Starting phenix.real_space_refine on Thu Jul 31 17:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2j_42916/07_2025/8v2j_42916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2j_42916/07_2025/8v2j_42916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2j_42916/07_2025/8v2j_42916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2j_42916/07_2025/8v2j_42916.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2j_42916/07_2025/8v2j_42916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2j_42916/07_2025/8v2j_42916.cif" } resolution = 2.9 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= 0.000 sd= 0.001 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 P 10 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 8537 2.51 5 N 2305 2.21 5 O 2634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13580 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3332 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 3334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3334 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3398 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3394 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.86, per 1000 atoms: 0.73 Number of scatterers: 13580 At special positions: 0 Unit cell: (74.7, 78.435, 191.73, 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) S 92 16.00 P 10 15.00 Mg 2 11.99 O 2634 8.00 N 2305 7.00 C 8537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 55.2% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.128A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.709A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.640A pdb=" N SER B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.319A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.620A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.061A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.906A pdb=" N TYR B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.709A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.564A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 392 removed outlier: 4.085A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.971A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.907A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 40 through 46 removed outlier: 4.134A pdb=" N LEU E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 108 through 127 removed outlier: 4.812A pdb=" N ASP E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 159 removed outlier: 3.625A pdb=" N SER E 145 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 196 removed outlier: 4.666A pdb=" N GLU E 194 " --> pdb=" O HIS E 190 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN E 195 " --> pdb=" O GLN E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 214 Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.703A pdb=" N LEU E 225 " --> pdb=" O THR E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.833A pdb=" N ARG E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.166A pdb=" N TYR E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 324 through 337 Processing helix chain 'E' and resid 338 through 341 Processing helix chain 'E' and resid 373 through 391 removed outlier: 3.935A pdb=" N LEU E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 401 removed outlier: 3.995A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 401 " --> pdb=" O TRP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 428 removed outlier: 3.877A pdb=" N PHE E 408 " --> pdb=" O ASP E 404 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 426 " --> pdb=" O TYR E 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 44 through 51 removed outlier: 4.042A pdb=" N SER A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 108 through 129 removed outlier: 3.884A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.659A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.649A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.104A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.608A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.909A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.065A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.891A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 44 through 51 removed outlier: 3.775A pdb=" N SER D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 82 through 85 removed outlier: 4.429A pdb=" N GLN D 85 " --> pdb=" O THR D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 82 through 85' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.197A pdb=" N ILE D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 128 " --> pdb=" O LYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 4.607A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.597A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.174A pdb=" N TYR D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.747A pdb=" N PHE D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 297 " --> pdb=" O ASN D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 338 removed outlier: 3.619A pdb=" N VAL D 328 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 401 removed outlier: 3.837A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.954A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 411 " --> pdb=" O TRP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 436 removed outlier: 3.730A pdb=" N PHE D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.315A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'E' and resid 90 through 92 removed outlier: 8.162A pdb=" N VAL E 91 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU E 65 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ILE E 64 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS E 6 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL E 66 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN E 8 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU E 3 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY E 132 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL E 5 