Starting phenix.real_space_refine on Thu Mar 5 12:51:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wmp_21850/03_2026/6wmp_21850_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wmp_21850/03_2026/6wmp_21850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wmp_21850/03_2026/6wmp_21850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wmp_21850/03_2026/6wmp_21850.map" model { file = "/net/cci-nas-00/data/ceres_data/6wmp_21850/03_2026/6wmp_21850_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wmp_21850/03_2026/6wmp_21850_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 46 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 13892 2.51 5 N 3913 2.21 5 O 4353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 158 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22296 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1694 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1765 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 225} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 8711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 8711 Classifications: {'peptide': 1196} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'PTRANS': 42, 'TRANS': 1153} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 679 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 543 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLU:plan': 37, 'ASN:plan1': 10, 'GLN:plan1': 8, 'TYR:plan': 4, 'ASP:plan': 19, 'ARG:plan': 9, 'HIS:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 369 Chain: "D" Number of atoms: 8637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8637 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1117} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 23, 'ASP:plan': 15, 'ASN:plan1': 5, 'TYR:plan': 2, 'GLN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 253 Chain: "E" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 515 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 68} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "G" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 483 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "R" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 223 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12627 SG CYS D 68 21.396 110.706 82.706 1.00 70.94 S ATOM 12641 SG CYS D 70 21.663 112.631 85.402 1.00 73.26 S ATOM 18295 SG CYS D 811 54.221 92.777 26.023 1.00 28.86 S ATOM 18814 SG CYS D 884 55.103 92.331 29.836 1.00 26.71 S ATOM 18870 SG CYS D 891 53.389 89.799 28.314 1.00 26.19 S ATOM 18890 SG CYS D 894 57.137 89.799 27.638 1.00 26.65 S Time building chain proxies: 5.00, per 1000 atoms: 0.22 Number of scatterers: 22296 At special positions: 0 Unit cell: (125.19, 162.64, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 46 15.00 Mg 1 11.99 O 4353 8.00 N 3913 7.00 C 13892 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: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1702 " pdb="ZN ZN D1702 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1702 " - pdb=" SG CYS D 68 " pdb=" ZN D1703 " pdb="ZN ZN D1703 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1703 " - pdb=" SG CYS D 894 " pdb="ZN ZN D1703 " - pdb=" SG CYS D 884 " pdb="ZN ZN D1703 " - pdb=" SG CYS D 811 " Number of angles added : 6 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 31 sheets defined 34.5% alpha, 12.2% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.512A pdb=" N LEU A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.735A pdb=" N PHE B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.724A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.613A pdb=" N ARG B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.681A pdb=" N LYS C 8 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.660A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.717A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 removed outlier: 4.138A pdb=" N GLN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 216 through 221 removed outlier: 4.068A pdb=" N ILE C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 221' Processing helix chain 'C' and resid 349 through 354 Processing helix chain 'C' and resid 360 through 373 removed outlier: 3.704A pdb=" N VAL C 371 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 removed outlier: 3.546A pdb=" N LEU C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 387 " --> pdb=" O VAL C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 411 Processing helix chain 'C' and resid 425 through 440 removed outlier: 3.713A pdb=" N VAL C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 482 removed outlier: 3.573A pdb=" N ARG C 473 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG C 479 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 512 removed outlier: 3.505A pdb=" N THR C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 530 removed outlier: 3.756A pdb=" N GLU C 526 " --> pdb=" O ASN C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.873A pdb=" N TYR C 558 " --> pdb=" O ALA C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 617 removed outlier: 3.633A pdb=" N ASN C 616 " --> pdb=" O ASP C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 653 No H-bonds generated for 'chain 'C' and resid 651 through 653' Processing helix chain 'C' and resid 678 through 689 removed outlier: 4.031A pdb=" N MET C 684 " --> pdb=" O ASN C 680 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 822 through 827 removed outlier: 3.610A pdb=" N LYS C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 827 " --> pdb=" O ARG C 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 822 through 827' Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 898 through 905 Processing helix chain 'C' and resid 946 through 978 removed outlier: 3.628A pdb=" N ILE C 969 " --> pdb=" O GLU C 965 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 971 " --> pdb=" O ALA C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 1031 through 1046 removed outlier: 3.677A pdb=" N LYS C1036 " --> pdb=" O TYR C1032 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C1038 " --> pdb=" O GLU C1034 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C1045 " --> pdb=" O ALA C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1120 removed outlier: 4.145A pdb=" N SER C1119 " --> pdb=" O LEU C1115 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C1120 " --> pdb=" O GLY C1116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1115 through 1120' Processing helix chain 'C' and resid 1123 through 1147 removed outlier: 3.683A pdb=" N ALA C1129 " --> pdb=" O GLN C1125 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C1142 " --> pdb=" O LEU C1138 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR C1145 " --> pdb=" O LYS C1141 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C1147 " --> pdb=" O GLU C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1164 removed outlier: 4.089A pdb=" N GLU C1160 " --> pdb=" O ARG C1156 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 1172 through 1176 removed outlier: 3.894A pdb=" N ALA C1175 " --> pdb=" O ASN C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1188 removed outlier: 3.615A pdb=" N LEU C1182 " --> pdb=" O ASP C1178 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR C1183 " --> pdb=" O GLU C1179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C1186 " --> pdb=" O LEU C1182 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1215 removed outlier: 3.751A pdb=" N ILE C1207 " --> pdb=" O LYS C1203 " (cutoff:3.500A) Processing helix chain 'C' and resid 1250 through 1254 removed outlier: 3.585A pdb=" N ASP C1253 " --> pdb=" O LEU C1250 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1294 removed outlier: 3.648A pdb=" N ALA C1289 " --> pdb=" O MET C1285 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C1290 " --> pdb=" O GLU C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1302 Processing helix chain 'C' and resid 1309 through 1323 removed outlier: 4.028A pdb=" N SER C1314 " --> pdb=" O ILE C1310 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C1315 " --> pdb=" O ALA C1311 " (cutoff:3.500A) Processing helix chain 'C' and resid 1332 through 1343 removed outlier: 3.705A pdb=" N ASN C1336 " --> pdb=" O PRO C1332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C1337 " --> pdb=" O GLU