Starting phenix.real_space_refine on Thu Jul 31 09:34:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc1_19042/07_2025/8rc1_19042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc1_19042/07_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_19042/07_2025/8rc1_19042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc1_19042/07_2025/8rc1_19042.map" model { file = "/net/cci-nas-00/data/ceres_data/8rc1_19042/07_2025/8rc1_19042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc1_19042/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.81, per 1000 atoms: 0.74 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: 3.79 Conformation dependent library (CDL) restraints added in 1.9 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: 1.59 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: 4.33 Time building geometry restraints manager: 4.19 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.100 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.550 ------------------------------------------------------------------------------- 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= 0.107 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 Details of bonding type rmsd hydrogen bonds : bond 0.19451 ( 747) hydrogen bonds : angle 6.60376 ( 2190) covalent geometry : bond 0.00209 (13544) covalent geometry : angle 0.47477 (18513) *********************** 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 : 1.585 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: 0.2639 time to fit residues: 82.7422 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 : 1.530 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.061315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051418 restraints weight = 42855.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.053461 restraints weight = 20321.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.054877 restraints weight = 11864.446| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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= 0.125 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 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 747) hydrogen bonds : angle 4.49760 ( 2190) covalent geometry : bond 0.00265 (13544) covalent geometry : angle 0.52542 (18513) *********************** 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 : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9196 (m) cc_final: 0.8877 (m) REVERT: A 69 ASP cc_start: 0.8048 (t0) cc_final: 0.7664 (t0) REVERT: A 183 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 203 MET cc_start: 0.8429 (mtm) cc_final: 0.8180 (mtm) REVERT: A 205 ASP cc_start: 0.7633 (t0) cc_final: 0.7384 (m-30) REVERT: A 301 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8199 (mp10) REVERT: A 302 MET cc_start: 0.8615 (mmt) cc_final: 0.8299 (mpp) REVERT: A 327 ASP cc_start: 0.9243 (m-30) cc_final: 0.9023 (m-30) REVERT: A 358 GLN cc_start: 0.9383 (tp-100) cc_final: 0.9022 (tp-100) REVERT: A 377 MET cc_start: 0.8931 (ttp) cc_final: 0.8688 (ttm) REVERT: A 411 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8114 (mm-30) REVERT: B 1 MET cc_start: 0.8294 (mmt) cc_final: 0.8014 (mmt) REVERT: B 321 MET cc_start: 0.8526 (pmm) cc_final: 0.8156 (pmm) REVERT: B 363 MET cc_start: 0.8761 (ptp) cc_final: 0.8415 (ptp) REVERT: C 36 MET cc_start: 0.8987 (tpp) cc_final: 0.8666 (tmm) REVERT: C 69 ASP cc_start: 0.8626 (t0) cc_final: 0.8280 (t70) REVERT: C 133 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8115 (mm110) REVERT: C 183 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8333 (mt-10) REVERT: C 213 CYS cc_start: 0.8613 (t) cc_final: 0.8303 (t) REVERT: C 417 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8468 (tm-30) REVERT: D 6 HIS cc_start: 0.8782 (t-90) cc_final: 0.8132 (t-170) REVERT: D 19 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8893 (mmmm) REVERT: D 73 MET cc_start: 0.9169 (mmm) cc_final: 0.8916 (mmm) REVERT: D 129 CYS cc_start: 0.8872 (t) cc_final: 0.8670 (m) REVERT: D 162 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8209 (mpp80) REVERT: D 257 MET cc_start: 0.8005 (mmm) cc_final: 0.7289 (mmm) REVERT: D 300 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8754 (mtm) REVERT: D 312 THR cc_start: 0.9129 (p) cc_final: 0.7814 (p) REVERT: D 321 MET cc_start: 0.8361 (ptp) cc_final: 0.8069 (ptp) REVERT: D 363 MET cc_start: 0.8157 (ptp) cc_final: 0.7850 (ptp) REVERT: D 403 MET cc_start: 0.8934 (mmm) cc_final: 0.8364 (mmm) outliers start: 27 outliers final: 17 residues processed: 169 average time/residue: 0.2091 time to fit residues: 54.8097 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 : 1.356 ------------------------------------------------------------------------------- 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: 9.9990 chunk 145 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.1642 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.059549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.049760 restraints weight = 44195.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051757 restraints weight = 20939.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053134 restraints weight = 12213.458| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13544 Z= 0.205 Angle : 0.551 7.177 18513 Z= 0.274 Chirality : 0.042 0.144 2141 Planarity : 0.004 0.037 2371 Dihedral : 10.483 171.634 2006 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.60 % Allowed : 9.52 % 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: 1.38 (0.21), residues: 1710 helix: 2.14 (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 0.005 0.001 HIS C 139 PHE 0.014 0.001 PHE B 367 TYR 0.012 0.001 TYR B 425 ARG 0.005 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 747) hydrogen bonds : angle 4.41740 ( 2190) covalent geometry : bond 0.00452 (13544) covalent geometry : angle 0.55139 (18513) *********************** 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 164 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9239 (m) cc_final: 0.8911 (m) REVERT: A 69 ASP cc_start: 0.8123 (t0) cc_final: 0.7756 (t0) REVERT: A 183 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 203 MET cc_start: 0.8530 (mtm) cc_final: 0.8302 (mtm) REVERT: A 205 ASP cc_start: 0.7849 (t0) cc_final: 0.7532 (m-30) REVERT: A 301 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8269 (mp10) REVERT: A 302 MET cc_start: 0.8644 (mmt) cc_final: 0.8367 (mpp) REVERT: A 377 MET cc_start: 0.9078 (ttp) cc_final: 0.8626 (ttm) REVERT: A 411 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B 1 MET cc_start: 0.8385 (mmt) cc_final: 0.8158 (mmt) REVERT: B 321 MET cc_start: 0.8602 (pmm) cc_final: 0.8218 (pmm) REVERT: B 363 MET cc_start: 0.8769 (ptp) cc_final: 0.8408 (ptt) REVERT: C 69 ASP cc_start: 0.8643 (t0) cc_final: 0.8308 (t70) REVERT: C 133 GLN cc_start: 0.8810 (mm-40) cc_final: 0.7996 (mm110) REVERT: C 183 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8431 (mt-10) REVERT: C 205 ASP cc_start: 0.7967 (t0) cc_final: 0.7636 (t0) REVERT: C 213 CYS cc_start: 0.8620 (t) cc_final: 0.8203 (t) REVERT: C 304 LYS cc_start: 0.8703 (tppt) cc_final: 0.8408 (tppt) REVERT: C 413 MET cc_start: 0.8635 (mmm) cc_final: 0.7959 (tpp) REVERT: C 417 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8440 (tm-30) REVERT: D 19 LYS cc_start: 0.9326 (mmmt) cc_final: 0.8938 (mmmm) REVERT: D 73 MET cc_start: 0.9224 (mmm) cc_final: 0.9020 (mmm) REVERT: D 129 CYS cc_start: 0.8920 (t) cc_final: 0.8641 (m) REVERT: D 162 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8186 (mpp80) REVERT: D 257 MET cc_start: 0.8010 (mmm) cc_final: 0.7260 (mmm) REVERT: D 300 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8679 (mtm) REVERT: D 312 THR cc_start: 0.9126 (p) cc_final: 0.7815 (p) REVERT: D 321 MET cc_start: 0.8486 (ptp) cc_final: 0.8159 (ptp) REVERT: D 363 MET cc_start: 0.8238 (ptp) cc_final: 0.7672 (ptt) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 0.2314 time to fit residues: 56.2665 Evaluate side-chains 153 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 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 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: 0.3980 chunk 140 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.061487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.051467 restraints weight = 42967.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053528 restraints weight = 20411.