cc_final: 0.8423 (t) REVERT: G 120 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7483 (mp) REVERT: G 122 ASP cc_start: 0.7368 (m-30) cc_final: 0.6889 (m-30) REVERT: H 67 MET cc_start: 0.7104 (mmt) cc_final: 0.6722 (tpt) REVERT: H 70 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: H 114 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6993 (tp30) outliers start: 71 outliers final: 36 residues processed: 242 average time/residue: 1.1542 time to fit residues: 308.0453 Evaluate side-chains 243 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 204 LYS 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 354 MET 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 71 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 80 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13784 Z= 0.322 Angle : 0.680 9.601 18618 Z= 0.350 Chirality : 0.049 0.268 1916 Planarity : 0.004 0.047 2508 Dihedral : 5.201 54.861 1791 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.39 % Allowed : 29.39 % Favored : 67.22 % 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: -0.06 (0.21), residues: 1648 helix: 1.26 (0.24), residues: 482 sheet: 0.57 (0.28), residues: 342 loop : -1.12 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 126 HIS 0.009 0.001 HIS D 99 PHE 0.023 0.002 PHE E 262 TYR 0.032 0.002 TYR B 208 ARG 0.013 0.001 ARG F 350 ********************** 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 245 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 1.834 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: 0.9009 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: A 191 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7630 (mt0) REVERT: A 294 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8383 (mp0) REVERT: A 307 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6848 (t80) REVERT: B 105 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: B 204 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8491 (mtmt) REVERT: B 224 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7632 (mptp) REVERT: B 330 GLU cc_start: 0.6781 (tp30) cc_final: 0.6166 (tp30) REVERT: C 62 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8447 (mptt) REVERT: C 114 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: C 120 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7537 (mp) REVERT: E 79 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8487 (pt0) REVERT: E 191 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7661 (mt0) REVERT: E 294 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8376 (mp0) REVERT: E 329 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6778 (mtp-110) REVERT: E 344 GLU cc_start: 0.7692 (tp30) cc_final: 0.7394 (tp30) REVERT: E 350 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6511 (ptp90) REVERT: F 179 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7550 (tp-100) REVERT: F 204 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8445 (mtmt) REVERT: F 224 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7650 (mptp) REVERT: F 330 GLU cc_start: 0.6797 (tp30) cc_final: 0.6186 (tp30) REVERT: F 352 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7655 (tt) REVERT: F 359 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6259 (tt0) REVERT: G 113 SER cc_start: 0.8679 (m) cc_final: 0.8453 (t) REVERT: G 115 ASP cc_start: 0.7141 (p0) cc_final: 0.6941 (p0) REVERT: G 120 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7483 (mp) REVERT: G 122 ASP cc_start: 0.7291 (m-30) cc_final: 0.6768 (m-30) REVERT: H 67 MET cc_start: 0.7122 (mmt) cc_final: 0.6780 (tpt) REVERT: H 70 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7713 (tm-30) outliers start: 49 outliers final: 33 residues processed: 234 average time/residue: 1.1415 time to fit residues: 295.1815 Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 204 LYS 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 354 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 179 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS E 235 ASN ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.188704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126999 restraints weight = 16971.447| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.42 r_work: 0.3508 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13784 Z= 0.191 Angle : 0.621 9.495 18618 Z= 0.318 Chirality : 0.046 0.266 1916 Planarity : 0.004 0.046 2508 Dihedral : 4.879 55.849 1791 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.32 % Allowed : 29.74 % Favored : 66.94 % 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: 0.18 (0.21), residues: 1648 helix: 1.51 (0.24), residues: 474 sheet: 0.71 (0.28), residues: 340 loop : -0.98 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 126 HIS 0.007 0.001 HIS H 99 PHE 0.022 0.001 PHE A 296 TYR 0.031 0.002 TYR F 208 ARG 0.012 0.001 ARG F 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5648.13 seconds wall clock time: 101 minutes 38.31 seconds (6098.31 seconds total)