C1333 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C1338 " --> pdb=" O SER C1334 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C1343 " --> pdb=" O ARG C1339 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 31 removed outlier: 3.932A pdb=" N SER D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.529A pdb=" N VAL D 95 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG D 96 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 129 through 138 removed outlier: 4.261A pdb=" N LYS D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 136 " --> pdb=" O ASN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 180 through 189 Processing helix chain 'D' and resid 191 through 204 removed outlier: 4.236A pdb=" N GLU D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 229 removed outlier: 4.263A pdb=" N LYS D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 228 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 234 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.631A pdb=" N VAL D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG D 273 " --> pdb=" O ARG D 269 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG D 276 " --> pdb=" O ASN D 272 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 307 removed outlier: 4.284A pdb=" N ASN D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.758A pdb=" N ASP D 327 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 368 through 375 removed outlier: 3.743A pdb=" N GLU D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 386 Processing helix chain 'D' and resid 391 through 401 removed outlier: 3.653A pdb=" N ALA D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 414 removed outlier: 3.717A pdb=" N ILE D 409 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 411 " --> pdb=" O TRP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.636A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'D' and resid 503 through 512 removed outlier: 3.835A pdb=" N GLY D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.815A pdb=" N VAL D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 595 through 611 Processing helix chain 'D' and resid 611 through 632 removed outlier: 3.812A pdb=" N THR D 615 " --> pdb=" O GLY D 611 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 668 removed outlier: 3.793A pdb=" N SER D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 677 removed outlier: 3.561A pdb=" N ARG D 676 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 695 removed outlier: 3.748A pdb=" N ASP D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 719 through 725 removed outlier: 3.501A pdb=" N ALA D 723 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.583A pdb=" N ALA D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 771 removed outlier: 4.067A pdb=" N THR D 771 " --> pdb=" O LEU D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 785 removed outlier: 3.720A pdb=" N ALA D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 784 " --> pdb=" O LEU D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 801 Processing helix chain 'D' and resid 865 through 871 removed outlier: 3.575A pdb=" N ASP D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 896 Processing helix chain 'D' and resid 910 through 917 removed outlier: 3.687A pdb=" N ILE D 914 " --> pdb=" O SER D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 926 removed outlier: 4.393A pdb=" N THR D 924 " --> pdb=" O GLU D 921 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 926 " --> pdb=" O GLY D 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 1125 through 1133 Processing helix chain 'D' and resid 1212 through 1230 removed outlier: 4.528A pdb=" N GLU D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE D1217 " --> pdb=" O GLY D1213 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D1228 " --> pdb=" O GLU D1224 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D1229 " --> pdb=" O ALA D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1241 through 1246 Processing helix chain 'D' and resid 1268 through 1275 removed outlier: 4.251A pdb=" N ILE D1273 " --> pdb=" O GLU D1269 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D1274 " --> pdb=" O LEU D1270 " (cutoff:3.500A) Processing helix chain 'D' and resid 1277 through 1282 Processing helix chain 'D' and resid 1298 through 1303 Processing helix chain 'D' and resid 1306 through 1312 Processing helix chain 'D' and resid 1315 through 1326 removed outlier: 4.160A pdb=" N GLU D1322 " --> pdb=" O ARG D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1334 through 1341 removed outlier: 3.554A pdb=" N ASN D1338 " --> pdb=" O GLY D1334 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE D1341 " --> pdb=" O GLU D1337 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1364 removed outlier: 3.959A pdb=" N ARG D1354 " --> pdb=" O GLY D1350 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D1359 " --> pdb=" O LYS D1355 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE D1360 " --> pdb=" O GLU D1356 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D1361 " --> pdb=" O SER D1357 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS D1362 " --> pdb=" O ALA D1358 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.608A pdb=" N CYS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 40 through 44 removed outlier: 3.735A pdb=" N LYS E 43 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS E 44 " --> pdb=" O ASN E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 44' Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.841A pdb=" N ILE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 6.244A pdb=" N GLU A 192 " --> pdb=" O PRO A 31 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR A 193 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A 185 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU A 195 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 183 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE A 197 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL A 181 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS A 199 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.733A pdb=" N LYS A 59 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A 148 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 57 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY A 150 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA A 55 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 removed outlier: 6.989A pdb=" N VAL A 112 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 15 removed outlier: 4.265A pdb=" N ASN B 11 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS B 23 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE B 197 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER B 25 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU B 195 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLU B 27 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 193 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 190 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 182 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.635A pdb=" N VAL B 145 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU B 142 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 57 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS B 144 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 51 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.924A pdb=" N ILE B 111 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.473A pdb=" N LYS C 13 " --> pdb=" O ALA C1195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 78 removed outlier: 5.865A pdb=" N TYR C 73 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG C 104 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C 75 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 130 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL C 101 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR C 128 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 103 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR C 126 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB2, first strand: chain 'C' and resid 454 through 457 Processing sheet with id=AB3, first strand: chain 'C' and resid 159 through 161 removed outlier: 3.676A pdb=" N ALA C 174 