Starting phenix.real_space_refine on Sun Jan 19 05:17:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc1_19042/01_2025/8rc1_19042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc1_19042/01_2025/8rc1_19042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rc1_19042/01_2025/8rc1_19042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc1_19042/01_2025/8rc1_19042.map" model { file = "/net/cci-nas-00/data/ceres_data/8rc1_19042/01_2025/8rc1_19042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc1_19042/01_2025/8rc1_19042.cif" } resolution = 3.7 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= -0.007 sd= 0.046 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 82 5.16 5 C 8417 2.51 5 N 2314 2.21 5 O 2410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13235 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3144 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 21, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 189 Chain: "B" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3192 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 20, 'TRANS': 409} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 16, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 149 Chain: "C" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3144 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 21, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 189 Chain: "D" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3188 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 20, 'TRANS': 409} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 153 Chain: "E" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 445 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'TRANS': 88} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'UNK:plan-1': 89} Unresolved non-hydrogen planarities: 89 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.22 Number of scatterers: 13235 At special positions: 0 Unit cell: (76.824, 76.824, 190.993, 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 82 16.00 P 10 15.00 Mg 2 11.99 O 2410 8.00 N 2314 7.00 C 8417 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: 3.51 Conformation dependent library (CDL) restraints added in 1.7 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 11 sheets defined 59.3% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.585A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.692A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.268A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.852A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.622A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.114A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 removed outlier: 4.212A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.279A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.692A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.707A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.201A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.998A 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 69 through 78 removed outlier: 4.490A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 126 removed outlier: 4.090A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.623A pdb=" N SER B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.943A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.759A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.922A 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 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.934A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.702A 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 391 removed outlier: 4.093A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.053A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.725A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.514A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 109 through 129 removed outlier: 4.164A pdb=" N GLU C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.162A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.085A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.633A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.909A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 401 removed outlier: 4.033A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.999A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.931A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 removed outlier: 3.668A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 46 through 49 Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 69 through 78 removed outlier: 4.569A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.940A pdb=" N GLU D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.917A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.578A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N CYS D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.670A pdb=" N ASN