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER E 138 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASN E 165 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE E 133 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE E 167 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU E 135 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL E 169 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N HIS E 137 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR E 199 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N CYS E 201 " --> pdb=" O PRO E 268 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N PHE E 270 " --> pdb=" O CYS E 201 " (cutoff:3.500A) removed outlier: 13.187A pdb=" N ASP E 203 " --> pdb=" O PHE E 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.851A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N SER A 165 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.769A pdb=" N ILE D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE D 67 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N VAL D 66 " --> pdb=" O CYS D 4 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL D 68 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HIS D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU D 3 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU D 136 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE D 5 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE D 138 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE D 7 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER D 140 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N VAL D 9 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN D 133 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE D 135 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE D 171 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS D 139 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS D 166 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE D 202 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU D 168 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL D 204 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER D 170 " --> pdb=" O VAL D 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'D' and resid 272 through 273 678 hydrogen bonds defined for protein. 2007 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: 4.48 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4412 1.34 - 1.46: 3143 1.46 - 1.58: 6174 1.58 - 1.71: 17 1.71 - 1.83: 144 Bond restraints: 13890 Sorted by residual: bond pdb=" N TYR E 310 " pdb=" CA TYR E 310 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N VAL E 313 " pdb=" CA VAL E 313 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.80e+00 bond pdb=" N SER E 322 " pdb=" CA SER E 322 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.27e-02 6.20e+03 9.11e+00 bond pdb=" N ASP A 46 " pdb=" CA ASP A 46 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.73e+00 bond pdb=" N MET E 323 " pdb=" CA MET E 323 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.42e+00 ... (remaining 13885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 18289 2.41 - 4.81: 490 4.81 - 7.22: 102 7.22 - 9.62: 6 9.62 - 12.03: 2 Bond angle restraints: 18889 Sorted by residual: angle pdb=" CA ILE D 219 " pdb=" C ILE D 219 " pdb=" O ILE D 219 " ideal model delta sigma weight residual 121.68 117.01 4.67 7.90e-01 1.60e+00 3.49e+01 angle pdb=" N LYS E 324 " pdb=" CA LYS E 324 " pdb=" C LYS E 324 " ideal model delta sigma weight residual 113.18 106.89 6.29 1.33e+00 5.65e-01 2.23e+01 angle pdb=" CB MET E 406 " pdb=" CG MET E 406 " pdb=" SD MET E 406 " ideal model delta sigma weight residual 112.70 124.73 -12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CA ARG D 221 " pdb=" C ARG D 221 " pdb=" N PRO D 222 " ideal model delta sigma weight residual 117.78 121.90 -4.12 1.06e+00 8.90e-01 1.51e+01 angle pdb=" CB MET A 203 " pdb=" CG MET A 203 " pdb=" SD MET A 203 " ideal model delta sigma weight residual 112.70 124.21 -11.51 3.00e+00 1.11e-01 1.47e+01 ... (remaining 18884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.51: 7895 31.51 - 63.01: 289 63.01 - 94.52: 32 94.52 - 126.02: 1 126.02 - 157.53: 6 Dihedral angle restraints: 8223 sinusoidal: 3233 harmonic: 4990 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -133.20 -157.53 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5' GTP D 501 " pdb=" O5' GTP D 501 " pdb=" PA GTP D 501 " pdb=" O3A GTP D 501 " ideal model delta sinusoidal sigma weight residual 69.27 -133.45 -157.28 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O5' GTP D 501 " pdb=" O3A GTP D 501 " pdb=" PA GTP D 501 " pdb=" PB GTP D 501 " ideal model delta sinusoidal sigma weight residual 274.12 139.23 134.89 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 8220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1627 0.059 - 0.118: 373 0.118 - 0.177: 74 0.177 - 0.236: 3 0.236 - 0.295: 1 Chirality restraints: 2078 Sorted by residual: chirality pdb=" CA ILE D 219 " pdb=" N ILE D 219 " pdb=" C ILE D 219 " pdb=" CB ILE D 219 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LYS E 324 " pdb=" N LYS E 324 " pdb=" C LYS E 324 " pdb=" CB LYS E 324 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA VAL E 313 " pdb=" N VAL E 313 " pdb=" C VAL E 313 " pdb=" CB VAL E 313 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 2075 not shown) Planarity restraints: 2463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 273 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO A 274 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 218 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C ASP D 218 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP D 218 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE D 219 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 128 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" CG ASP B 128 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP B 128 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 128 " -0.016 2.00e-02 2.50e+03 ... (remaining 