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 187 " --> pdb=" O TRP C 195 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 204 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 583 through 584 removed outlier: 7.191A pdb=" N LEU C 590 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 609 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA C 592 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU C 607 " --> pdb=" O ALA C 592 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR C 594 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU C 605 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS C 596 " --> pdb=" O THR C 603 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 636 through 640 Processing sheet with id=AB6, first strand: chain 'C' and resid 719 through 720 removed outlier: 6.382A pdb=" N ILE C 719 " --> pdb=" O LEU C 785 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 751 through 754 removed outlier: 6.889A pdb=" N ARG C 734 " --> pdb=" O VAL C 730 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL C 730 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 736 " --> pdb=" O ALA C 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AB9, first strand: chain 'C' and resid 800 through 801 removed outlier: 7.383A pdb=" N ILE C 818 " --> pdb=" O SER C1091 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C1093 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 820 " --> pdb=" O VAL C1093 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 819 " --> pdb=" O CYS C1111 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR C1238 " --> pdb=" O PHE C 806 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 832 through 843 removed outlier: 6.462A pdb=" N SER C 832 " --> pdb=" O LYS C1071 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS C1071 " --> pdb=" O SER C 832 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS C 834 " --> pdb=" O ALA C1069 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA C1069 " --> pdb=" O HIS C 834 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU C 836 " --> pdb=" O PHE C1067 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE C1067 " --> pdb=" O GLU C 836 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE C 838 " --> pdb=" O LYS C1065 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS C1065 " --> pdb=" O PHE C 838 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS C 840 " --> pdb=" O THR C1063 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR C1063 " --> pdb=" O CYS C 840 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA C 842 " --> pdb=" O LEU C1061 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN C 932 " --> pdb=" O PHE C1067 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C1069 " --> pdb=" O VAL C 930 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL C 930 " --> pdb=" O ALA C1069 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N LYS C1071 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY C 928 " --> pdb=" O LYS C1071 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 889 through 891 Processing sheet with id=AC3, first strand: chain 'C' and resid 1257 through 1258 removed outlier: 6.573A pdb=" N CYS D 364 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE D 440 " --> pdb=" O CYS D 364 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU D 366 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1280 through 1281 removed outlier: 3.784A pdb=" N GLN C1280 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1347 through 1352 removed outlier: 3.586A pdb=" N ASP C1348 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE D 17 " --> pdb=" O ASP C1352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 32 through 35 removed outlier: 4.302A pdb=" N SER D 32 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS D 102 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY D 34 " --> pdb=" O HIS D 102 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 101 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 158 removed outlier: 5.585A pdb=" N VAL D 144 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER D 177 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AD1, first strand: chain 'D' and resid 806 through 808 Processing sheet with id=AD2, first strand: chain 'D' and resid 817 through 819 Processing sheet with id=AD3, first strand: chain 'D' and resid 1152 through 1153 removed outlier: 3.882A pdb=" N GLY D1153 " --> pdb=" O GLN D1161 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1265 through 1267 659 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5372 1.33 - 1.45: 4423 1.45 - 1.57: 12665 1.57 - 1.69: 90 1.69 - 1.82: 149 Bond restraints: 22699 Sorted by residual: bond pdb=" C PHE D 435 " pdb=" N GLU D 436 " ideal model delta sigma weight residual 1.332 1.260 0.072 1.44e-02 4.82e+03 2.51e+01 bond pdb=" CA TYR D 114 " pdb=" C TYR D 114 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.80e-02 3.09e+03 1.77e+01 bond pdb=" CA ASN D 536 " pdb=" C ASN D 536 " ideal model delta sigma weight residual 1.522 1.453 0.069 1.72e-02 3.38e+03 1.59e+01 bond pdb=" CA ASN B 218 " pdb=" C ASN B 218 " ideal model delta sigma weight residual 1.522 1.456 0.065 1.72e-02 3.38e+03 1.45e+01 bond pdb=" N ASN B 202 " pdb=" CA ASN B 202 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.35e-02 5.49e+03 6.56e+00 ... (remaining 22694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 29976 2.30 - 4.60: 851 4.60 - 6.90: 85 6.90 - 9.20: 19 9.20 - 11.50: 4 Bond angle restraints: 30935 Sorted by residual: angle pdb=" C ASP C 519 " pdb=" N GLN C 520 " pdb=" CA GLN C 520 " ideal model delta sigma weight residual 121.54 111.81 9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" N ASP B 176 " pdb=" CA ASP B 176 " pdb=" C ASP B 176 " ideal model delta sigma weight residual 111.02 117.02 -6.00 1.25e+00 6.40e-01 2.31e+01 angle pdb=" N VAL B 172 " pdb=" CA VAL B 172 " pdb=" C VAL B 172 " ideal model delta sigma weight residual 109.34 99.36 9.98 2.08e+00 2.31e-01 2.30e+01 angle pdb=" C PRO B 171 " pdb=" N VAL B 172 " pdb=" CA VAL B 172 " ideal model delta sigma weight residual 121.97 129.90 -7.93 1.80e+00 3.09e-01 1.94e+01 angle pdb=" N GLY C 643 " pdb=" CA GLY C 643 " pdb=" C GLY C 643 " ideal model delta sigma weight residual 115.08 109.89 5.19 1.19e+00 7.06e-01 1.90e+01 ... (remaining 30930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 11601 18.07 - 36.13: 1508 36.13 - 54.20: 465 54.20 - 72.26: 123 72.26 - 90.33: 25 Dihedral angle restraints: 13722 sinusoidal: 5424 harmonic: 8298 Sorted by residual: dihedral pdb=" CA SER B 170 " pdb=" C SER B 170 " pdb=" N PRO B 171 " pdb=" CA PRO B 171 " ideal model delta harmonic sigma weight residual 180.00 -117.75 -62.25 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA LYS D1286 " pdb=" C LYS D1286 " pdb=" N GLU D1287 " pdb=" CA GLU D1287 " ideal model delta harmonic sigma weight residual 180.00 -147.84 -32.16 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA ILE C 198 " pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta harmonic sigma weight residual -180.00 -148.20 -31.80 0 5.00e+00 4.00e-02 4.05e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2529 0.056 - 0.113: 966 0.113 - 0.169: 144 0.169 - 0.225: 11 0.225 - 0.281: 3 Chirality restraints: 3653 Sorted by residual: chirality pdb=" CA PHE C 60 " pdb=" N PHE C 60 " pdb=" C PHE C 60 " pdb=" CB PHE C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA SER B 170 " pdb=" N SER B 170 " pdb=" C SER B 170 " pdb=" CB SER B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA HIS C1256 " pdb=" N HIS C1256 " pdb=" C HIS C1256 " pdb=" CB HIS C1256 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3650 not shown) Planarity restraints: 3857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 170 " -0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO B 171 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO B 171 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 171 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 880 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO D 881 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 881 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 881 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 830 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO D 831 