D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.835A pdb=" N MET D 299 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 373 through 391 removed outlier: 4.247A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 4.017A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 428 removed outlier: 3.602A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 87 removed outlier: 3.537A pdb=" N UNK E 18 " --> pdb=" O UNK E 14 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N UNK E 23 " --> pdb=" O UNK E 19 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N UNK E 24 " --> pdb=" O UNK E 20 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK E 25 " --> pdb=" O UNK E 21 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.900A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 3.625A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.253A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 198 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.894A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.004A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 272 removed outlier: 8.433A pdb=" N LYS C 352 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS C 315 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY C 354 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU C 317 " --> pdb=" O GLY C 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.176A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.176A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 51 through 53 758 hydrogen bonds defined for protein. 2190 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: 4.62 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4323 1.34 - 1.46: 3049 1.46 - 1.58: 6024 1.58 - 1.69: 16 1.69 - 1.81: 132 Bond restraints: 13544 Sorted by residual: bond pdb=" C5 GDP D 501 " pdb=" C4 GDP D 501 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.48e+00 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C ILE B 356 " pdb=" O ILE B 356 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.11e-01 bond pdb=" CA ILE A 171 " pdb=" CB ILE A 171 " ideal model delta sigma weight residual 1.527 1.538 -0.011 1.31e-02 5.83e+03 6.80e-01 bond pdb=" CA ILE C 171 " pdb=" CB ILE C 171 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.62e-01 ... (remaining 13539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 18128 1.30 - 2.60: 289 2.60 - 3.90: 74 3.90 - 5.21: 15 5.21 - 6.51: 7 Bond angle restraints: 18513 Sorted by residual: angle pdb=" N ALA D 271 " pdb=" CA ALA D 271 " pdb=" C ALA D 271 " ideal model delta sigma weight residual 109.81 114.97 -5.16 2.21e+00 2.05e-01 5.45e+00 angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 104.58 6.42 3.00e+00 1.11e-01 4.59e+00 angle pdb=" C2' GTP C 501 " pdb=" C3' GTP C 501 " pdb=" C4' GTP C 501 " ideal model delta sigma weight residual 111.00 104.71 6.29 3.00e+00 1.11e-01 4.39e+00 angle pdb=" N ASP C 33 " pdb=" CA ASP C 33 " pdb=" C ASP C 33 " ideal model delta sigma weight residual 113.20 110.68 2.52 1.21e+00 6.83e-01 4.35e+00 angle pdb=" C GLY A 436 " pdb=" N VAL A 437 " pdb=" CA VAL A 437 " ideal model delta sigma weight residual 120.50 123.24 -2.74 1.34e+00 5.57e-01 4.18e+00 ... (remaining 18508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 7868 34.96 - 69.93: 41 69.93 - 104.89: 3 104.89 - 139.85: 7 139.85 - 174.82: 2 Dihedral angle restraints: 7921 sinusoidal: 2679 harmonic: 5242 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 -115.92 -174.82 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.13 171.72 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O3B GTP C 501 " pdb=" O3A GTP C 501 " pdb=" PB GTP C 501 " pdb=" PA GTP C 501 " ideal model delta sinusoidal sigma weight residual 291.08 153.68 137.40 1 2.00e+01 2.50e-03 4.17e+01 ... (remaining 7918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1227 0.026 - 0.052: 532 0.052 - 0.078: 229 0.078 - 0.104: 107 0.104 - 0.130: 46 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CA VAL C 363 " pdb=" N VAL C 363 " pdb=" C VAL C 363 " pdb=" CB VAL C 363 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE D 4 " pdb=" N ILE D 4 " pdb=" C ILE D 4 " pdb=" CB ILE D 4 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 2138 not shown) Planarity restraints: 2371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 267 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO C 268 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 357 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO D 358 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 358 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 358 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 170 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO D 171 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 171 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 171 " -0.015 5.00e-02 4.00e+02 ... (remaining 2368 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 111 2.58 - 3.16: 11051 3.16 - 3.74: 