2460 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 85 2.56 - 3.14: 10839 3.14 - 3.73: 22247 3.73 - 4.31: 31147 4.31 - 4.90: 52203 Nonbonded interactions: 116521 Sorted by model distance: nonbonded pdb=" O1G GTP D 501 " pdb="MG MG D 502 " model vdw 1.970 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 1.996 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 2.004 2.170 nonbonded pdb=" O2B GTP D 501 " pdb="MG MG D 502 " model vdw 2.024 2.170 nonbonded pdb=" OE2 GLU D 71 " pdb="MG MG D 502 " model vdw 2.030 2.170 ... (remaining 116516 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 1 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 441 or resid 501 through 502)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 1 through 335 or (resid 336 and (name N or name CA or name \ C or name O or name CB )) or resid 337 through 429 or resid 501)) selection = (chain 'E' and (resid 1 through 281 or (resid 282 through 283 and (name N or nam \ e CA or name C or name O or name CB )) or resid 284 through 429 or resid 501)) } 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: 8.120 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.710 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 0.006 0.068 13890 Z= 0.282 Angle : 0.953 12.025 18889 Z= 0.515 Chirality : 0.052 0.295 2078 Planarity : 0.006 0.075 2463 Dihedral : 16.662 157.528 5027 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.42 % Allowed : 14.67 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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 (0.20), residues: 1720 helix: 0.93 (0.18), residues: 776 sheet: -0.81 (0.33), residues: 244 loop : -0.53 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 397 HIS 0.010 0.001 HIS B 37 PHE 0.026 0.002 PHE E 81 TYR 0.032 0.002 TYR D 24 ARG 0.010 0.001 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.06520 ( 678) hydrogen bonds : angle 5.45602 ( 2007) covalent geometry : bond 0.00580 (13890) covalent geometry : angle 0.95305 (18889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 391 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: B 22 GLU cc_start: 0.6762 (tt0) cc_final: 0.6287 (mt-10) REVERT: B 60 VAL cc_start: 0.8124 (t) cc_final: 0.7816 (t) REVERT: B 73 MET cc_start: 0.6968 (mtp) cc_final: 0.6705 (mtp) REVERT: B 83 GLN cc_start: 0.8242 (tt0) cc_final: 0.7995 (tt0) REVERT: B 94 GLN cc_start: 0.7285 (mt0) cc_final: 0.6205 (tm-30) REVERT: B 135 LEU cc_start: 0.7870 (tp) cc_final: 0.7667 (tp) REVERT: B 157 GLU cc_start: 0.7474 (tp30) cc_final: 0.7059 (mt-10) REVERT: B 161 ASP cc_start: 0.7680 (t70) cc_final: 0.7040 (p0) REVERT: B 192 LEU cc_start: 0.7150 (mp) cc_final: 0.6914 (mt) REVERT: B 242 PHE cc_start: 0.7718 (m-80) cc_final: 0.7493 (m-80) REVERT: B 280 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7496 (mp10) REVERT: B 309 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6749 (mtt180) REVERT: B 318 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7452 (mtp180) REVERT: B 376 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6141 (mm-30) REVERT: B 383 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6757 (tm-30) REVERT: E 88 ASP cc_start: 0.6708 (t0) cc_final: 0.6108 (t0) REVERT: E 112 LEU cc_start: 0.7328 (mm) cc_final: 0.7111 (mt) REVERT: E 114 ASP cc_start: 0.7263 (m-30) cc_final: 0.7024 (m-30) REVERT: E 123 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5902 (mm-30) REVERT: E 161 ASP cc_start: 0.7912 (t70) cc_final: 0.7349 (p0) REVERT: E 241 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.7060 (mtm110) REVERT: E 291 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7058 (pp30) REVERT: E 298 ASN cc_start: 0.7321 (t0) cc_final: 0.6799 (t0) REVERT: E 344 TRP cc_start: 0.7940 (p-90) cc_final: 0.7670 (p-90) REVERT: E 362 LYS cc_start: 0.7553 (mmtm) cc_final: 0.6702 (ttpt) REVERT: E 383 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6787 (tm-30) REVERT: E 406 MET cc_start: 0.6374 (tpp) cc_final: 0.6062 (tpp) REVERT: A 24 TYR cc_start: 0.7326 (m-10) cc_final: 0.6633 (m-10) REVERT: A 172 TYR cc_start: 0.7257 (t80) cc_final: 0.5895 (t80) REVERT: A 279 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7243 (mp0) REVERT: A 280 LYS cc_start: 0.3971 (mmtt) cc_final: 0.3455 (tptp) REVERT: A 386 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6949 (mm-30) REVERT: D 1 MET cc_start: 0.1859 (tmm) cc_final: 0.1653 (tmm) REVERT: D 49 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.4917 (t80) REVERT: D 55 GLU cc_start: 0.7762 (tt0) cc_final: 0.6682 (mp0) REVERT: D 214 ARG cc_start: 0.7636 (ttm170) cc_final: 0.7368 (ttm110) REVERT: D 220 GLU cc_start: 0.7421 (tp30) cc_final: 0.7125 (pt0) REVERT: D 279 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7204 (mp0) REVERT: D 326 LYS cc_start: 0.7876 (tttt) cc_final: 0.6735 (mptt) REVERT: D 370 LYS cc_start: 0.6751 (tptt) cc_final: 0.6339 (tptp) REVERT: D 390 ARG cc_start: 0.6934 (mtm110) cc_final: 0.6523 (ttp80) REVERT: D 392 ASP cc_start: 0.7652 (m-30) cc_final: 0.7341 (m-30) outliers start: 6 outliers final: 1 residues processed: 393 average time/residue: 1.3385 time to fit residues: 570.5751 Evaluate side-chains 239 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain D residue 49 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.0370 chunk 154 optimal weight: 0.2980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 131 GLN B 165 ASN B 204 ASN B 247 ASN B 375 GLN B 396 HIS E 6 HIS E 131 GLN A 15 GLN A 128 GLN A 206 ASN A 293 ASN A 358 GLN D 101 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 206 ASN D 266 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108813 restraints weight = 19447.144| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.71 r_work: 0.3474 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13890 Z= 0.153 Angle : 0.576 8.817 18889 Z= 0.296 Chirality : 0.045 0.144 2078 Planarity : 0.004 0.039 2463 Dihedral : 10.835 157.546 1927 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.36 % Allowed : 15.50 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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: 