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.054896 restraints weight = 11944.788| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1917 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= 0.107 Angle : 0.491 6.765 18513 Z= 0.243 Chirality : 0.040 0.150 2141 Planarity : 0.003 0.038 2371 Dihedral : 10.261 168.301 2006 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.95 % Allowed : 10.66 % Favored : 87.39 % 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: 1.36 (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 0.011 0.001 TRP D 397 HIS 0.006 0.001 HIS D 137 PHE 0.012 0.001 PHE D 367 TYR 0.008 0.001 TYR B 310 ARG 0.003 0.000 ARG A 422 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 747) hydrogen bonds : angle 4.08657 ( 2190) covalent geometry : bond 0.00230 (13544) covalent geometry : angle 0.49100 (18513) *********************** 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 : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9183 (m) cc_final: 0.8844 (m) REVERT: A 69 ASP cc_start: 0.7977 (t0) cc_final: 0.7635 (t0) REVERT: A 183 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 203 MET cc_start: 0.8429 (mtm) cc_final: 0.8205 (mtm) REVERT: A 205 ASP cc_start: 0.7711 (t0) cc_final: 0.7442 (m-30) REVERT: A 302 MET cc_start: 0.8567 (mmt) cc_final: 0.8327 (mpp) REVERT: B 1 MET cc_start: 0.8348 (mmt) cc_final: 0.8024 (mmt) REVERT: B 224 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8369 (p0) REVERT: B 321 MET cc_start: 0.8454 (pmm) cc_final: 0.8018 (pmm) REVERT: B 363 MET cc_start: 0.8728 (ptp) cc_final: 0.8347 (ptt) REVERT: C 36 MET cc_start: 0.9031 (tpp) cc_final: 0.8289 (tmm) REVERT: C 69 ASP cc_start: 0.8588 (t0) cc_final: 0.8190 (t70) REVERT: C 183 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8355 (mt-10) REVERT: C 205 ASP cc_start: 0.7886 (t0) cc_final: 0.7543 (t0) REVERT: C 213 CYS cc_start: 0.8567 (t) cc_final: 0.8144 (t) REVERT: C 304 LYS cc_start: 0.8676 (tppt) cc_final: 0.8412 (tppt) REVERT: C 413 MET cc_start: 0.8616 (mmm) cc_final: 0.8132 (tpp) REVERT: C 417 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 432 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7530 (t80) REVERT: D 19 LYS cc_start: 0.9291 (mmmt) cc_final: 0.8880 (mmmm) REVERT: D 129 CYS cc_start: 0.8907 (t) cc_final: 0.8641 (m) REVERT: D 162 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8205 (mpp80) REVERT: D 257 MET cc_start: 0.7894 (mmm) cc_final: 0.6952 (mmm) REVERT: D 300 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8526 (mtm) REVERT: D 312 THR cc_start: 0.9048 (p) cc_final: 0.7468 (p) REVERT: D 321 MET cc_start: 0.8424 (ptp) cc_final: 0.8193 (ptp) REVERT: D 363 MET cc_start: 0.8215 (ptp) cc_final: 0.7569 (ptt) outliers start: 24 outliers final: 16 residues processed: 157 average time/residue: 0.2264 time to fit residues: 54.6273 Evaluate side-chains 148 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 48 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** B 347 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052046 restraints weight = 42739.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054125 restraints weight = 20255.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055509 restraints weight = 11774.951| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13544 Z= 0.101 Angle : 0.482 7.166 18513 Z= 0.236 Chirality : 0.040 0.196 2141 Planarity : 0.003 0.038 2371 Dihedral : 10.080 164.845 2005 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.44 % Allowed : 10.58 % Favored : 86.98 % 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: 1.40 (0.21), residues: 1710 helix: 2.16 (0.19), residues: 784 sheet: 0.09 (0.33), residues: 270 loop : -0.16 (0.24), residues: 656 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 310 ARG 0.003 0.000 ARG D 241 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 747) hydrogen bonds : angle 3.93517 ( 2190) covalent geometry : bond 0.00214 (13544) covalent geometry : angle 0.48215 (18513) *********************** 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 171 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9186 (m) cc_final: 0.8832 (m) REVERT: A 69 ASP cc_start: 0.7753 (t0) cc_final: 0.7416 (t0) REVERT: A 183 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 203 MET cc_start: 0.8412 (mtm) cc_final: 0.8159 (mtm) REVERT: A 205 ASP cc_start: 0.7670 (t0) cc_final: 0.7292 (m-30) REVERT: A 302 MET cc_start: 0.8548 (mmt) cc_final: 0.8319 (mpp) REVERT: B 293 MET cc_start: 0.8697 (mmm) cc_final: 0.8379 (mmm) REVERT: B 363 MET cc_start: 0.8712 (ptp) cc_final: 0.8258 (ptt) REVERT: B 407 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: C 36 MET cc_start: 0.8971 (tpp) cc_final: 0.8215 (tmm) REVERT: C 69 ASP cc_start: 0.8536 (t0) cc_final: 0.8144 (t70) REVERT: C 172 TYR cc_start: 0.8042 (t80) cc_final: 0.7707 (t80) REVERT: C 183 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8323 (mt-10) REVERT: C 205 ASP cc_start: 0.7851 (t0) cc_final: 0.7449 (t0) REVERT: C 213 CYS cc_start: 0.8753 (t) cc_final: 0.8353 (t) REVERT: C 327 ASP cc_start: 0.9177 (m-30) cc_final: 0.8911 (p0) REVERT: C 413 MET cc_start: 0.8627 (mmm) cc_final: 0.8220 (tpp) REVERT: C 417 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 432 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.7613 (t80) REVERT: D 6 HIS cc_start: 0.8839 (t-90) cc_final: 0.8200 (t-170) REVERT: D 129 CYS cc_start: 0.8906 (t) cc_final: 0.8608 (m) REVERT: D 162 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8199 (mpp80) REVERT: D 257 MET cc_start: 0.7770 (mmm) cc_final: 0.6811 (mmm) REVERT: D 300 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8491 (mpp) REVERT: D 312 THR cc_start: 0.8934 (p) cc_final: 0.7308 (p) REVERT: D 321 MET cc_start: 0.8481 (ptp) cc_final: 0.8130 (ptp) REVERT: D 363 MET cc_start: 0.8167 (ptp) cc_final: 0.7539 (ptt) outliers start: 30 outliers final: 16 residues processed: 165 average time/residue: 0.2270 time to fit residues: 58.3229 Evaluate side-chains 148 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 407 GLU 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: 10.0000 chunk 99 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 3 optimal weight: 0.0040 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 ** 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 = 0.3268 r_free = 0.3268 target = 0.060772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.051052 restraints weight = 43780.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053082 restraints weight = 20674.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.054479 restraints weight = 12019.087| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13544 Z= 0.145 Angle : 0.513 8.729 18513 Z= 0.253 Chirality : 0.041 0.156 2141 Planarity : 0.004 0.074 2371 Dihedral : 10.021 164.927 2005 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.85 % Allowed : 10.98 % Favored : 86.17 % 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: 2.16 (0.19), residues: 786 sheet: -0.00 (0.33), residues: 282 loop : -0.04 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 397 HIS 0.005 0.001 HIS D 28 PHE 0.012 0.001 PHE D 367 TYR 0.009 0.001 TYR B 425 ARG 0.020 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 747) hydrogen bonds : angle 3.94741 ( 2190) covalent geometry : bond 0.00320 (13544) covalent geometry : angle 0.51329 (18513) *********************** 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 166 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9212 (m) cc_final: 0.8861 (m) REVERT: A 69 ASP cc_start: 0.7862 (t0) cc_final: 0.7484 (t0) REVERT: A 183 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 203 MET cc_start: 0.8427 (mtm) cc_final: 0.8183 (mtm) REVERT: A 205 ASP cc_start: 0.7723 (t0) cc_final: 0.7366 (m-30) REVERT: B 293 MET cc_start: 0.8709 (mmm) cc_final: 0.8413 (mtp) REVERT: B 363 MET cc_start: 0.8684 (ptp) cc_final: 0.8363 (ptt) REVERT: B 374 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8885 (pt) REVERT: C 36 MET cc_start: 0.8960 (tpp) cc_final: 0.8194 (tmm) REVERT: C 69 ASP cc_start: 0.8532 (t0) cc_final: 0.8167 (t70) REVERT: C 172 TYR cc_start: 0.7915 (t80) cc_final: 0.7408 (t80) REVERT: C 183 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8353 (mt-10) REVERT: C 205 ASP cc_start: 0.7835 (t0) cc_final: 0.7429 (t0) REVERT: C 304 LYS cc_start: 0.8714 (tppt) cc_final: 0.8415 (tppt) REVERT: C 413 MET cc_start: 0.8600 (mmm) cc_final: 0.8238 (tpp) REVERT: C 417 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 432 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7596 (t80) REVERT: D 6 HIS cc_start: 0.8860 (t-90) cc_final: 0.8218 (t-170) REVERT: D 129 CYS cc_start: 0.8902 (t) cc_final: 0.8620 (m) REVERT: D 162 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8176 (mpp80) REVERT: D 257 MET cc_start: 0.7836 (mmm) cc_final: 0.6862 (mmm) REVERT: D 300 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8514 (mpp) REVERT: D 312 THR cc_start: 0.8974 (p) cc_final: 0.7346 (p) REVERT: D 363 MET cc_start: 0.8161 (ptp) cc_final: 0.7546 (ptt) outliers start: 35 outliers final: 20 residues processed: 161 average time/residue: 0.2167 time to fit residues: 55.8515 Evaluate side-chains 154 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 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: 0.0070 chunk 135 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.061274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051459 restraints weight = 43456.