21199 3.74 - 4.32: 28039 4.32 - 4.90: 48268 Nonbonded interactions: 108668 Sorted by model distance: nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.994 2.170 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 1.994 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 2.026 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.053 2.170 nonbonded pdb=" OD2 ASP B 67 " pdb=" OG1 THR B 72 " model vdw 2.255 3.040 ... (remaining 108663 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 333 or (resid 334 through 336 and (name N or nam \ e CA or name C or name O or name CB )) or resid 337 through 430 or resid 501)) selection = chain 'D' } 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 group one per residue 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: 18.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.670 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.002 0.024 13544 Z= 0.141 Angle : 0.475 6.507 18513 Z= 0.245 Chirality : 0.039 0.130 2141 Planarity : 0.003 0.029 2371 Dihedral : 11.146 174.815 4551 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.71 % Allowed : 3.91 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.21), residues: 1710 helix: 2.42 (0.19), residues: 762 sheet: 0.38 (0.34), residues: 268 loop : -0.15 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 21 HIS 0.003 0.001 HIS A 139 PHE 0.008 0.001 PHE B 260 TYR 0.008 0.001 TYR B 310 ARG 0.002 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9195 (m) cc_final: 0.8846 (m) REVERT: A 69 ASP cc_start: 0.8098 (t0) cc_final: 0.7733 (t0) REVERT: A 183 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8088 (mt-10) REVERT: A 302 MET cc_start: 0.8704 (mmt) cc_final: 0.8424 (mpp) REVERT: A 377 MET cc_start: 0.8880 (ttp) cc_final: 0.8658 (ttm) REVERT: A 378 LEU cc_start: 0.9426 (mt) cc_final: 0.9225 (mt) REVERT: A 411 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 19 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8655 (mmmm) REVERT: B 252 LYS cc_start: 0.9366 (tttt) cc_final: 0.8708 (tttm) REVERT: B 289 LEU cc_start: 0.9548 (mt) cc_final: 0.9155 (mp) REVERT: B 321 MET cc_start: 0.8463 (pmm) cc_final: 0.7944 (pmm) REVERT: B 363 MET cc_start: 0.8800 (ptp) cc_final: 0.8394 (ptp) REVERT: C 69 ASP cc_start: 0.8659 (t0) cc_final: 0.8331 (t0) REVERT: C 133 GLN cc_start: 0.9016 (mm110) cc_final: 0.8192 (mm110) REVERT: C 183 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8375 (mt-10) REVERT: C 213 CYS cc_start: 0.8714 (t) cc_final: 0.8504 (t) REVERT: C 301 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7751 (pm20) REVERT: C 304 LYS cc_start: 0.8904 (tppt) cc_final: 0.8408 (tppt) REVERT: C 377 MET cc_start: 0.8785 (ttp) cc_final: 0.7928 (tmm) REVERT: C 392 ASP cc_start: 0.8541 (t70) cc_final: 0.8074 (t0) REVERT: C 417 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8600 (tm-30) REVERT: D 6 HIS cc_start: 0.8802 (t-90) cc_final: 0.8322 (t-170) REVERT: D 19 LYS cc_start: 0.9339 (mmmt) cc_final: 0.9079 (mmmm) REVERT: D 58 LYS cc_start: 0.8440 (mmtp) cc_final: 0.7973 (pttt) REVERT: D 103 LYS cc_start: 0.8865 (tttp) cc_final: 0.8508 (ttmm) REVERT: D 129 CYS cc_start: 0.8932 (t) cc_final: 0.8659 (m) REVERT: D 162 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8239 (mpp80) REVERT: D 257 MET cc_start: 0.7730 (mmm) cc_final: 0.6552 (mmm) REVERT: D 312 THR cc_start: 0.9141 (p) cc_final: 0.7782 (p) REVERT: D 350 LYS cc_start: 0.8880 (tptt) cc_final: 0.7942 (tppt) REVERT: D 403 MET cc_start: 0.8918 (mmm) cc_final: 0.7962 (mmm) REVERT: D 407 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8370 (mt-10) outliers start: 21 outliers final: 7 residues processed: 216 average time/residue: 0.2553 time to fit residues: 79.6540 Evaluate side-chains 139 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 162 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.0870 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN B 48 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 300 ASN D 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.061249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.051414 restraints weight = 42878.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053474 restraints weight = 19977.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054888 restraints weight = 11534.571| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13544 Z= 0.179 Angle : 0.525 6.836 18513 Z= 0.264 Chirality : 0.041 0.168 2141 Planarity : 0.004 0.035 2371 Dihedral : 10.578 173.129 2009 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.20 % Allowed : 7.57 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.21), residues: 1710 helix: 2.26 (0.19), residues: 774 sheet: 0.16 (0.33), residues: 276 loop : -0.22 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.007 0.001 HIS B 6 PHE 0.015 0.001 PHE D 367 TYR 0.011 0.001 TYR C 272 ARG 0.005 0.000 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9206 (m) cc_final: 0.8886 (m) REVERT: A 69 ASP cc_start: 0.8052 (t0) cc_final: 0.7666 (t0) REVERT: A 183 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 203 MET cc_start: 0.8440 (mtm) cc_final: 0.8188 (mtm) REVERT: A 205 ASP cc_start: 0.7646 (t0) cc_final: 0.7375 (m-30) REVERT: A 301 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8206 (mp10) REVERT: A 302 MET cc_start: 0.8626 (mmt) cc_final: 0.8296 (mpp) REVERT: A 327 ASP cc_start: 0.9253 (m-30) cc_final: 0.9032 (m-30) REVERT: A 358 GLN cc_start: 0.9381 (tp-100) cc_final: 0.9017 (tp-100) REVERT: A 377 MET cc_start: 0.8934 (ttp) cc_final: 0.8686 (ttm) REVERT: A 411 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8133 (mm-30) REVERT: B 1 MET cc_start: 0.8303 (mmt) cc_final: 0.8016 (mmt) REVERT: B 321 MET cc_start: 0.8528 (pmm) cc_final: 0.8150 (pmm) REVERT: B 363 MET cc_start: 0.8767 (ptp) cc_final: 0.8416 (ptp) REVERT: C 36 MET cc_start: 0.8987 (tpp) cc_final: 0.8663 (tmm) REVERT: C 69 ASP cc_start: 0.8630 (t0) cc_final: 0.8278 (t70) REVERT: C 133 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8101 (mm110) REVERT: C 183 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8336 (mt-10) REVERT: C 213 CYS cc_start: 0.8630 (t) cc_final: 0.8319 (t) REVERT: C 304 LYS cc_start: 0.8383 (tppt) cc_final: 0.8182 (tppt) REVERT: C 417 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8469 (tm-30) REVERT: D 6 HIS cc_start: 0.8789 (t-90) cc_final: 0.8129 (t-170) REVERT: D 19 LYS cc_start: 0.9288 (mmmt) cc_final: 0.8887 (mmmm) REVERT: D 73 MET cc_start: 0.9176 (mmm) cc_final: 0.8925 (mmm) REVERT: D 129 CYS cc_start: 0.8875 (t) cc_final: 0.8662 (m) REVERT: D 162 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8208 (mpp80) REVERT: D 257 MET cc_start: 0.8009 (mmm) cc_final: 0.7290 (mmm) REVERT: D 300 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8751 (mtm) REVERT: D 312 THR cc_start: 0.9130 (p) cc_final: 0.7815 (p) REVERT: D 321 MET cc_start: 0.8367 (ptp) cc_final: 0.8066 (ptp) REVERT: D 363 MET cc_start: 0.8167 (ptp) cc_final: 0.7853 (ptp) REVERT: D 403 MET cc_start: 0.8942 (mmm) cc_final: 0.8367 (mmm) outliers start: 27 outliers final: 17 residues processed: 169 average time/residue: 0.2266 time to fit residues: 58.9740 Evaluate side-chains 152 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 153 optimal weight: 0.0270 chunk 79 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 102 optimal weight: 0.0170 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049959 restraints weight = 44091.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.051937 restraints weight = 20891.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.053274 restraints weight = 12263.104| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13544 Z= 0.281 Angle : 0.544 7.259 18513 Z= 0.270 Chirality : 0.042 0.142 2141 Planarity : 0.004 0.037 2371 Dihedral : 10.470 171.594 2006 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.52 % Allowed : 9.60 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.21), residues: 1710 helix: 2.16 (0.19), residues: 786 sheet: 0.03 (0.33), residues: 272 loop : -0.16 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 397 HIS 0.004 0.001 HIS C 139 PHE 0.014 0.001 PHE B 367 TYR 0.011 0.001 TYR B 425 ARG 0.006 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9236 (m) cc_final: 0.8907 (m) REVERT: A 69 ASP cc_start: 0.8116 (t0) cc_final: 0.7744 (t0) REVERT: A 183 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8197 (mt-10) REVERT: A 203 MET cc_start: 0.8523 (mtm) cc_final: 0.8293 (mtm) REVERT: A 205 ASP cc_start: 0.7900 (t0) cc_final: 0.7603 (m-30) REVERT: A 301 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8257 (mp10) REVERT: A 302 MET cc_start: 0.8637 (mmt) cc_final: 0.8360 (mpp) REVERT: A 377 MET cc_start: 0.9076 (ttp) cc_final: 0.8611 (ttm) REVERT: A 411 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B 1 MET cc_start: 0.8387 (mmt) cc_final: 0.8156 (mmt) REVERT: B 321 MET cc_start: 0.8585 (pmm) cc_final: 0.8193 (pmm) REVERT: B 363 MET cc_start: 0.8775 (ptp) cc_final: 0.8409 (ptt) REVERT: C 69 ASP cc_start: 0.8640 (t0) cc_final: 0.8297 (t70) REVERT: C 133 GLN cc_start: 0.8803 (mm-40) cc_final: 0.7991 (mm110) REVERT: C 183 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8435 (mt-10) REVERT: C 205 ASP cc_start: 0.7943 (t0) cc_final: 0.7594 (t0) REVERT: C 213 CYS cc_start: 0.8623 (t) cc_final: 0.8204 (t) REVERT: C 304 LYS cc_start: 0.8701 (tppt) cc_final: 0.8340 (tppt) REVERT: C 413 MET cc_start: 0.8632 (mmm) cc_final: 0.7960 (tpp) REVERT: C 417 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8436 (tm-30) REVERT: D 19 LYS cc_start: 0.9322 (mmmt) cc_final: 0.8933 (mmmm) REVERT: D 73 MET cc_start: 0.9233 (mmm) cc_final: 0.9027 (mmm) REVERT: D 129 CYS cc_start: 0.8933 (t) cc_final: 0.8639 (m) REVERT: D 162 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8188 (mpp80) REVERT: D 257 MET cc_start: 0.8010 (mmm) cc_final: 0.7263 (mmm) REVERT: D 300 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8672 (mtm) REVERT: D 312 THR cc_start: 0.9122 (p) cc_final: 0.7803 (p) REVERT: D 321 MET cc_start: 0.8482 (ptp) cc_final: 0.8155 (ptp) REVERT: D 363 MET cc_start: 0.8238 (ptp) cc_final: 0.7666 (ptt) outliers start: 31 outliers final: 22 residues processed: 157 average time/residue: 0.2275 time to fit residues: 55.0736 Evaluate side-chains 152 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.051642 restraints weight = 42860.