0.57 (0.20), residues: 1720 helix: 1.38 (0.18), residues: 806 sheet: -0.53 (0.30), residues: 296 loop : -0.38 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS B 105 PHE 0.016 0.002 PHE B 20 TYR 0.020 0.002 TYR D 24 ARG 0.005 0.001 ARG D 390 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 678) hydrogen bonds : angle 4.71068 ( 2007) covalent geometry : bond 0.00350 (13890) covalent geometry : angle 0.57587 (18889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 1.450 Fit side-chains REVERT: B 22 GLU cc_start: 0.7524 (tt0) cc_final: 0.7220 (mt-10) REVERT: B 41 ASP cc_start: 0.7116 (t0) cc_final: 0.6899 (t0) REVERT: B 44 LEU cc_start: 0.8105 (mt) cc_final: 0.7893 (mp) REVERT: B 94 GLN cc_start: 0.7257 (mt0) cc_final: 0.6045 (tm-30) REVERT: B 164 MET cc_start: 0.8291 (ttt) cc_final: 0.8037 (ttt) REVERT: B 280 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7797 (mp10) REVERT: B 383 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 406 MET cc_start: 0.7095 (tpp) cc_final: 0.6630 (tpp) REVERT: E 22 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: E 41 ASP cc_start: 0.7370 (t0) cc_final: 0.7135 (t0) REVERT: E 86 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7616 (ttp-110) REVERT: E 88 ASP cc_start: 0.7575 (t0) cc_final: 0.7130 (t0) REVERT: E 114 ASP cc_start: 0.7733 (m-30) cc_final: 0.7418 (m-30) REVERT: E 178 THR cc_start: 0.9160 (p) cc_final: 0.8951 (m) REVERT: E 298 ASN cc_start: 0.8232 (t0) cc_final: 0.7876 (t0) REVERT: E 362 LYS cc_start: 0.7632 (mmtm) cc_final: 0.6841 (ttpt) REVERT: E 383 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7727 (tm-30) REVERT: E 415 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8071 (mtp) REVERT: A 24 TYR cc_start: 0.8424 (m-10) cc_final: 0.7980 (m-10) REVERT: A 172 TYR cc_start: 0.7988 (t80) cc_final: 0.6726 (t80) REVERT: A 280 LYS cc_start: 0.5696 (mmtt) cc_final: 0.4934 (tptp) REVERT: A 386 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7810 (mm-30) REVERT: D 1 MET cc_start: 0.2812 (OUTLIER) cc_final: 0.2428 (tmm) REVERT: D 154 MET cc_start: 0.8882 (mmm) cc_final: 0.8601 (mmp) REVERT: D 214 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7880 (ttm110) REVERT: D 326 LYS cc_start: 0.8784 (tttt) cc_final: 0.7594 (mptm) REVERT: D 392 ASP cc_start: 0.8196 (m-30) cc_final: 0.6986 (m-30) REVERT: D 413 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8116 (ptp) REVERT: D 433 GLU cc_start: 0.7905 (tp30) cc_final: 0.7558 (tp30) outliers start: 63 outliers final: 22 residues processed: 281 average time/residue: 1.2639 time to fit residues: 387.8788 Evaluate side-chains 225 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 375 GLN Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 132 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 298 ASN E 8 GLN E 134 GLN E 424 GLN A 128 GLN A 216 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.117163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104467 restraints weight = 19447.168| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.78 r_work: 0.3399 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13890 Z= 0.144 Angle : 0.554 8.438 18889 Z= 0.284 Chirality : 0.044 0.189 2078 Planarity : 0.004 0.066 2463 Dihedral : 11.108 174.671 1925 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.15 % Allowed : 17.65 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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: 0.65 (0.20), residues: 1720 helix: 1.52 (0.18), residues: 804 sheet: -0.35 (0.32), residues: 272 loop : -0.53 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 344 HIS 0.004 0.001 HIS E 396 PHE 0.016 0.002 PHE D 149 TYR 0.015 0.001 TYR D 24 ARG 0.004 0.001 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 678) hydrogen bonds : angle 4.61761 ( 2007) covalent geometry : bond 0.00328 (13890) covalent geometry : angle 0.55395 (18889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 1.475 Fit side-chains REVERT: B 3 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6448 (mm-30) REVERT: B 15 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: B 41 ASP cc_start: 0.7008 (t0) cc_final: 0.6745 (t0) REVERT: B 44 LEU cc_start: 0.8455 (mt) cc_final: 0.8195 (mp) REVERT: B 94 GLN cc_start: 0.7300 (mt0) cc_final: 0.6112 (tm-30) REVERT: B 280 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7854 (mp10) REVERT: B 343 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7398 (pm20) REVERT: B 361 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4931 (mt) REVERT: B 383 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7679 (tm-30) REVERT: B 406 MET cc_start: 0.7350 (tpp) cc_final: 0.6980 (tpp) REVERT: E 22 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: E 162 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7599 (mmm160) REVERT: E 164 MET cc_start: 0.7514 (mmm) cc_final: 0.7296 (mmt) REVERT: E 178 THR cc_start: 0.9219 (p) cc_final: 0.8943 (m) REVERT: E 213 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.7984 (ttm-80) REVERT: E 250 LEU cc_start: 0.7933 (pp) cc_final: 0.7562 (pt) REVERT: E 298 ASN cc_start: 0.8540 (t0) cc_final: 0.8262 (t0) REVERT: E 383 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7664 (tm-30) REVERT: E 392 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8720 (mtpt) REVERT: E 415 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8120 (mtp) REVERT: A 24 TYR cc_start: 0.8483 (m-10) cc_final: 0.8043 (m-10) REVERT: A 49 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5305 (t80) REVERT: A 161 TYR cc_start: 0.8702 (m-80) cc_final: 0.8411 (m-80) REVERT: A 172 TYR cc_start: 0.7931 (t80) cc_final: 0.6845 (t80) REVERT: A 214 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8407 (ttp-110) REVERT: A 272 TYR cc_start: 0.8769 (t80) cc_final: 0.8415 (t80) REVERT: A 280 LYS cc_start: 0.5684 (mmtt) cc_final: 0.4849 (tptp) REVERT: A 386 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7901 (mm-30) REVERT: D 1 MET cc_start: 0.2125 (OUTLIER) cc_final: 0.1793 (tmm) REVERT: D 154 MET cc_start: 0.8870 (mmm) cc_final: 