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053504 restraints weight = 20373.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054914 restraints weight = 11801.823| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13544 Z= 0.128 Angle : 0.513 7.787 18513 Z= 0.251 Chirality : 0.041 0.151 2141 Planarity : 0.004 0.037 2371 Dihedral : 9.915 164.848 2005 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.36 % Allowed : 12.04 % Favored : 85.60 % 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: 1.41 (0.21), residues: 1710 helix: 2.15 (0.19), residues: 784 sheet: 0.01 (0.33), residues: 282 loop : -0.08 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 397 HIS 0.007 0.001 HIS B 6 PHE 0.011 0.001 PHE D 367 TYR 0.009 0.001 TYR B 310 ARG 0.014 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 747) hydrogen bonds : angle 3.90294 ( 2190) covalent geometry : bond 0.00285 (13544) covalent geometry : angle 0.51337 (18513) *********************** 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 160 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9204 (m) cc_final: 0.8849 (m) REVERT: A 69 ASP cc_start: 0.7863 (t0) cc_final: 0.7482 (t0) REVERT: A 183 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8234 (mt-10) REVERT: A 203 MET cc_start: 0.8430 (mtm) cc_final: 0.8198 (mtm) REVERT: A 205 ASP cc_start: 0.7706 (t0) cc_final: 0.7324 (m-30) REVERT: A 302 MET cc_start: 0.8593 (tpp) cc_final: 0.8321 (mmt) REVERT: A 417 GLU cc_start: 0.7627 (mp0) cc_final: 0.7347 (mp0) REVERT: B 363 MET cc_start: 0.8767 (ptp) cc_final: 0.8113 (ptt) REVERT: B 374 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8861 (pt) REVERT: C 36 MET cc_start: 0.8962 (tpp) cc_final: 0.8189 (tmm) REVERT: C 69 ASP cc_start: 0.8581 (t0) cc_final: 0.8193 (t70) REVERT: C 172 TYR cc_start: 0.7867 (t80) cc_final: 0.7227 (t80) REVERT: C 183 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8348 (mt-10) REVERT: C 304 LYS cc_start: 0.8688 (tppt) cc_final: 0.8435 (tppt) REVERT: C 413 MET cc_start: 0.8557 (mmm) cc_final: 0.6872 (tpp) REVERT: C 432 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7624 (t80) REVERT: D 6 HIS cc_start: 0.8875 (t-90) cc_final: 0.8264 (t-170) REVERT: D 129 CYS cc_start: 0.8907 (t) cc_final: 0.8609 (m) REVERT: D 162 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8195 (mpp80) REVERT: D 257 MET cc_start: 0.7842 (mmm) cc_final: 0.6865 (mmm) REVERT: D 300 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8350 (mpp) REVERT: D 312 THR cc_start: 0.8956 (p) cc_final: 0.7337 (p) REVERT: D 363 MET cc_start: 0.8126 (ptp) cc_final: 0.7625 (ptt) outliers start: 29 outliers final: 20 residues processed: 154 average time/residue: 0.2634 time to fit residues: 64.4526 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 : 1.729 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 25 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.060384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.050490 restraints weight = 43604.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.052508 restraints weight = 20809.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053902 restraints weight = 12176.765| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13544 Z= 0.176 Angle : 0.542 7.601 18513 Z= 0.268 Chirality : 0.042 0.151 2141 Planarity : 0.004 0.034 2371 Dihedral : 9.865 164.641 2001 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 1.36 (0.21), residues: 1710 helix: 2.06 (0.19), residues: 786 sheet: -0.03 (0.33), residues: 282 loop : -0.04 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 397 HIS 0.006 0.001 HIS B 6 PHE 0.011 0.001 PHE D 367 TYR 0.010 0.001 TYR B 425 ARG 0.010 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 747) hydrogen bonds : angle 4.01737 ( 2190) covalent geometry : bond 0.00388 (13544) covalent geometry : angle 0.54155 (18513) *********************** 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 160 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9227 (m) cc_final: 0.8892 (m) REVERT: A 69 ASP cc_start: 0.7972 (t70) cc_final: 0.7590 (t0) REVERT: A 183 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8106 (mt-10) REVERT: A 203 MET cc_start: 0.8440 (mtm) cc_final: 0.8213 (mtm) REVERT: B 363 MET cc_start: 0.8753 (ptp) cc_final: 0.8296 (ptt) REVERT: B 374 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8888 (pt) REVERT: C 36 MET cc_start: 0.8955 (tpp) cc_final: 0.8198 (tmm) REVERT: C 69 ASP cc_start: 0.8643 (t0) cc_final: 0.8250 (t70) REVERT: C 183 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8358 (mt-10) REVERT: C 304 LYS cc_start: 0.8726 (tppt) cc_final: 0.8459 (tppt) REVERT: C 413 MET cc_start: 0.8216 (mmm) cc_final: 0.7858 (tpp) REVERT: C 432 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7636 (t80) REVERT: D 6 HIS cc_start: 0.8889 (t-90) cc_final: 0.8275 (t-170) REVERT: D 129 CYS cc_start: 0.8917 (t) cc_final: 0.8619 (m) REVERT: D 162 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8206 (mpp80) REVERT: D 257 MET cc_start: 0.7872 (mmm) cc_final: 0.6893 (mmm) REVERT: D 300 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8479 (mtm) REVERT: D 312 THR cc_start: 0.9005 (p) cc_final: 0.7380 (p) REVERT: D 363 MET cc_start: 0.8133 (ptp) cc_final: 0.7649 (ptt) outliers start: 32 outliers final: 22 residues processed: 154 average time/residue: 0.2024 time to fit residues: 49.6299 Evaluate side-chains 150 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.061813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052036 restraints weight = 43160.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.054057 restraints weight = 20401.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055465 restraints weight = 11932.544| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13544 Z= 0.107 Angle : 0.521 8.114 18513 Z= 0.252 Chirality : 0.041 0.171 2141 Planarity : 0.004 0.044 2371 Dihedral : 9.708 164.615 2001 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.03 % Allowed : 12.29 % 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: 1.41 (0.21), residues: 1710 helix: 2.12 (0.19), residues: 780 sheet: 0.04 (0.33), residues: 282 loop : -0.03 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 397 HIS 0.006 0.001 HIS B 6 PHE 0.012 0.001 PHE B 367 TYR 0.008 0.001 TYR B 425 ARG 0.009 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 747) hydrogen bonds : angle 3.91594 ( 2190) covalent geometry : bond 0.00234 (13544) covalent geometry : angle 0.52101 (18513) *********************** 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 159 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9194 (m) cc_final: 0.8832 (m) REVERT: A 69 ASP cc_start: 0.7844 (t70) cc_final: 0.7467 (t0) REVERT: A 183 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8227 (mt-10) REVERT: A 203 MET cc_start: 0.8426 (mtm) cc_final: 0.8214 (mtm) REVERT: A 302 MET cc_start: 0.8704 (tpp) cc_final: 0.8429 (mmt) REVERT: B 363 MET cc_start: 0.8749 (ptp) cc_final: 0.8261 (ptt) REVERT: B 403 MET cc_start: 0.8884 (mmm) cc_final: 0.8379 (mmm) REVERT: B 407 GLU cc_start: 0.8709 (tt0) cc_final: 0.8493 (tt0) REVERT: C 36 MET cc_start: 0.8925 (tpp) cc_final: 0.8157 (tmm) REVERT: C 69 ASP cc_start: 0.8551 (t0) cc_final: 0.8169 (t70) REVERT: C 172 TYR cc_start: 0.7831 (t80) cc_final: 0.7150 (t80) REVERT: C 183 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8309 (mt-10) REVERT: C 304 LYS cc_start: 0.8663 (tppt) cc_final: 0.8409 (tppt) REVERT: C 432 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7563 (t80) REVERT: D 6 HIS cc_start: 0.8864 (t-90) cc_final: 0.8310 (t-170) REVERT: D 129 CYS cc_start: 0.8901 (t) cc_final: 0.8581 (m) REVERT: D 162 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8217 (mpp80) REVERT: D 257 MET cc_start: 0.7807 (mmm) cc_final: 0.6848 (mmm) REVERT: D 300 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8461 (mpp) REVERT: D 312 THR cc_start: 0.8944 (p) cc_final: 0.7313 (p) REVERT: D 363 MET cc_start: 0.8183 (ptp) cc_final: 0.7670 (ptt) outliers start: 25 outliers final: 18 residues processed: 155 average time/residue: 0.2900 time to fit residues: 72.6218 Evaluate side-chains 151 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 76 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 152 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3243 r_free = 0.3243 target = 0.059684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.050021 restraints weight = 43811.