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.053683 restraints weight = 20286.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.055090 restraints weight = 11847.367| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13544 Z= 0.149 Angle : 0.492 6.790 18513 Z= 0.243 Chirality : 0.040 0.151 2141 Planarity : 0.004 0.037 2371 Dihedral : 10.263 168.347 2006 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 10.74 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.21), residues: 1710 helix: 2.14 (0.19), residues: 786 sheet: 0.06 (0.33), residues: 260 loop : -0.21 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 397 HIS 0.005 0.001 HIS D 137 PHE 0.012 0.001 PHE B 367 TYR 0.008 0.001 TYR B 310 ARG 0.011 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9180 (m) cc_final: 0.8840 (m) REVERT: A 69 ASP cc_start: 0.7987 (t0) cc_final: 0.7627 (t0) REVERT: A 183 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 203 MET cc_start: 0.8430 (mtm) cc_final: 0.8201 (mtm) REVERT: A 205 ASP cc_start: 0.7702 (t0) cc_final: 0.7432 (m-30) REVERT: A 302 MET cc_start: 0.8566 (mmt) cc_final: 0.8321 (mpp) REVERT: B 1 MET cc_start: 0.8354 (mmt) cc_final: 0.8035 (mmt) REVERT: B 224 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8357 (p0) REVERT: B 321 MET cc_start: 0.8462 (pmm) cc_final: 0.8012 (pmm) REVERT: B 363 MET cc_start: 0.8728 (ptp) cc_final: 0.8347 (ptt) REVERT: C 36 MET cc_start: 0.9010 (tpp) cc_final: 0.8256 (tmm) REVERT: C 69 ASP cc_start: 0.8584 (t0) cc_final: 0.8188 (t70) REVERT: C 183 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8356 (mt-10) REVERT: C 213 CYS cc_start: 0.8580 (t) cc_final: 0.8154 (t) REVERT: C 304 LYS cc_start: 0.8705 (tppt) cc_final: 0.8311 (tppt) REVERT: C 413 MET cc_start: 0.8628 (mmm) cc_final: 0.8153 (tpp) REVERT: C 417 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8349 (tm-30) REVERT: C 432 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.7535 (t80) REVERT: D 19 LYS cc_start: 0.9289 (mmmt) cc_final: 0.8875 (mmmm) REVERT: D 129 CYS cc_start: 0.8897 (t) cc_final: 0.8627 (m) REVERT: D 162 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8198 (mpp80) REVERT: D 257 MET cc_start: 0.7885 (mmm) cc_final: 0.6941 (mmm) REVERT: D 300 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8531 (mtm) REVERT: D 312 THR cc_start: 0.9041 (p) cc_final: 0.7461 (p) REVERT: D 321 MET cc_start: 0.8411 (ptp) cc_final: 0.8134 (ptp) REVERT: D 363 MET cc_start: 0.8214 (ptp) cc_final: 0.7577 (ptt) outliers start: 24 outliers final: 16 residues processed: 156 average time/residue: 0.2616 time to fit residues: 62.6607 Evaluate side-chains 147 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 77 optimal weight: 0.0470 chunk 114 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.052295 restraints weight = 42650.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.054361 restraints weight = 20093.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055762 restraints weight = 11618.377| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13544 Z= 0.138 Angle : 0.488 7.270 18513 Z= 0.238 Chirality : 0.040 0.202 2141 Planarity : 0.004 0.042 2371 Dihedral : 10.091 164.853 2005 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.60 % Allowed : 10.66 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.21), residues: 1710 helix: 2.16 (0.19), residues: 784 sheet: 0.10 (0.33), residues: 260 loop : -0.20 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 397 HIS 0.006 0.001 HIS D 28 PHE 0.010 0.001 PHE D 367 TYR 0.008 0.001 TYR B 200 ARG 0.005 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9180 (m) cc_final: 0.8828 (m) REVERT: A 69 ASP cc_start: 0.7757 (t0) cc_final: 0.7416 (t0) REVERT: A 183 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 203 MET cc_start: 0.8410 (mtm) cc_final: 0.8174 (mtm) REVERT: A 205 ASP cc_start: 0.7677 (t0) cc_final: 0.7330 (m-30) REVERT: A 301 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8022 (mp10) REVERT: A 302 MET cc_start: 0.8547 (mmt) cc_final: 0.8283 (mpp) REVERT: B 73 MET cc_start: 0.8894 (mmt) cc_final: 0.8595 (mmt) REVERT: B 293 MET cc_start: 0.8700 (mmm) cc_final: 0.8382 (mmm) REVERT: B 363 MET cc_start: 0.8716 (ptp) cc_final: 0.8263 (ptt) REVERT: C 36 MET cc_start: 0.8949 (tpp) cc_final: 0.8181 (tmm) REVERT: C 69 ASP cc_start: 0.8536 (t0) cc_final: 0.8132 (t70) REVERT: C 172 TYR cc_start: 0.7890 (t80) cc_final: 0.7352 (t80) REVERT: C 183 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8312 (mt-10) REVERT: C 203 MET cc_start: 0.8812 (mtm) cc_final: 0.8048 (mtm) REVERT: C 327 ASP cc_start: 0.9182 (m-30) cc_final: 0.8906 (p0) REVERT: C 413 MET cc_start: 0.8636 (mmm) cc_final: 0.8236 (tpp) REVERT: C 417 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8306 (tm-30) REVERT: C 432 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7593 (t80) REVERT: D 6 HIS cc_start: 0.8826 (t-90) cc_final: 0.8183 (t-170) REVERT: D 129 CYS cc_start: 0.8907 (t) cc_final: 0.8611 (m) REVERT: D 162 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8175 (mpp80) REVERT: D 257 MET cc_start: 0.7771 (mmm) cc_final: 0.6811 (mmm) REVERT: D 300 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8488 (mpp) REVERT: D 312 THR cc_start: 0.8936 (p) cc_final: 0.7319 (p) REVERT: D 321 MET cc_start: 0.8465 (ptp) cc_final: 0.8115 (ptp) REVERT: D 363 MET cc_start: 0.8165 (ptp) cc_final: 0.7539 (ptt) outliers start: 32 outliers final: 16 residues processed: 165 average time/residue: 0.2200 time to fit residues: 56.5188 Evaluate side-chains 147 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 157 optimal weight: 0.0010 chunk 109 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.061254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.051539 restraints weight = 43453.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.053535 restraints weight = 20450.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054934 restraints weight = 12059.951| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13544 Z= 0.188 Angle : 0.503 8.716 18513 Z= 0.246 Chirality : 0.040 0.159 2141 Planarity : 0.003 0.036 2371 Dihedral : 9.989 165.005 2005 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.60 % Allowed : 11.64 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.21), residues: 1710 helix: 2.18 (0.19), residues: 784 sheet: 0.01 (0.33), residues: 282 loop : -0.07 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 397 HIS 0.004 0.001 HIS D 28 PHE 0.012 0.001 PHE D 367 TYR 0.008 0.001 TYR B 310 ARG 0.006 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9211 (m) cc_final: 0.8853 (m) REVERT: A 69 ASP cc_start: 0.7842 (t0) cc_final: 0.7461 (t0) REVERT: A 183 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8188 (mt-10) REVERT: A 203 MET cc_start: 0.8426 (mtm) cc_final: 0.8180 (mtm) REVERT: A 205 ASP cc_start: 0.7698 (t0) cc_final: 0.7291 (m-30) REVERT: A 302 MET cc_start: 0.8565 (mmt) cc_final: 0.8329 (mpp) REVERT: B 6 HIS cc_start: 0.9084 (t70) cc_final: 0.8870 (t-170) REVERT: B 73 MET cc_start: 0.8933 (mmt) cc_final: 0.8637 (mmt) REVERT: B 363 MET cc_start: 0.8687 (ptp) cc_final: 0.8364 (ptt) REVERT: B 374 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8854 (pt) REVERT: C 36 MET cc_start: 0.8946 (tpp) cc_final: 0.8158 (tmm) REVERT: C 69 ASP cc_start: 0.8518 (t0) cc_final: 0.8145 (t70) REVERT: C 172 TYR cc_start: 0.7845 (t80) cc_final: 0.7321 (t80) REVERT: C 183 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8339 (mt-10) REVERT: C 203 MET cc_start: 0.8851 (mtm) cc_final: 0.8044 (mtm) REVERT: C 304 LYS cc_start: 0.8684 (tppt) cc_final: 0.8305 (tppt) REVERT: C 327 ASP cc_start: 0.9180 (m-30) cc_final: 0.8964 (p0) REVERT: C 413 MET cc_start: 0.8617 (mmm) cc_final: 0.8232 (tpp) REVERT: C 417 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 432 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7555 (t80) REVERT: D 6 HIS cc_start: 0.8857 (t-90) cc_final: 0.8197 (t-170) REVERT: D 129 CYS cc_start: 0.8913 (t) cc_final: 0.8597 (m) REVERT: D 162 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8189 (mpp80) REVERT: D 257 MET cc_start: 0.7816 (mmm) cc_final: 0.6826 (mmm) REVERT: D 300 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8439 (mtm) REVERT: D 312 THR cc_start: 0.8955 (p) cc_final: 0.7324 (p) REVERT: D 321 MET cc_start: 0.8487 (ptp) cc_final: 0.8240 (ptp) REVERT: D 363 MET cc_start: 0.8170 (ptp) cc_final: 0.7525 (ptt) outliers start: 32 outliers final: 16 residues processed: 160 average time/residue: 0.2195 time to fit residues: 55.2869 Evaluate side-chains 150 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 135 optimal weight: 0.0670 chunk 179 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.050220 restraints weight = 43732.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.052111 restraints weight = 20755.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053533 restraints weight = 12398.112| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13544 Z= 0.281 Angle : 0.547 7.656 18513 Z= 0.272 Chirality : 0.042 0.155 2141 Planarity : 0.004 0.034 2371 Dihedral : 9.956 164.662 2001 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 11.96 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.21), residues: 1710 helix: 2.11 (0.19), residues: 786 sheet: -0.02 (0.33), residues: 282 loop : -0.06 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 397 HIS 0.004 0.001 HIS C 139 PHE 0.011 0.001 PHE D 367 TYR 0.011 0.001 TYR B 425 ARG 0.008 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9240 (m) cc_final: 0.8916 (m) REVERT: A 69 ASP cc_start: 0.7991 (t70) cc_final: 