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 831 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 831 " 0.033 5.00e-02 4.00e+02 ... (remaining 3854 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 187 2.55 - 3.14: 17133 3.14 - 3.73: 31835 3.73 - 4.31: 48493 4.31 - 4.90: 80911 Nonbonded interactions: 178559 Sorted by model distance: nonbonded pdb=" OH TYR B 133 " pdb=" O LYS B 137 " model vdw 1.965 3.040 nonbonded pdb=" O TRP C 809 " pdb=" OG1 THR D 631 " model vdw 2.020 3.040 nonbonded pdb=" OG1 THR D 813 " pdb=" OD1 ASP D 815 " model vdw 2.032 3.040 nonbonded pdb=" OD1 ASP D 458 " pdb="MG MG D1701 " model vdw 2.076 2.170 nonbonded pdb=" O ALA B 123 " pdb=" OG1 THR B 125 " model vdw 2.081 3.040 ... (remaining 178554 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.360 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.012 0.407 22705 Z= 0.479 Angle : 0.943 17.429 30941 Z= 0.520 Chirality : 0.056 0.281 3653 Planarity : 0.006 0.124 3857 Dihedral : 18.703 90.328 8368 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.62 % Favored : 86.17 % Rotamer: Outliers : 12.01 % Allowed : 22.03 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.30 (0.11), residues: 2863 helix: -3.58 (0.11), residues: 972 sheet: -2.93 (0.25), residues: 305 loop : -3.72 (0.12), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1343 TYR 0.023 0.003 TYR C1101 PHE 0.029 0.003 PHE C 60 TRP 0.018 0.002 TRP C 809 HIS 0.007 0.002 HIS C 450 Details of bonding type rmsd covalent geometry : bond 0.01106 (22699) covalent geometry : angle 0.92966 (30935) hydrogen bonds : bond 0.22339 ( 716) hydrogen bonds : angle 8.33365 ( 1944) metal coordination : bond 0.20145 ( 6) metal coordination : angle 11.59325 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 301 time to evaluate : 0.769 Fit side-chains REVERT: B 183 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7111 (ptp90) REVERT: B 187 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6044 (ttm170) REVERT: C 135 MET cc_start: 0.8964 (ttm) cc_final: 0.8397 (ttp) REVERT: C 161 PHE cc_start: 0.7073 (m-10) cc_final: 0.6870 (m-10) REVERT: C 210 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6908 (mt) REVERT: C 417 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7475 (m) REVERT: C 457 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7834 (ttp-170) REVERT: D 140 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7238 (tm-30) REVERT: D 195 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7626 (mt-10) REVERT: D 280 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6345 (mp) REVERT: D 282 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: D 462 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: D 464 MET cc_start: 0.8879 (mtt) cc_final: 0.8495 (mtt) REVERT: D 746 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7283 (ptpt) REVERT: D 748 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7136 (p0) REVERT: D 778 LYS cc_start: 0.7975 (tptt) cc_final: 0.7522 (ttmt) REVERT: D 822 ILE cc_start: 0.8854 (mt) cc_final: 0.8647 (mt) REVERT: D 1295 MET cc_start: 0.8029 (mtt) cc_final: 0.7821 (mtm) REVERT: D 1325 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8249 (mm) outliers start: 255 outliers final: 154 residues processed: 511 average time/residue: 0.6180 time to fit residues: 362.4556 Evaluate side-chains 417 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 252 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 722 ARG Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 813 ASN Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 1064 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1106 THR Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1135 SER Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1198 VAL Chi-restraints excluded: chain C residue 1219 ASN Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1260 THR Chi-restraints excluded: chain C residue 1262 SER Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1314 SER Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1343 ARG Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 746 LYS Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 750 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 762 GLU Chi-restraints excluded: chain D residue 773 THR Chi-restraints excluded: chain D residue 815 ASP Chi-restraints excluded: chain D residue 824 GLU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 833 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 910 SER Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1301 SER Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1306 SER Chi-restraints excluded: chain D residue 1309 SER Chi-restraints excluded: chain D residue 1317 THR Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1339 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 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 ASN B 11 ASN B 219 GLN C 20 HIS C 31 GLN C 58 GLN C 138 ASN C 425 ASN C 520 GLN C 748 ASN C 810 ASN C 874 HIS C 934 GLN C1130 HIS C1219 ASN C1268 GLN C1336 ASN D 102 HIS D 111 HIS D 156 GLN D 264 ASN D 292 ASN D 362 HIS D 394 GLN D 495 GLN D 543 HIS D 736 GLN D 774 HIS D1232 GLN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.157625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121627 restraints weight = 25419.546| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.51 r_work: 0.3244 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22705 Z= 0.132 Angle : 0.640 8.482 30941 Z= 0.343 Chirality : 0.044 0.185 3653 Planarity : 0.005 0.089 3857 Dihedral : 13.912 70.483 3874 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.01 % Favored : 90.88 % Rotamer: Outliers : 7.16 % Allowed : 25.47 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.13), residues: 2863 helix: -2.04 (0.15), residues: 966 sheet: -2.02 (0.26), residues: 317 loop : -3.00 (0.13), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1150 TYR 0.018 0.001 TYR D 138 PHE 0.021 0.001 PHE C 60 TRP 0.022 0.001 TRP C 809 HIS 0.012 0.001 HIS C1256 Details of bonding type rmsd covalent geometry : bond 0.00285 (22699) covalent geometry : angle 0.63939 (30935) hydrogen bonds : bond 0.04129 ( 716) hydrogen bonds : angle 5.09804 ( 1944) metal coordination : bond 0.01368 ( 6) metal coordination : angle 2.75741 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 287 time to evaluate : 0.891 Fit side-chains REVERT: A 164 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: B 4 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6138 (mp0) REVERT: B 126 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5102 (pm20) REVERT: B 176 ASP cc_start: 0.7689 (t70) cc_final: 0.7217 (t70) REVERT: C 91 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7632 (mtp180) REVERT: C 135 MET cc_start: 0.9177 (ttm) cc_final: 0.8810 (ttp) REVERT: C 418 LYS cc_start: 0.8188 (mmpt) cc_final: 0.7976 (mmpt) REVERT: C 434 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: C 646 ILE cc_start: 0.8542 (tt) cc_final: 0.8040 (pp) REVERT: C 1266 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7924 (t) REVERT: D 140 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: D 193 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: D 195 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: D 302 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7093 (t0) REVERT: D 306 ASP cc_start: 0.7722 (p0) cc_final: 0.7479 (p0) REVERT: D 310 ARG cc_start: 0.7261 (ttt-90) cc_final: 0.7028 (ttt180) REVERT: D 384 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7486 (tmm-80) REVERT: D 678 ASN cc_start: 0.8020 (m-40) cc_final: 0.7810 (m-40) REVERT: D 762 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: D 778 LYS cc_start: 0.8070 (tptt) cc_final: 0.7416 (ttpt) REVERT: D 1289 GLU cc_start: 0.7531 (mp0) cc_final: 0.7314 (mp0) REVERT: D 1325 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8080 (mm) REVERT: D 1363 MET cc_start: 0.6915 (mtm) cc_final: 0.6598 (mtt) outliers start: 152 outliers final: 58 residues processed: 396 average time/residue: 0.6737 time to fit residues: 303.6109 Evaluate side-chains 319 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 250 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1219 ASN Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 750 THR Chi-restraints excluded: chain D residue 762 GLU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1267 