Starting phenix.real_space_refine on Mon Sep 14 19:05:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p18_20233/09_2026/6p18_20233.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p18_20233/09_2026/6p18_20233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6p18_20233/09_2026/6p18_20233.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p18_20233/09_2026/6p18_20233.cif" model { file = "/net/cci-nas-00/data/ceres_data/6p18_20233/09_2026/6p18_20233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p18_20233/09_2026/6p18_20233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p18_20233/09_2026/6p18_20233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p18_20233/09_2026/6p18_20233.map" } resolution = 3.5 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= 0.008 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 123 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20120 2.51 5 N 5793 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32673 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1153 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "2" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1142 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10568 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2665 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 6, 'TRANS': 318} Chain breaks: 2 Chain: "P" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1165 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "Q" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1261 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 244 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 8} 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 16874 SG CYS D 70 58.979 119.013 85.312 1.00 46.06 S ATOM 16888 SG CYS D 72 60.321 122.141 84.051 1.00 47.41 S ATOM 16996 SG CYS D 85 58.195 120.359 81.163 1.00 51.55 S ATOM 17020 SG CYS D 88 61.752 119.701 81.629 1.00 46.73 S ATOM 22708 SG CYS D 814 58.114 52.188 74.105 1.00 40.48 S ATOM 23273 SG CYS D 888 60.903 55.573 74.913 1.00 31.50 S ATOM 23324 SG CYS D 895 58.341 53.893 77.348 1.00 27.28 S ATOM 23345 SG CYS D 898 60.983 51.584 76.680 1.00 26.31 S Time building chain proxies: 6.04, per 1000 atoms: 0.18 Number of scatterers: 32673 At special positions: 0 Unit cell: (158.834, 179.088, 172.692, 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 143 16.00 P 123 15.00 Mg 1 11.99 O 6491 8.00 N 5793 7.00 C 20120 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 12 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 47 sheets defined 43.7% alpha, 13.1% beta 50 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.531A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.222A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.657A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.044A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.884A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.799A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.192A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.887A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.737A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.552A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.629A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.812A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.065A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 removed outlier: 4.095A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.777A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.921A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.694A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.606A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.907A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.522A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.573A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.596A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.763A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.991A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.325A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.941A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.798A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.343A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1361 through 1375 removed outlier: 4.515A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 114 through 135 removed outlier: 3.690A pdb=" N ASP F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 216 through 232 Processing helix chain 'F' and resid 243 through 257 removed outlier: 3.673A pdb=" N LYS F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 294 removed outlier: 4.195A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.681A pdb=" N LEU F 330 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.576A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.528A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.642A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 4.309A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 444 removed outlier: 4.644A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 467 Processing helix chain 'P' and resid 9 through 29 removed outlier: 3.801A pdb=" N SER P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 44 Processing helix chain 'P' and resid 59 through 74 removed outlier: 3.779A pdb=" N GLY P 63 " --> pdb=" O ASN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 89 Processing helix chain 'P' and resid 93 through 103 removed outlier: 3.500A pdb=" N ILE P 97 " --> pdb=" O SER P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 150 Proline residue: P 143 - end of helix Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 38 through 48 Processing helix chain 'Q' and resid 60 through 74 Processing helix chain 'Q' and resid 77 through 89 Processing helix chain 'Q' and resid 93 through 104 Processing helix chain 'Q' and resid 122 through 151 removed outlier: 3.536A pdb=" N CYS Q 126 " --> pdb=" O SER Q 122 " (cutoff:3.500A) Proline residue: Q 143 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 6.812A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.518A pdb=" N GLU A 60 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.560A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 16 removed outlier: 4.013A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 105 removed outlier: 6.286A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.509A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.186A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.440A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.891A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 98 