0.7624 (t0) REVERT: A 183 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8115 (mt-10) REVERT: A 203 MET cc_start: 0.8456 (mtm) cc_final: 0.8219 (mtm) REVERT: A 302 MET cc_start: 0.8560 (mmt) cc_final: 0.8345 (mpp) REVERT: B 363 MET cc_start: 0.8762 (ptp) cc_final: 0.8238 (ptt) REVERT: B 374 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8898 (pt) REVERT: C 36 MET cc_start: 0.8950 (tpp) cc_final: 0.8181 (tmm) REVERT: C 69 ASP cc_start: 0.8682 (t0) cc_final: 0.8275 (t70) REVERT: C 183 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8373 (mt-10) REVERT: C 304 LYS cc_start: 0.8680 (tppt) cc_final: 0.8335 (tppt) REVERT: C 392 ASP cc_start: 0.8297 (t0) cc_final: 0.8050 (t70) REVERT: C 413 MET cc_start: 0.8565 (mmm) cc_final: 0.6819 (tpp) REVERT: C 432 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7591 (t80) REVERT: D 129 CYS cc_start: 0.8904 (t) cc_final: 0.8593 (m) REVERT: D 162 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8187 (mpp80) REVERT: D 257 MET cc_start: 0.7915 (mmm) cc_final: 0.6928 (mmm) REVERT: D 300 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8521 (mtm) REVERT: D 312 THR cc_start: 0.9020 (p) cc_final: 0.7394 (p) REVERT: D 321 MET cc_start: 0.8491 (ptp) cc_final: 0.8272 (ptp) REVERT: D 363 MET cc_start: 0.8180 (ptp) cc_final: 0.7581 (ptt) outliers start: 32 outliers final: 21 residues processed: 154 average time/residue: 0.2080 time to fit residues: 51.0513 Evaluate side-chains 147 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.060683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.050755 restraints weight = 43474.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.052756 restraints weight = 20746.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054186 restraints weight = 12211.112| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13544 Z= 0.211 Angle : 0.531 10.369 18513 Z= 0.259 Chirality : 0.041 0.170 2141 Planarity : 0.004 0.043 2371 Dihedral : 9.871 164.252 2001 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.20 % Allowed : 12.12 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.21), residues: 1710 helix: 2.09 (0.19), residues: 782 sheet: -0.02 (0.33), residues: 282 loop : -0.01 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 397 HIS 0.007 0.001 HIS B 6 PHE 0.014 0.001 PHE B 367 TYR 0.009 0.001 TYR B 425 ARG 0.006 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9218 (m) cc_final: 0.8877 (m) REVERT: A 69 ASP cc_start: 0.7894 (t70) cc_final: 0.7515 (t0) REVERT: A 183 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8296 (mt-10) REVERT: A 203 MET cc_start: 0.8433 (mtm) cc_final: 0.8199 (mtm) REVERT: B 257 MET cc_start: 0.8946 (mmm) cc_final: 0.8739 (mmm) REVERT: B 363 MET cc_start: 0.8703 (ptp) cc_final: 0.8191 (ptt) REVERT: B 374 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8891 (pt) REVERT: C 36 MET cc_start: 0.8939 (tpp) cc_final: 0.8178 (tmm) REVERT: C 69 ASP cc_start: 0.8645 (t0) cc_final: 0.8249 (t70) REVERT: C 183 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8354 (mt-10) REVERT: C 304 LYS cc_start: 0.8709 (tppt) cc_final: 0.8346 (tppt) REVERT: C 392 ASP cc_start: 0.8287 (t0) cc_final: 0.8049 (t70) REVERT: C 413 MET cc_start: 0.8205 (mmm) cc_final: 0.7837 (tpp) REVERT: C 432 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.7596 (t80) REVERT: D 6 HIS cc_start: 0.8888 (t-90) cc_final: 0.8303 (t-170) REVERT: D 129 CYS cc_start: 0.8918 (t) cc_final: 0.8614 (m) REVERT: D 162 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8124 (mpp80) REVERT: D 257 MET cc_start: 0.7875 (mmm) cc_final: 0.6911 (mmm) REVERT: D 300 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8559 (mtm) REVERT: D 312 THR cc_start: 0.9008 (p) cc_final: 0.7388 (p) REVERT: D 363 MET cc_start: 0.8183 (ptp) cc_final: 0.7578 (ptt) outliers start: 27 outliers final: 22 residues processed: 154 average time/residue: 0.2202 time to fit residues: 53.1670 Evaluate side-chains 151 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 48 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.062058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.052044 restraints weight = 43119.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054097 restraints weight = 20519.