0.8629 (mmp) REVERT: D 326 LYS cc_start: 0.8925 (tttt) cc_final: 0.7658 (mmtp) outliers start: 60 outliers final: 19 residues processed: 248 average time/residue: 1.2540 time to fit residues: 340.1109 Evaluate side-chains 213 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 101 optimal weight: 0.0570 chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS E 28 HIS E 37 HIS A 128 GLN A 300 ASN D 101 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101043 restraints weight = 19691.753| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.76 r_work: 0.3338 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13890 Z= 0.177 Angle : 0.578 7.740 18889 Z= 0.299 Chirality : 0.045 0.170 2078 Planarity : 0.004 0.036 2463 Dihedral : 11.272 176.428 1925 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.43 % Allowed : 18.06 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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: 0.55 (0.20), residues: 1720 helix: 1.37 (0.18), residues: 812 sheet: -0.30 (0.32), residues: 272 loop : -0.54 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 344 HIS 0.005 0.001 HIS E 396 PHE 0.016 0.002 PHE D 149 TYR 0.012 0.002 TYR D 24 ARG 0.004 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 678) hydrogen bonds : angle 4.72780 ( 2007) covalent geometry : bond 0.00412 (13890) covalent geometry : angle 0.57847 (18889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 1.417 Fit side-chains REVERT: B 3 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6426 (mm-30) REVERT: B 44 LEU cc_start: 0.8403 (mt) cc_final: 0.8156 (mp) REVERT: B 125 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7598 (mp0) REVERT: B 280 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7895 (mp10) REVERT: B 343 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7368 (pm20) REVERT: B 361 LEU cc_start: 0.5234 (OUTLIER) cc_final: 0.4983 (mt) REVERT: B 383 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 406 MET cc_start: 0.7458 (tpp) cc_final: 0.7089 (tpp) REVERT: E 22 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: E 122 LYS cc_start: 0.8133 (pttm) cc_final: 0.7660 (ptmt) REVERT: E 164 MET cc_start: 0.7767 (mmm) cc_final: 0.7459 (mmt) REVERT: E 249 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7424 (p0) REVERT: E 288 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7331 (tp30) REVERT: E 298 ASN cc_start: 0.8548 (t0) cc_final: 0.8268 (t0) REVERT: E 361 LEU cc_start: 0.4545 (OUTLIER) cc_final: 0.4231 (mt) REVERT: E 383 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7755 (tm-30) REVERT: E 392 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8752 (mtpt) REVERT: E 415 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8301 (mtp) REVERT: A 24 TYR cc_start: 0.8442 (m-10) cc_final: 0.8108 (m-10) REVERT: A 49 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5121 (t80) REVERT: A 55 GLU cc_start: 0.7978 (tp30) cc_final: 0.7743 (tp30) REVERT: A 172 TYR cc_start: 0.7919 (t80) cc_final: 0.7708 (t80) REVERT: A 279 GLU cc_start: 0.7956 (mp0) cc_final: 0.7721 (mp0) REVERT: A 280 LYS cc_start: 0.5844 (mmtt) cc_final: 0.4923 (tptp) REVERT: A 285 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7417 (tp-100) REVERT: A 386 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 154 MET cc_start: 0.8931 (mmm) cc_final: 0.8610 (mmp) REVERT: D 254 GLU cc_start: 0.4531 (mm-30) cc_final: 0.3889 (mm-30) REVERT: D 326 LYS cc_start: 0.9055 (tttt) cc_final: 0.7733 (mmtp) REVERT: D 340 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8523 (t) outliers start: 64 outliers final: 27 residues processed: 239 average time/residue: 1.1796 time to fit residues: 310.0834 Evaluate side-chains 224 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 347 ASN B 348 ASN E 37 HIS E 426 GLN A 128 GLN A 309 HIS D 91 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098678 restraints weight = 19797.935| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.75 r_work: 0.3295 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13890 Z= 0.195 Angle : 0.590 7.671 18889 Z= 0.306 Chirality : 0.045 0.169 2078 Planarity : 0.004 0.037 2463 Dihedral : 11.399 178.615 1923 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.36 % Allowed : 19.17 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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 (0.20), residues: 1720 helix: 1.19 (0.18), residues: 812 sheet: -0.40 (0.32), residues: 264 loop : -0.58 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 388 HIS 0.006 0.001 HIS E 396 PHE 0.016 0.002 PHE D 149 TYR 0.023 0.002 TYR D 24 ARG 0.004 0.001 ARG E 77 Details of bonding type rmsd hydrogen bonds : bond 0.04962 ( 678) hydrogen bonds : angle 4.82886 ( 2007) covalent geometry : bond 0.00456 (13890) covalent geometry : angle 0.59045 (18889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 1.429 Fit side-chains REVERT: B 125 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8023 (mp0) REVERT: B 280 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7843 (mp10) REVERT: B 291 GLN cc_start: 0.8504 (pp30) cc_final: 0.8011 (mm-40) REVERT: B 343 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7179 (pm20) REVERT: B 361 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.5174 (mt) REVERT: B 406 MET cc_start: 0.7491 (tpp) cc_final: 0.7109 (tpp) REVERT: E 22 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: E 41 ASP cc_start: 0.7313 (t70) cc_final: 0.7066 (t0) REVERT: E 122 LYS cc_start: 0.8249 (pttm) cc_final: 0.7813 (ptmm) REVERT: E 164 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7574 (mmt) REVERT: E 213 ARG cc_start: 0.8442 (ttp-170) cc_final: 0.8202 (ttp-110) REVERT: E 298 ASN cc_start: 0.8569 (t0) cc_final: 0.8341 (t0) REVERT: E 361 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.5015 (mt) REVERT: E 383 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7756 (tm-30) REVERT: E 392 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8743 (mtpt) REVERT: A 24 TYR cc_start: 0.8476 (m-10) cc_final: 0.8078 (m-10) REVERT: A 49 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.4776 (t80) REVERT: A 55 GLU cc_start: 0.7961 (tp30) cc_final: 0.7712 (tp30) REVERT: A 172 TYR cc_start: 0.7850 (t80) cc_final: 0.7638 (t80) REVERT: A 280 LYS cc_start: 0.6222 (mmtt) cc_final: 0.5321 (tptp) REVERT: A 285 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7530 (tp40) REVERT: A 386 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7969 (mm-30) REVERT: D 154 MET cc_start: 0.8800 (mmm) cc_final: 0.8465 (mmp) REVERT: D 254 GLU cc_start: 0.4795 (mm-30) cc_final: 0.4074 (mm-30) REVERT: D 326 LYS cc_start: 0.9001 (tttt) cc_final: 0.7720 (mmtp) REVERT: D 340 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8516 (t) outliers start: 63 outliers final: 30 residues processed: 238 average time/residue: 1.1981 time to fit residues: 312.7201 Evaluate side-chains 223 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 0.0670 chunk 116 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 139 optimal weight: 0.0770 chunk 93 optimal weight: 0.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 300 ASN D 18 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099241 restraints weight = 19866.409| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.75 r_work: 0.3300 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13890 Z= 0.164 Angle : 0.562 7.462 18889 Z= 0.290 Chirality : 0.044 0.138 2078 Planarity : 0.004 0.034 2463 Dihedral : 11.349 179.838 1923 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.15 % Allowed : 20.69 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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: 0.42 (0.20), residues: 1720 helix: 1.24 (0.18), residues: 816 sheet: -0.44 (0.31), residues: 272 loop : -0.54 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 388 HIS 0.005 0.001 HIS E 396 PHE 0.019 0.002 PHE D 49 TYR 0.017 0.001 TYR D 24 ARG 0.003 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 678) hydrogen bonds : angle 4.74490 ( 2007) covalent geometry : bond 0.00381 (13890) covalent geometry : angle 0.56168 (18889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 1.548 Fit side-chains REVERT: B 280 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7862 (mp10) REVERT: B 291 GLN cc_start: 0.8505 (pp30) cc_final: 0.7972 (mm-40) REVERT: B 406 MET cc_start: 0.7384 (tpp) cc_final: 0.7021 (tpp) REVERT: E 22 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: E 122 LYS cc_start: 0.8244 (pttm) cc_final: 0.7855 (ptmm) REVERT: E 164 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7507 (mmt) REVERT: E 298 ASN cc_start: 0.8544 (t0) cc_final: 0.8196 (t0) REVERT: E 358 PRO cc_start: 0.7196 (Cg_endo) cc_final: 0.6850 (Cg_exo) REVERT: E 383 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 24 TYR cc_start: 0.8473 (m-10) cc_final: 0.8147 (m-10) REVERT: A 49 PHE cc_start: 0.6171 (OUTLIER) cc_final: 0.4864 (t80) REVERT: A 73 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8190 (m) REVERT: A 280 LYS cc_start: 0.6274 (mmtt) cc_final: 0.5355 (tptp) REVERT: A 285 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7533 (tp40) REVERT: A 386 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 85 GLN cc_start: 0.8408 (mm110) cc_final: 0.8027 (mt0) REVERT: D 154 MET cc_start: 0.8909 (mmm) cc_final: 0.8601 (mmp) REVERT: D 254 GLU cc_start: 0.4778 (mm-30) cc_final: 0.4070 (mm-30) REVERT: D 326 LYS cc_start: 0.9009 (tttt) cc_final: 0.7886 (tptt) outliers start: 60 outliers final: 30 residues processed: 227 average time/residue: 1.1412 time to fit residues: 285.3669 Evaluate side-chains 216 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 12 CYS Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS E 298 ASN A 128 GLN A 300 ASN D 18 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098523 restraints weight = 19694.858| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.76 r_work: 0.3292 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13890 Z= 0.175 Angle : 0.571 8.048 18889 Z= 0.294 Chirality : 0.044 0.143 2078 Planarity : 0.004 0.033 2463 Dihedral : 11.383 179.567 1923 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.01 % Allowed : 21.31 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1720 helix: 1.18 (0.18), residues: 816 sheet: -0.51 (0.30), residues: 276 loop : -0.50 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 388 HIS 0.005 0.001 HIS E 396 PHE 0.016 0.002 PHE D 149 TYR 0.016 0.001 TYR D 24 ARG 0.003 0.000 ARG E 213 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 678) hydrogen bonds : angle 4.76946 ( 2007) covalent geometry : bond 0.00407 (13890) covalent geometry : angle 0.57070 (18889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.454 Fit side-chains REVERT: B 41 ASP cc_start: 0.7124 (t0) cc_final: 0.6919 (t0) REVERT: B 280 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7898 (mp10) REVERT: B 291 GLN cc_start: 0.8511 (pp30) cc_final: 0.8034 (mm-40) REVERT: B 406 MET cc_start: 0.7397 (tpp) cc_final: 0.7039 (tpp) REVERT: E 22 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: E 41 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: E 74 ASP cc_start: 0.8149 (m-30) cc_final: 0.7937 (m-30) REVERT: E 122 LYS cc_start: 0.8325 (pttm) cc_final: 0.7930 (ptmm) REVERT: E 213 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8003 (ttm110) REVERT: E 298 ASN cc_start: 0.8377 (t0) cc_final: 0.8054 (t0) REVERT: E 358 PRO cc_start: 0.7041 (Cg_endo) cc_final: 0.6654 (Cg_exo) REVERT: E 361 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4758 (mt) REVERT: E 383 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7786 (tm-30) REVERT: E 392 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8727 (mtpt) REVERT: A 24 TYR cc_start: 0.8495 (m-10) cc_final: 0.8156 (m-10) REVERT: A 49 PHE cc_start: 0.6082 (OUTLIER) cc_final: 0.4741 (t80) REVERT: A 73 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8237 (m) REVERT: A 90 GLU cc_start: 0.8189 (tt0) cc_final: 0.7887 (tt0) REVERT: A 215 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7911 (mtm110) REVERT: A 280 LYS cc_start: 0.6326 (mmtt) cc_final: 0.5395 (tptp) REVERT: A 285 