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051948 restraints weight = 20826.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053292 restraints weight = 12282.053| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13544 Z= 0.196 Angle : 0.571 8.804 18513 Z= 0.281 Chirality : 0.042 0.158 2141 Planarity : 0.004 0.035 2371 Dihedral : 9.699 164.050 2001 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.87 % Allowed : 12.53 % Favored : 85.60 % 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: 1.33 (0.21), residues: 1710 helix: 2.01 (0.19), residues: 786 sheet: -0.02 (0.33), residues: 282 loop : -0.03 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 397 HIS 0.005 0.001 HIS B 6 PHE 0.013 0.001 PHE B 367 TYR 0.010 0.001 TYR B 425 ARG 0.008 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 747) hydrogen bonds : angle 4.06431 ( 2190) covalent geometry : bond 0.00433 (13544) covalent geometry : angle 0.57057 (18513) ********************** 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 151 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9278 (m) cc_final: 0.9032 (m) REVERT: A 69 ASP cc_start: 0.8003 (t70) cc_final: 0.7633 (t0) REVERT: A 183 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 203 MET cc_start: 0.8465 (mtm) cc_final: 0.8217 (mtm) REVERT: A 302 MET cc_start: 0.8951 (tpp) cc_final: 0.8409 (mpp) REVERT: B 224 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8433 (p0) REVERT: B 363 MET cc_start: 0.8778 (ptp) cc_final: 0.8323 (ptt) REVERT: B 403 MET cc_start: 0.8758 (mmm) cc_final: 0.8326 (mmm) REVERT: C 25 CYS cc_start: 0.9192 (m) cc_final: 0.8986 (m) REVERT: C 36 MET cc_start: 0.8940 (tpp) cc_final: 0.8143 (tmm) REVERT: C 69 ASP cc_start: 0.8686 (t0) cc_final: 0.8286 (t70) REVERT: C 183 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 304 LYS cc_start: 0.8706 (tppt) cc_final: 0.8391 (tppt) REVERT: C 432 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.7650 (t80) REVERT: D 6 HIS cc_start: 0.8923 (t-90) cc_final: 0.8268 (t-170) REVERT: D 19 LYS cc_start: 0.9391 (mmmt) cc_final: 0.8988 (mmmm) REVERT: D 129 CYS cc_start: 0.8919 (t) cc_final: 0.8590 (m) REVERT: D 162 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8210 (mpp80) REVERT: D 257 MET cc_start: 0.7902 (mmm) cc_final: 0.6885 (mmm) REVERT: D 300 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8662 (mtm) REVERT: D 312 THR cc_start: 0.9023 (p) cc_final: 0.7391 (p) REVERT: D 363 MET cc_start: 0.8121 (ptp) cc_final: 0.7622 (ptt) outliers start: 23 outliers final: 18 residues processed: 148 average time/residue: 0.2116 time to fit residues: 49.7351 Evaluate side-chains 149 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 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 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 148 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 177 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.061567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051637 restraints weight = 43461.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053666 restraints weight = 20637.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055043 restraints weight = 12091.669| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13544 Z= 0.111 Angle : 0.534 12.925 18513 Z= 0.256 Chirality : 0.041 0.165 2141 Planarity : 0.004 0.040 2371 Dihedral : 9.529 163.882 2001 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.87 % Allowed : 12.61 % Favored : 85.52 % 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: 2.12 (0.19), residues: 778 sheet: -0.03 (0.33), residues: 282 loop : -0.04 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 397 HIS 0.005 0.001 HIS B 6 PHE 0.010 0.001 PHE D 367 TYR 0.008 0.001 TYR B 425 ARG 0.009 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 747) hydrogen bonds : angle 3.93664 ( 2190) covalent geometry : bond 0.00244 (13544) covalent geometry : angle 0.53394 (18513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.14 seconds wall clock time: 72 minutes 4.84 seconds (4324.84 seconds total)