SER Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 245 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 233 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN C 72 HIS C 219 GLN D 394 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 ASN D 495 GLN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118264 restraints weight = 25438.030| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.53 r_work: 0.3194 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22705 Z= 0.233 Angle : 0.699 9.129 30941 Z= 0.368 Chirality : 0.048 0.222 3653 Planarity : 0.005 0.094 3857 Dihedral : 13.164 68.896 3691 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.76 % Favored : 89.10 % Rotamer: Outliers : 6.64 % Allowed : 27.50 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.14), residues: 2863 helix: -1.77 (0.15), residues: 978 sheet: -1.88 (0.27), residues: 314 loop : -2.82 (0.13), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 439 TYR 0.021 0.002 TYR D 138 PHE 0.022 0.002 PHE C 60 TRP 0.014 0.002 TRP C 809 HIS 0.007 0.001 HIS C1256 Details of bonding type rmsd covalent geometry : bond 0.00562 (22699) covalent geometry : angle 0.69660 (30935) hydrogen bonds : bond 0.04922 ( 716) hydrogen bonds : angle 4.92627 ( 1944) metal coordination : bond 0.00669 ( 6) metal coordination : angle 3.95639 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 253 time to evaluate : 0.885 Fit side-chains REVERT: B 176 ASP cc_start: 0.7823 (t70) cc_final: 0.7458 (t70) REVERT: B 194 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: B 210 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8426 (ttp-170) REVERT: C 91 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7742 (mtp180) REVERT: C 135 MET cc_start: 0.9179 (ttm) cc_final: 0.8567 (ttp) REVERT: C 434 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: C 646 ILE cc_start: 0.8587 (tt) cc_final: 0.8212 (pt) REVERT: C 1148 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7751 (pptt) REVERT: C 1266 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7903 (t) REVERT: D 42 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6522 (tp) REVERT: D 140 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: D 195 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: D 302 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6946 (t0) REVERT: D 306 ASP cc_start: 0.7935 (p0) cc_final: 0.7663 (p0) REVERT: D 310 ARG cc_start: 0.7282 (ttt-90) cc_final: 0.7025 (ttt-90) REVERT: D 384 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7452 (tmm-80) REVERT: D 762 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: D 778 LYS cc_start: 0.8208 (tptt) cc_final: 0.7494 (ttmt) REVERT: D 1363 MET cc_start: 0.7017 (mtm) cc_final: 0.6668 (mtt) outliers start: 141 outliers final: 82 residues processed: 348 average time/residue: 0.6649 time to fit residues: 264.2969 Evaluate side-chains 331 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 239 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1099 MET Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1219 ASN Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1262 SER Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 762 GLU Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1224 GLU Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1309 SER Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 143 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN C 72 HIS C 874 HIS D 394 GLN D 495 GLN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122304 restraints weight = 25367.778| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.54 r_work: 0.3214 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22705 Z= 0.121 Angle : 0.588 9.061 30941 Z= 0.313 Chirality : 0.043 0.184 3653 Planarity : 0.004 0.084 3857 Dihedral : 12.762 70.434 3684 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.77 % Favored : 91.16 % Rotamer: Outliers : 5.60 % Allowed : 28.34 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.14), residues: 2863 helix: -1.21 (0.16), residues: 981 sheet: -1.45 (0.28), residues: 319 loop : -2.52 (0.14), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 439 TYR 0.018 0.001 TYR D 138 PHE 0.018 0.001 PHE C 60 TRP 0.017 0.001 TRP C 809 HIS 0.010 0.001 HIS C1256 Details of bonding type rmsd covalent geometry : bond 0.00270 (22699) covalent geometry : angle 0.58732 (30935) hydrogen bonds : bond 0.03591 ( 716) hydrogen bonds : angle 4.55666 ( 1944) metal coordination : bond 0.00430 ( 6) metal coordination : angle 2.38086 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 260 time to evaluate : 0.878 Fit side-chains REVERT: A 164 GLU cc_start: 0.7626 (mp0) cc_final: 0.7373 (mt-10) REVERT: C 91 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7684 (mtp180) REVERT: C 123 ARG cc_start: 0.4993 (OUTLIER) cc_final: 0.4359 (mtt-85) REVERT: C 135 MET cc_start: 0.9189 (ttm) cc_final: 0.8404 (ttp) REVERT: C 434 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: C 598 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8571 (m) REVERT: C 646 ILE cc_start: 0.8493 (tt) cc_final: 0.8222 (pt) REVERT: C 1120 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7905 (mtt180) REVERT: C 1157 LYS cc_start: 0.8164 (mppt) cc_final: 0.7927 (mptt) REVERT: C 1266 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7834 (t) REVERT: D 42 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6411 (tp) REVERT: D 140 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: D 193 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: D 195 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: D 280 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5826 (mp) REVERT: D 302 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7249 (t0) REVERT: D 384 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7317 (tmm-80) REVERT: D 495 GLN cc_start: 0.8351 (mt0) cc_final: 0.7899 (mm-40) REVERT: D 762 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: D 778 LYS cc_start: 0.8118 (tptt) cc_final: 0.7469 (ttpt) REVERT: D 827 GLU cc_start: 0.7050 (pm20) cc_final: 0.6763 (pm20) REVERT: D 859 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8597 (tp) REVERT: D 1287 GLU cc_start: 0.4533 (OUTLIER) cc_final: 0.3752 (mm-30) REVERT: D 1363 MET cc_start: 0.6962 (mtm) cc_final: 0.6649 (mtt) outliers start: 119 outliers final: 55 residues processed: 342 average time/residue: 0.7440 time to fit residues: 287.4798 Evaluate side-chains 303 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1099 MET Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1140 LYS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1262 SER Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 762 GLU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1309 SER Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 196 optimal weight: 5.9990 chunk 123 optimal weight: 50.0000 chunk 182 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 121 GLN C 72 HIS C 77 GLN C 874 HIS D 394 GLN D 591 ASN D 679 ASN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117026 restraints weight = 25386.708| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.53 r_work: 0.3140 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 22705 Z= 0.324 Angle : 0.756 9.060 30941 Z= 0.397 Chirality : 0.051 0.216 3653 Planarity : 0.006 0.099 3857 Dihedral : 13.053 68.330 3670 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.07 % Favored : 88.82 % Rotamer: Outliers : 7.53 % Allowed : 27.40 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.14), residues: 2863 helix: -1.48 (0.15), residues: 981 sheet: -1.45 (0.29), residues: 305 loop : -2.59 (0.14), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 121 TYR 0.027 0.002 TYR D 138 PHE 0.020 0.002 PHE C 60 TRP 0.013 0.002 TRP C 809 HIS 0.006 0.002 HIS C 450 Details of bonding type rmsd covalent geometry : bond 0.00794 (22699) covalent geometry : angle 0.75400 (30935) hydrogen bonds : bond 0.05266 ( 716) hydrogen bonds : angle 4.83724 ( 1944) metal coordination : bond 0.00819 ( 6) metal coordination : angle 4.27794 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 241 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7058 (pp20) cc_final: 0.6621 (pp20) REVERT: A 174 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8437 (t0) REVERT: B 114 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6490 (pt0) REVERT: C 91 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7730 (mtp180) REVERT: C 123 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.4163 (mtt-85) REVERT: C 135 MET cc_start: 0.9138 (ttm) cc_final: 0.8610 (ttp) REVERT: C 434 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: C 646 ILE cc_start: 0.8668 (tt) cc_final: 0.8317 (pt) REVERT: C 1120 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8095 (mtt180) REVERT: C 1148 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7826 (pptt) REVERT: C 1157 LYS cc_start: 0.8265 (mppt) cc_final: 0.7992 (mptt) REVERT: C 1266 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7889 (t) REVERT: D 40 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: D 42 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6449 (tp) REVERT: D 45 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5599 (mmt180) REVERT: D 140 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: D 193 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: D 195 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: D 280 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5941 (mp) REVERT: D 302 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7010 (t70) REVERT: D 506 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.7953 (tp) REVERT: D 721 MET cc_start: 0.8822 (mtp) cc_final: 0.8500 (mtm) REVERT: D 762 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8379 (pt0) REVERT: D 778 LYS cc_start: 0.8236 (tptt) cc_final: 0.7523 (ttmt) REVERT: D 822 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8046 (pt) REVERT: D 859 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8652 (tp) REVERT: D 1229 TYR cc_start: 0.8426 (m-80) cc_final: 0.8131 (m-80) REVERT: D 1287 GLU cc_start: 0.4787 (OUTLIER) cc_final: 0.3936 (mm-30) REVERT: D 1363 MET cc_start: 0.7070 (mtp) cc_final: 0.6835 (mtt) outliers start: 160 outliers final: 92 residues processed: 355 average time/residue: 0.6611 time to fit residues: 268.5137 Evaluate side-chains 350 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 238 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1099 MET Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1140 LYS Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1198 VAL Chi-restraints excluded: chain C residue 1219 ASN Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1262 SER Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain C residue 1342 VAL Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 762 GLU Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1267 SER Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1309 SER Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Chi-restraints excluded: chain E residue 60 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 261 optimal weight: 50.0000 chunk 118 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 121 GLN C 72 HIS C 874 HIS D 394 GLN D 591 ASN D 679 ASN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121018 restraints weight = 25394.906| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.50 r_work: 0.3184 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22705 Z= 0.144 Angle : 0.618 10.430 30941 Z= 0.329 Chirality : 0.044 0.191 3653 Planarity : 0.004 0.088 3857 Dihedral : 12.774 69.615 3670 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.84 % Favored : 91.09 % Rotamer: Outliers : 6.36 % Allowed : 28.58 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.15), residues: 2863 helix: -1.05 (0.16), residues: 973 sheet: -1.29 (0.29), residues: 316 loop : -2.38 (0.14), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 439 TYR 0.014 0.001 TYR C1136 PHE 0.018 0.001 PHE C 60 TRP 0.016 0.001 TRP C 809 HIS 0.010 0.001 HIS C1256 Details of bonding type rmsd covalent geometry : bond 0.00332 (22699) covalent geometry : angle 0.61744 (30935) hydrogen bonds : bond 0.03824 ( 716) hydrogen bonds : angle 4.53549 ( 1944) metal coordination : bond 0.00472 ( 6) metal coordination : angle 2.54678 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 250 time to evaluate : 0.833 Fit side-chains REVERT: A 162 GLU cc_start: 0.7079 (pp20) cc_final: 0.6664 (pp20) REVERT: A 164 GLU cc_start: 0.7635 (mp0) cc_final: 0.7374 (mt-10) REVERT: A 174 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8392 (t0) REVERT: B 142 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: B 176 ASP cc_start: 0.7819 (t70) cc_final: 0.7351 (t70) REVERT: B 210 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8248 (ttp-170) REVERT: C 91 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7675 (mtp180) REVERT: C 123 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.4582 (mtt-85) REVERT: C 135 MET cc_start: 0.9151 (ttm) cc_final: 0.8360 (ttp) REVERT: C 434 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: C 598 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8591 (m) REVERT: C 646 ILE cc_start: 0.8529 (tt) cc_final: 0.8224 (pt) REVERT: C 1120 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7963 (mtt180) REVERT: C 1148 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7737 (pptt) REVERT: C 1266 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7868 (t) REVERT: D 40 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: D 42 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6542 (tp) REVERT: D 45 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5654 (mmt180) REVERT: D 140 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: D 193 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: D 195 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: D 280 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.5861 (mp) REVERT: D 302 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7095 (t0) REVERT: D 384 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7042 (ttm170) REVERT: D 392 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7218 (mm) REVERT: D 394 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: D 495 GLN cc_start: 0.8422 (mt0) cc_final: 0.7975 (mm-40) REVERT: D 721 MET cc_start: 0.8783 (mtp) cc_final: 0.8477 (mtm) REVERT: D 778 LYS cc_start: 0.8134 (tptt) cc_final: 0.7475 (ttpt) REVERT: D 802 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: D 859 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8648 (tp) REVERT: D 1287 GLU cc_start: 0.4357 (OUTLIER) cc_final: 0.3589 (mm-30) REVERT: D 1363 MET cc_start: 0.7009 (mtp) cc_final: 0.6792 (mtt) outliers start: 135 outliers final: 73 residues processed: 345 average time/residue: 0.6842 time to fit residues: 268.2119 Evaluate side-chains 331 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 235 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1099 MET Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1140 LYS Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1198 VAL Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1262 SER Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 591 ASN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 802 GLN Chi-restraints excluded: chain D residue 820 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1224 GLU Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1309 SER Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Chi-restraints excluded: chain E residue 60 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 164 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 170 optimal weight: 0.0970 chunk 279 optimal weight: 6.9990 chunk 265 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 121 GLN C 72 HIS C 223 ASN C 874 HIS D 394 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 ASN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122219 restraints weight = 25238.400| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.48 r_work: 0.3238 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.003 0.041 22705 Z= 0.127 Angle : 0.597 11.566 30941 Z= 0.317 Chirality : 0.043 0.190 3653 Planarity : 0.004 0.083 3857 Dihedral : 12.573 68.659 3666 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.98 % Favored : 90.92 % Rotamer: Outliers : 6.07 % Allowed : 28.81 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.15), residues: 2863 helix: -0.84 (0.17), residues: 979 sheet: -1.10 (0.30), residues: 310 loop : -2.28 (0.14), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 310 TYR 0.022 0.001 TYR D 138 PHE 0.018 0.001 PHE C 60 