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7605 (tp40) REVERT: A 386 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8046 (mm-30) REVERT: D 85 GLN cc_start: 0.8369 (mm110) cc_final: 0.8066 (mt0) REVERT: D 154 MET cc_start: 0.8795 (mmm) cc_final: 0.8483 (mmp) REVERT: D 254 GLU cc_start: 0.4913 (mm-30) cc_final: 0.4125 (mm-30) REVERT: D 279 GLU cc_start: 0.7480 (mp0) cc_final: 0.7142 (mp0) REVERT: D 326 LYS cc_start: 0.9044 (tttt) cc_final: 0.7935 (tptt) outliers start: 58 outliers final: 35 residues processed: 226 average time/residue: 1.2015 time to fit residues: 298.4517 Evaluate side-chains 229 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 12 CYS Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.0060 chunk 39 optimal weight: 0.0770 chunk 141 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 67 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 300 ASN D 18 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101517 restraints weight = 19627.263| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.75 r_work: 0.3337 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13890 Z= 0.122 Angle : 0.530 7.561 18889 Z= 0.271 Chirality : 0.042 0.137 2078 Planarity : 0.004 0.032 2463 Dihedral : 11.188 177.695 1923 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.11 % Allowed : 22.84 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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: 0.63 (0.20), residues: 1720 helix: 1.43 (0.19), residues: 804 sheet: -0.32 (0.31), residues: 272 loop : -0.43 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 388 HIS 0.004 0.001 HIS E 396 PHE 0.021 0.001 PHE D 49 TYR 0.015 0.001 TYR D 24 ARG 0.003 0.000 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 678) hydrogen bonds : angle 4.63785 ( 2007) covalent geometry : bond 0.00273 (13890) covalent geometry : angle 0.52972 (18889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.435 Fit side-chains REVERT: B 3 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6475 (mm-30) REVERT: B 41 ASP cc_start: 0.7092 (t0) cc_final: 0.6870 (t0) REVERT: B 267 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7656 (ptp) REVERT: B 406 MET cc_start: 0.7318 (tpp) cc_final: 0.6964 (tpp) REVERT: B 415 MET cc_start: 0.7958 (mmm) cc_final: 0.7716 (mmm) REVERT: E 22 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: E 74 ASP cc_start: 0.8121 (m-30) cc_final: 0.7847 (m-30) REVERT: E 122 LYS cc_start: 0.8341 (pttm) cc_final: 0.7899 (ptmm) REVERT: E 213 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7918 (ttm110) REVERT: E 298 ASN cc_start: 0.8366 (t0) cc_final: 0.8054 (t0) REVERT: E 358 PRO cc_start: 0.7254 (Cg_endo) cc_final: 0.6918 (Cg_exo) REVERT: E 383 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7752 (tm-30) REVERT: E 392 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8715 (mtpt) REVERT: A 24 TYR cc_start: 0.8459 (m-10) cc_final: 0.8127 (m-10) REVERT: A 49 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.4900 (t80) REVERT: A 73 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8157 (m) REVERT: A 90 GLU cc_start: 0.8171 (tt0) cc_final: 0.7852 (tt0) REVERT: A 280 LYS cc_start: 0.6308 (mmtt) cc_final: 0.5413 (tptp) REVERT: A 285 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7672 (tp-100) REVERT: A 386 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 417 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: D 154 MET cc_start: 0.8924 (mmm) cc_final: 0.8670 (mmp) REVERT: D 254 GLU cc_start: 0.4592 (mm-30) cc_final: 0.3860 (mm-30) REVERT: D 279 GLU cc_start: 0.7488 (mp0) cc_final: 0.7137 (mp0) REVERT: D 326 LYS cc_start: 0.9017 (tttt) cc_final: 0.7882 (mptt) REVERT: D 340 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8512 (t) outliers start: 45 outliers final: 21 residues processed: 224 average time/residue: 1.2378 time to fit residues: 304.1276 Evaluate side-chains 215 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS E 347 ASN A 128 GLN A 300 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098214 restraints weight = 19675.801| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.73 r_work: 0.3286 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13890 Z= 0.192 Angle : 0.594 8.114 18889 Z= 0.307 Chirality : 0.045 0.202 2078 Planarity : 0.004 0.035 2463 Dihedral : 11.376 178.775 1923 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.32 % Allowed : 23.46 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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: 0.42 (0.20), residues: 1720 helix: 1.20 (0.18), residues: 806 sheet: -0.43 (0.31), residues: 270 loop : -0.46 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 388 HIS 0.006 0.001 HIS E 396 PHE 0.017 0.002 PHE D 149 TYR 0.025 0.002 TYR D 24 ARG 0.009 0.001 ARG E 282 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 678) hydrogen bonds : angle 4.77817 ( 2007) covalent geometry : bond 0.00452 (13890) covalent geometry : angle 0.59441 (18889) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 1.491 Fit side-chains REVERT: B 41 ASP cc_start: 0.7159 (t0) cc_final: 0.6933 (t0) REVERT: B 291 GLN cc_start: 0.8523 (pp30) cc_final: 0.8001 (mm-40) REVERT: B 406 MET cc_start: 0.7374 (tpp) cc_final: 0.7023 (tpp) REVERT: E 22 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: E 41 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6831 (m-30) REVERT: E 74 ASP cc_start: 0.8061 (m-30) cc_final: 0.7843 (m-30) REVERT: E 115 SER cc_start: 0.7533 (t) cc_final: 0.7296 (m) REVERT: E 122 LYS cc_start: 0.8344 (pttm) cc_final: 0.7935 (ptmm) REVERT: E 213 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8019 (ttp80) REVERT: E 282 ARG cc_start: 0.6114 (mtp-110) cc_final: 0.5883 (ptm160) REVERT: E 298 ASN cc_start: 0.8389 (t0) cc_final: 0.8055 (t0) REVERT: E 358 PRO cc_start: 0.7224 (Cg_endo) cc_final: 0.6880 (Cg_exo) REVERT: E 383 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7735 (tm-30) REVERT: E 392 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8705 (mtpt) REVERT: A 24 TYR cc_start: 0.8498 (m-10) cc_final: 0.8143 (m-10) REVERT: A 49 