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055485 restraints weight = 12021.107| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13544 Z= 0.157 Angle : 0.520 10.988 18513 Z= 0.250 Chirality : 0.041 0.164 2141 Planarity : 0.004 0.039 2371 Dihedral : 9.684 164.506 2001 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.36 % Allowed : 12.29 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.21), residues: 1710 helix: 2.10 (0.19), residues: 780 sheet: -0.04 (0.33), residues: 282 loop : -0.02 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 397 HIS 0.007 0.001 HIS B 6 PHE 0.017 0.001 PHE A 169 TYR 0.008 0.001 TYR B 425 ARG 0.009 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9171 (m) cc_final: 0.8807 (m) REVERT: A 69 ASP cc_start: 0.7811 (t70) cc_final: 0.7433 (t0) REVERT: A 183 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 203 MET cc_start: 0.8405 (mtm) cc_final: 0.8199 (mtm) REVERT: B 224 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8345 (p0) REVERT: B 363 MET cc_start: 0.8606 (ptp) cc_final: 0.7905 (ptt) REVERT: B 374 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8868 (pt) REVERT: B 403 MET cc_start: 0.8882 (mmm) cc_final: 0.8394 (mmm) REVERT: C 36 MET cc_start: 0.8894 (tpp) cc_final: 0.8135 (tmm) REVERT: C 69 ASP cc_start: 0.8376 (t0) cc_final: 0.8047 (t70) REVERT: C 183 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8324 (mt-10) REVERT: C 304 LYS cc_start: 0.8692 (tppt) cc_final: 0.8328 (tppt) REVERT: C 392 ASP cc_start: 0.8215 (t0) cc_final: 0.7892 (t70) REVERT: C 432 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7617 (t80) REVERT: D 6 HIS cc_start: 0.8851 (t-90) cc_final: 0.8338 (t-170) REVERT: D 129 CYS cc_start: 0.8911 (t) cc_final: 0.8600 (m) REVERT: D 162 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8221 (mpp80) REVERT: D 257 MET cc_start: 0.7795 (mmm) cc_final: 0.6829 (mmm) REVERT: D 300 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8494 (mpp) REVERT: D 312 THR cc_start: 0.8928 (p) cc_final: 0.7304 (p) REVERT: D 363 MET cc_start: 0.8145 (ptp) cc_final: 0.7938 (ptp) outliers start: 29 outliers final: 20 residues processed: 155 average time/residue: 0.2147 time to fit residues: 52.7539 Evaluate side-chains 153 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 0.0870 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.051709 restraints weight = 43212.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053698 restraints weight = 20540.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055050 restraints weight = 12180.013| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13544 Z= 0.183 Angle : 0.538 11.682 18513 Z= 0.260 Chirality : 0.041 0.155 2141 Planarity : 0.004 0.039 2371 Dihedral : 9.584 164.691 2001 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.03 % Allowed : 12.61 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.21), residues: 1710 helix: 2.08 (0.19), residues: 788 sheet: -0.05 (0.33), residues: 282 loop : 0.02 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 397 HIS 0.006 0.001 HIS B 6 PHE 0.018 0.001 PHE A 169 TYR 0.011 0.001 TYR C 172 ARG 0.009 0.000 ARG C 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9176 (m) cc_final: 0.8816 (m) REVERT: A 69 ASP cc_start: 0.7828 (t70) cc_final: 0.7451 (t0) REVERT: A 183 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 203 MET cc_start: 0.8431 (mtm) cc_final: 0.8197 (mtm) REVERT: A 302 MET cc_start: 0.8668 (tpp) cc_final: 0.8079 (mpp) REVERT: B 363 MET cc_start: 0.8594 (ptp) cc_final: 0.8037 (ptt) REVERT: B 374 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8874 (pt) REVERT: B 403 MET cc_start: 0.8829 (mmm) cc_final: 0.8444 (mmm) REVERT: C 36 MET cc_start: 0.8883 (tpp) cc_final: 0.8131 (tmm) REVERT: C 69 ASP cc_start: 0.8582 (t0) cc_final: 0.8204 (t70) REVERT: C 183 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8339 (mt-10) REVERT: C 392 ASP cc_start: 0.8256 (t0) cc_final: 0.7991 (t70) REVERT: C 432 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7583 (t80) REVERT: D 6 HIS cc_start: 0.8860 (t-90) cc_final: 0.8330 (t-170) REVERT: D 129 CYS cc_start: 0.8920 (t) cc_final: 0.8602 (m) REVERT: D 162 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8174 (mpp80) REVERT: D 257 MET cc_start: 0.7820 (mmm) cc_final: 0.6838 (mmm) REVERT: D 300 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8552 (mpp) REVERT: D 312 THR cc_start: 0.8928 (p) cc_final: 0.7313 (p) REVERT: D 363 MET cc_start: 0.8155 (ptp) cc_final: 0.7663 (ptt) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.2169 time to fit residues: 51.7798 Evaluate side-chains 150 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 148 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 133 optimal weight: 0.0980 chunk 177 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051663 restraints weight = 44054.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053733 restraints weight = 20611.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055182 restraints weight = 11962.718| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13544 Z= 0.140 Angle : 0.522 11.337 18513 Z= 0.250 Chirality : 0.040 0.160 2141 Planarity : 0.003 0.040 2371 Dihedral : 9.371 165.072 2001 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.71 % Allowed : 12.86 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.21), residues: 1710 helix: 2.12 (0.19), residues: 784 sheet: 0.02 (0.33), residues: 282 loop : 0.06 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 388 HIS 0.006 0.001 HIS B 6 PHE 0.018 0.001 PHE A 169 TYR 0.007 0.001 TYR A 108 ARG 0.007 0.000 ARG C 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.51 seconds wall clock time: 62 minutes 33.38 seconds (3753.38 seconds total)