TRP 0.015 0.001 TRP C 809 HIS 0.008 0.001 HIS C1256 Details of bonding type rmsd covalent geometry : bond 0.00291 (22699) covalent geometry : angle 0.59632 (30935) hydrogen bonds : bond 0.03558 ( 716) hydrogen bonds : angle 4.39726 ( 1944) metal coordination : bond 0.00396 ( 6) metal coordination : angle 2.25500 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 252 time to evaluate : 0.828 Fit side-chains REVERT: A 162 GLU cc_start: 0.7047 (pp20) cc_final: 0.6629 (pp20) REVERT: A 164 GLU cc_start: 0.7596 (mp0) cc_final: 0.7353 (mt-10) REVERT: A 174 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8367 (t0) REVERT: B 103 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6530 (pt0) REVERT: B 210 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8105 (ttp-110) REVERT: C 91 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7632 (mtp180) REVERT: C 123 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.4584 (mtt-85) REVERT: C 135 MET cc_start: 0.9168 (ttm) cc_final: 0.8366 (ttp) REVERT: C 434 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: C 646 ILE cc_start: 0.8493 (tt) cc_final: 0.8263 (pt) REVERT: C 1120 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7930 (mtt180) REVERT: C 1148 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7607 (pptt) REVERT: C 1266 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7795 (t) REVERT: D 40 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: D 42 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6530 (tp) REVERT: D 45 ARG cc_start: 0.5877 (OUTLIER) cc_final: 0.5673 (mmt180) REVERT: D 140 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: D 193 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: D 195 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: D 280 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5870 (mp) REVERT: D 302 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7157 (t0) REVERT: D 384 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7267 (tmm-80) REVERT: D 394 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6740 (mp10) REVERT: D 495 GLN cc_start: 0.8379 (mt0) cc_final: 0.7958 (mm-40) REVERT: D 653 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 721 MET cc_start: 0.8766 (mtp) cc_final: 0.8399 (mtm) REVERT: D 778 LYS cc_start: 0.8144 (tptt) cc_final: 0.7492 (ttpt) REVERT: D 802 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: D 859 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8629 (tp) REVERT: D 1229 TYR cc_start: 0.8243 (m-80) cc_final: 0.7838 (m-80) REVERT: D 1287 GLU cc_start: 0.4801 (OUTLIER) cc_final: 0.4044 (mm-30) REVERT: D 1290 TYR cc_start: 0.8165 (p90) cc_final: 0.7963 (p90) outliers start: 129 outliers final: 76 residues processed: 343 average time/residue: 0.7369 time to fit residues: 286.7857 Evaluate side-chains 335 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 238 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1099 MET Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1140 LYS Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 802 GLN Chi-restraints excluded: chain D residue 820 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1309 SER Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 60 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 205 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 273 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 121 GLN C 72 HIS C 223 ASN C 874 HIS D 394 GLN D 417 HIS D 591 ASN D 679 ASN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118235 restraints weight = 25273.530| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.57 r_work: 0.3180 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22705 Z= 0.261 Angle : 0.705 11.689 30941 Z= 0.371 Chirality : 0.048 0.204 3653 Planarity : 0.005 0.091 3857 Dihedral : 12.799 67.822 3666 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.30 % Favored : 89.56 % Rotamer: Outliers : 6.78 % Allowed : 28.44 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.15), residues: 2863 helix: -1.09 (0.16), residues: 978 sheet: -1.19 (0.29), residues: 309 loop : -2.32 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 310 TYR 0.037 0.002 TYR D 138 PHE 0.019 0.002 PHE C 60 TRP 0.012 0.002 TRP C 809 HIS 0.007 0.001 HIS C1256 Details of bonding type rmsd covalent geometry : bond 0.00637 (22699) covalent geometry : angle 0.70345 (30935) hydrogen bonds : bond 0.04702 ( 716) hydrogen bonds : angle 4.62459 ( 1944) metal coordination : bond 0.00677 ( 6) metal coordination : angle 3.60878 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 246 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7097 (pp20) cc_final: 0.6639 (pp20) REVERT: B 103 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6695 (pt0) REVERT: B 114 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6624 (pt0) REVERT: B 210 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8101 (ttp-110) REVERT: C 123 ARG cc_start: 0.5404 (OUTLIER) cc_final: 0.4576 (mtt-85) REVERT: C 135 MET cc_start: 0.9150 (ttm) cc_final: 0.8615 (ttp) REVERT: C 434 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: C 646 ILE cc_start: 0.8645 (tt) cc_final: 0.8325 (pt) REVERT: C 1071 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8775 (mttp) REVERT: C 1120 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8045 (mtt180) REVERT: C 1148 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7641 (pptt) REVERT: C 1266 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7844 (t) REVERT: C 1286 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: D 40 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: D 42 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6505 (tp) REVERT: D 45 ARG cc_start: 0.5894 (OUTLIER) cc_final: 0.5609 (mmt180) REVERT: D 140 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: D 193 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: D 195 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: D 280 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5926 (mp) REVERT: D 384 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6984 (ttm170) REVERT: D 403 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: D 734 MET cc_start: 0.8154 (mtp) cc_final: 0.7748 (ttm) REVERT: D 778 LYS cc_start: 0.8210 (tptt) cc_final: 0.7503 (ttmt) REVERT: D 802 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: D 1229 TYR cc_start: 0.8368 (m-80) cc_final: 0.8086 (m-80) REVERT: D 1268 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8031 (mt) REVERT: D 1287 GLU cc_start: 0.4860 (OUTLIER) cc_final: 0.4103 (mm-30) REVERT: D 1305 GLU cc_start: 0.7998 (pp20) cc_final: 0.7502 (pt0) outliers start: 144 outliers final: 86 residues processed: 346 average time/residue: 0.6896 time to fit residues: 271.6789 Evaluate side-chains 343 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 235 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1099 MET Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1140 LYS Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1198 VAL Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1250 LEU Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1286 GLU Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 802 GLN Chi-restraints excluded: chain D residue 820 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1309 SER Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Chi-restraints excluded: chain E residue 4 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 121 GLN C 72 HIS C 874 HIS D 394 GLN D 591 ASN D 679 ASN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123197 restraints weight = 25291.272| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.57 r_work: 0.3211 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22705 Z= 0.116 Angle : 0.590 14.178 30941 Z= 0.312 Chirality : 0.043 0.183 3653 Planarity : 0.004 0.083 3857 Dihedral : 12.465 68.521 3664 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.31 % Favored : 91.62 % Rotamer: Outliers : 5.08 % Allowed : 30.18 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.15), residues: 2863 helix: -0.68 (0.17), residues: 989 sheet: -1.10 (0.30), residues: 315 loop : -2.14 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 310 TYR 0.040 0.001 TYR D 138 PHE 0.018 0.001 PHE C 60 TRP 0.020 0.001 TRP C 809 HIS 0.010 0.001 HIS C1256 Details of bonding type rmsd covalent