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.4723 (t80) REVERT: A 73 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8208 (m) REVERT: A 90 GLU cc_start: 0.8162 (tt0) cc_final: 0.7832 (tt0) REVERT: A 215 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7832 (mtm110) REVERT: A 280 LYS cc_start: 0.6486 (mmtt) cc_final: 0.5447 (tptt) REVERT: A 285 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7643 (tp40) REVERT: A 386 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 417 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: D 254 GLU cc_start: 0.4906 (mm-30) cc_final: 0.4101 (mm-30) REVERT: D 279 GLU cc_start: 0.7429 (mp0) cc_final: 0.7110 (mp0) REVERT: D 326 LYS cc_start: 0.9023 (tttt) cc_final: 0.7730 (mmtp) REVERT: D 340 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8541 (t) outliers start: 48 outliers final: 29 residues processed: 215 average time/residue: 1.2510 time to fit residues: 294.2183 Evaluate side-chains 221 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 12 CYS Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.0060 chunk 1 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 132 optimal weight: 0.0670 chunk 97 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 300 ASN D 18 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100297 restraints weight = 19526.348| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.73 r_work: 0.3321 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13890 Z= 0.139 Angle : 0.564 8.553 18889 Z= 0.290 Chirality : 0.043 0.196 2078 Planarity : 0.004 0.035 2463 Dihedral : 11.266 177.260 1923 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.84 % Allowed : 23.88 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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: 0.56 (0.20), residues: 1720 helix: 1.32 (0.19), residues: 804 sheet: -0.23 (0.31), residues: 264 loop : -0.47 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 388 HIS 0.005 0.001 HIS B 37 PHE 0.016 0.001 PHE D 49 TYR 0.022 0.001 TYR D 24 ARG 0.012 0.000 ARG E 282 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 678) hydrogen bonds : angle 4.70648 ( 2007) covalent geometry : bond 0.00317 (13890) covalent geometry : angle 0.56396 (18889) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 1.582 Fit side-chains REVERT: B 41 ASP cc_start: 0.7114 (t0) cc_final: 0.6885 (t0) REVERT: B 111 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7359 (mt-10) REVERT: B 291 GLN cc_start: 0.8516 (pp30) cc_final: 0.7963 (mm-40) REVERT: B 363 MET cc_start: 0.8192 (mtp) cc_final: 0.7945 (mtm) REVERT: B 406 MET cc_start: 0.7352 (tpp) cc_final: 0.7009 (tpp) REVERT: E 22 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: E 41 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: E 122 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7945 (ptmm) REVERT: E 172 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8048 (m) REVERT: E 213 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8001 (ttm110) REVERT: E 279 GLN cc_start: 0.7656 (pm20) cc_final: 0.7115 (mp10) REVERT: E 282 ARG cc_start: 0.6219 (mtp-110) cc_final: 0.5837 (ptm160) REVERT: E 298 ASN cc_start: 0.8381 (t0) cc_final: 0.8055 (t0) REVERT: E 358 PRO cc_start: 0.7206 (Cg_endo) cc_final: 0.6889 (Cg_exo) REVERT: E 383 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7728 (tm-30) REVERT: E 392 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8713 (mtpt) REVERT: A 24 TYR cc_start: 0.8460 (m-10) cc_final: 0.8120 (m-10) REVERT: A 49 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.4921 (t80) REVERT: A 73 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8174 (m) REVERT: A 90 GLU cc_start: 0.8147 (tt0) cc_final: 0.7814 (tt0) REVERT: A 161 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: A 280 LYS cc_start: 0.6509 (mmtt) cc_final: 0.5477 (tptt) REVERT: A 285 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7719 (tp-100) REVERT: A 386 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 417 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: D 254 GLU cc_start: 0.4723 (mm-30) cc_final: 0.3941 (mm-30) REVERT: D 279 GLU cc_start: 0.7507 (mp0) cc_final: 0.7142 (mp0) REVERT: D 326 LYS cc_start: 0.9022 (tttt) cc_final: 0.7835 (mptt) REVERT: D 340 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8547 (t) outliers start: 41 outliers final: 22 residues processed: 210 average time/residue: 1.1993 time to fit residues: 276.6936 Evaluate side-chains 211 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 12 CYS Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 134 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 114 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 124 optimal weight: 0.0170 chunk 123 optimal weight: 0.4980 chunk 118 optimal weight: 0.5980 chunk 148 optimal weight: 0.0370 chunk 68 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN A 128 GLN A 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.114856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102322 restraints weight = 19454.942| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.73 r_work: 0.3354 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13890 Z= 0.126 Angle : 0.553 8.851 18889 Z= 0.284 Chirality : 0.043 0.184 2078 Planarity : 0.004 0.034 2463 Dihedral : 11.143 176.923 1923 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.35 % Allowed : 24.57 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % 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: 0.64 (0.20), residues: 1720 helix: 1.43 (0.19), residues: 802 sheet: -0.33 (0.31), residues: 270 loop : -0.42 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 388 HIS 0.005 0.001 HIS B 37 PHE 0.023 0.001 PHE D 49 TYR 0.022 0.001 TYR D 24 ARG 0.010 0.000 ARG E 282 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 678) hydrogen bonds : angle 4.61508 ( 2007) covalent geometry : bond 0.00284 (13890) covalent geometry : angle 0.55265 (18889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9411.31 seconds wall clock time: 161 minutes 17.92 seconds (9677.92 seconds total)