geometry : bond 0.00262 (22699) covalent geometry : angle 0.58902 (30935) hydrogen bonds : bond 0.03296 ( 716) hydrogen bonds : angle 4.35530 ( 1944) metal coordination : bond 0.00335 ( 6) metal coordination : angle 1.89186 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 256 time to evaluate : 0.877 Fit side-chains REVERT: A 121 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: A 162 GLU cc_start: 0.7168 (pp20) cc_final: 0.6741 (pp20) REVERT: B 103 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6462 (pt0) REVERT: B 162 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: B 191 ASP cc_start: 0.8639 (m-30) cc_final: 0.8301 (m-30) REVERT: C 91 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7740 (mtp180) REVERT: C 123 ARG cc_start: 0.5362 (OUTLIER) cc_final: 0.4502 (mtt-85) REVERT: C 135 MET cc_start: 0.9192 (ttm) cc_final: 0.8891 (ttp) REVERT: C 349 ILE cc_start: 0.6437 (pt) cc_final: 0.6202 (pt) REVERT: C 434 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: C 451 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8264 (tp) REVERT: C 646 ILE cc_start: 0.8469 (tt) cc_final: 0.8255 (pt) REVERT: C 921 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.6911 (ttm-80) REVERT: C 1120 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7917 (mtt180) REVERT: C 1148 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7790 (pptt) REVERT: C 1266 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7823 (t) REVERT: D 40 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: D 42 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6475 (tp) REVERT: D 45 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.5624 (mmt180) REVERT: D 140 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: D 144 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.6916 (p) REVERT: D 193 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: D 195 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: D 302 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7228 (t0) REVERT: D 384 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6896 (ttm170) REVERT: D 495 GLN cc_start: 0.8255 (mt0) cc_final: 0.7847 (mm-40) REVERT: D 653 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7215 (tm-30) REVERT: D 721 MET cc_start: 0.8777 (mtp) cc_final: 0.8458 (mtm) REVERT: D 778 LYS cc_start: 0.8067 (tptt) cc_final: 0.7397 (ttpt) REVERT: D 1229 TYR cc_start: 0.8185 (m-80) cc_final: 0.7808 (m-80) REVERT: D 1287 GLU cc_start: 0.4914 (OUTLIER) cc_final: 0.4238 (mm-30) REVERT: E 14 GLU cc_start: 0.6240 (tt0) cc_final: 0.5580 (pm20) outliers start: 108 outliers final: 69 residues processed: 333 average time/residue: 0.6907 time to fit residues: 262.1734 Evaluate side-chains 329 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 241 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1099 MET Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1140 LYS Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 820 SER Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 833 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 261 optimal weight: 50.0000 chunk 232 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 121 GLN C 72 HIS C 874 HIS D 394 GLN D 679 ASN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.154051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117714 restraints weight = 25389.977| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.56 r_work: 0.3142 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 22705 Z= 0.285 Angle : 0.730 13.193 30941 Z= 0.383 Chirality : 0.050 0.219 3653 Planarity : 0.005 0.091 3857 Dihedral : 12.740 67.777 3663 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.34 % Favored : 89.52 % Rotamer: Outliers : 5.18 % Allowed : 29.76 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.15), residues: 2863 helix: -1.01 (0.16), residues: 975 sheet: -1.21 (0.29), residues: 311 loop : -2.25 (0.14), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 439 TYR 0.044 0.002 TYR D 138 PHE 0.018 0.002 PHE C 60 TRP 0.012 0.002 TRP C 809 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00695 (22699) covalent geometry : angle 0.72847 (30935) hydrogen bonds : bond 0.04879 ( 716) hydrogen bonds : angle 4.63177 ( 1944) metal coordination : bond 0.00703 ( 6) metal coordination : angle 3.76754 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 239 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 121 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6629 (tp40) REVERT: A 162 GLU cc_start: 0.7078 (pp20) cc_final: 0.6711 (pp20) REVERT: B 103 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6640 (pt0) REVERT: C 123 ARG cc_start: 0.5411 (OUTLIER) cc_final: 0.4575 (mtt-85) REVERT: C 135 MET cc_start: 0.9150 (ttm) cc_final: 0.8658 (ttp) REVERT: C 434 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: C 646 ILE cc_start: 0.8643 (tt) cc_final: 0.8319 (pt) REVERT: C 1071 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8748 (mttp) REVERT: C 1120 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8061 (mtt180) REVERT: C 1148 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7694 (pptt) REVERT: C 1266 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7846 (t) REVERT: D 42 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6508 (tp) REVERT: D 45 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.5527 (mmt180) REVERT: D 140 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: D 193 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: D 195 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: D 310 ARG cc_start: 0.7121 (mtm180) cc_final: 0.6916 (mtm180) REVERT: D 384 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6874 (ttm170) REVERT: D 721 MET cc_start: 0.8805 (mtp) cc_final: 0.8447 (mtm) REVERT: D 734 MET cc_start: 0.8159 (mtp) cc_final: 0.7771 (ttm) REVERT: D 778 LYS cc_start: 0.8221 (tptt) cc_final: 0.7509 (ttmt) REVERT: D 1229 TYR cc_start: 0.8341 (m-80) cc_final: 0.8068 (m-80) REVERT: D 1287 GLU cc_start: 0.4917 (OUTLIER) cc_final: 0.4144 (mm-30) REVERT: D 1305 GLU cc_start: 0.7993 (pp20) cc_final: 0.7486 (pt0) outliers start: 110 outliers final: 74 residues processed: 318 average time/residue: 0.6968 time to fit residues: 252.1882 Evaluate side-chains 321 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 232 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1099 MET Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1140 LYS Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1198 VAL Chi-restraints excluded: chain C residue 1219 ASN Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1326 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 820 SER Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 833 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1224 GLU Chi-restraints excluded: chain D residue 1227 SER Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1331 ASN Chi-restraints excluded: chain E residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 272 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 144 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 121 GLN C 72 HIS C 874 HIS D 394 GLN D 679 ASN ** D1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118830 restraints weight = 25264.466| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.50 r_work: 0.3149 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 22705 Z= 0.197 Angle : 0.841 58.911 30941 Z= 0.461 Chirality : 0.046 0.381 3653 Planarity : 0.005 0.091 3857 Dihedral : 12.735 67.768 3663 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.51 % Favored : 89.38 % Rotamer: Outliers : 5.04 % Allowed : 29.90 % Favored : 65.07 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.15), residues: 2863 helix: -1.00 (0.16), residues: 976 sheet: -1.24 (0.29), residues: 311 loop : -2.26 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 439 TYR 0.041 0.002 TYR D 138 PHE 0.020 0.002 PHE C 60 TRP 0.009 0.001 TRP C 809 HIS 0.008 0.001 HIS C1256 Details of bonding type rmsd covalent geometry : bond 0.00467 (22699) covalent geometry : angle 0.83950 (30935) hydrogen bonds : bond 0.04580 ( 716) hydrogen bonds : angle 4.61697 ( 1944) metal coordination : bond 0.00479 ( 6) metal coordination : angle 3.67923 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8483.38 seconds wall clock time: 144 minutes 56.82 seconds (8696.82 seconds total)