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.151A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.640A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AC1, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.966A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.089A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.526A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.526A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.783A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.962A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1065 through 1066 removed outlier: 7.099A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.677A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 877 " --> pdb=" O GLY C 926 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.850A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.548A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.623A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.689A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.228A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.942A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.513A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.645A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.503A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 984 " --> pdb=" O GLU D 993 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 966 removed outlier: 4.040A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.962A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.571A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AE9, first strand: chain 'D' and resid 1164 through 1165 Processing sheet with id=AF1, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 4.008A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 108 through 109 1363 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 8.79 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8109 1.33 - 1.45: 6360 1.45 - 1.57: 18478 1.57 - 1.69: 244 1.69 - 1.81: 249 Bond restraints: 33440 Sorted by residual: bond pdb=" C3' DC 2 55 " pdb=" C2' DC 2 55 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA 1 12 " pdb=" C2' DA 1 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC 2 27 " pdb=" C2' DC 2 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC 2 47 " pdb=" C2' DC 2 47 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.85e+00 bond pdb=" C3' DA 1 24 " pdb=" C2' DA 1 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.47e+00 ... (remaining 33435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 44514 2.17 - 4.34: 1032 4.34 - 6.51: 91 6.51 - 8.68: 28 8.68 - 10.85: 11 Bond angle restraints: 45676 Sorted by residual: angle pdb=" C GLY B 209 " pdb=" N THR B 210 " pdb=" CA THR B 210 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C MET F 322 " pdb=" N ASN F 323 " pdb=" CA ASN F 323 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.80e+01 angle pdb=" O4' DG 1 43 " pdb=" C4' DG 1 43 " pdb=" C3' DG 1 43 " ideal model delta sigma weight residual 106.00 102.90 3.10 6.00e-01 2.78e+00 2.67e+01 angle pdb=" O4' DA 2 21 " pdb=" C4' DA 2 21 " pdb=" C3' DA 2 21 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 angle pdb=" N LYS C 991 " pdb=" CA LYS C 991 " pdb=" C LYS C 991 " ideal model delta sigma weight residual 113.28 107.33 5.95 1.22e+00 6.72e-01 2.38e+01 ... (remaining 45671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17307 17.93 - 35.86: 2097 35.86 - 53.78: 640 53.78 - 71.71: 163 71.71 - 89.64: 31 Dihedral angle restraints: 20238 sinusoidal: 9221 harmonic: 11017 Sorted by residual: dihedral pdb=" C4' U R 1 " pdb=" C3' U R 1 " pdb=" C2' U R 1 " pdb=" C1' U R 1 " ideal model delta sinusoidal sigma weight residual 36.34 -36.59 72.94 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' G R 2 " pdb=" C3' G R 2 " pdb=" C2' G R 2 " pdb=" C1' G R 2 " ideal model delta sinusoidal sigma weight residual 36.35 -34.12 70.47 1 3.10e+00 1.04e-01 6.65e+02 dihedral pdb=" O4' U R 1 " pdb=" C4' U R 1 " pdb=" C3' U R 1 " pdb=" C2' U R 1 " ideal model delta sinusoidal sigma weight residual -35.15 25.04 -60.19 1 4.00e+00 6.25e-02 3.02e+02 ... (remaining 20235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4429 0.073 - 0.145: 671 0.145 - 0.218: 54 0.218 - 0.291: 16 0.291 - 0.364: 5 Chirality restraints: 5175 Sorted by residual: chirality pdb=" CB ILE D 707 " pdb=" CA ILE D 707 " pdb=" CG1 ILE D 707 " pdb=" CG2 ILE D 707 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL D1280 " pdb=" CA VAL D1280 " pdb=" CG1 VAL D1280 " pdb=" CG2 VAL D1280 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 5172 not shown) Planarity restraints: 5519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 324 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO F 325 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 325 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 325 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO C 190 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO C 520 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.039 5.00e-02 4.00e+02 ... (remaining 5516 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 564 2.67 - 3.23: 27476 3.23 - 3.78: 51384 3.78 - 4.34: 67563 4.34 - 4.90: 109894 Nonbonded interactions: 256881 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.110 2.170 nonbonded pdb=" O3' A R 11 " pdb="MG MG D1503 " model vdw 2.116 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.144 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.191 2.170 nonbonded pdb=" OE2 GLU D 981 " pdb=" OG SER D 994 " model vdw 2.302 3.040 ... (remaining 256876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = (chain 'P' and resid 7 through 150) selection = (chain 'Q' and resid 7 through 150) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 37.380 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.005 0.246 33448 Z= 0.267 Angle : 0.827 28.967 45688 Z= 0.501 Chirality : 0.053 0.364 5175 Planarity : 0.006 0.080 5519 Dihedral : 17.398 89.640 13144 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.80 (0.10), residues: 3802 helix: -2.17 (0.09), residues: 1574 sheet: -2.23 (0.23), residues: 399 loop : -2.89 (0.11), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 69 TYR 0.021 0.001 TYR D 679 PHE 0.028 0.002 PHE F 266 TRP 0.025 0.001 TRP F 326 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.25 (33440) covalent geometry : angle 0.78596 / 0.50 (45676) hydrogen bonds : bond 0.16515 / 18.10 ( 1481) hydrogen bonds : angle 7.31176 / 9.40 ( 4166) metal coordination : bond 0.17411 / 14.81 ( 8) metal coordination : angle 15.91434 / 24.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 582 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7947 (ttpp) REVERT: A 117 HIS cc_start: 0.7606 (p-80) cc_final: 0.7341 (p-80) REVERT: B 229 GLU cc_start: 0.7479 (tp30) cc_final: 0.7140 (tp30) REVERT: C 524 ILE cc_start: 0.8837 (tt) cc_final: 0.8593 (tt) REVERT: C 696 ASP cc_start: 0.7953 (t70) cc_final: 0.7636 (t70) REVERT: C 952 GLN cc_start: 0.8164 (mt0) cc_final: 0.7928 (mt0) REVERT: D 140 TYR cc_start: 0.7162 (m-10) cc_final: 0.6832 (m-80) REVERT: D 802 ASP cc_start: 0.7850 (m-30) cc_final: 0.7609 (m-30) REVERT: D 984 LEU cc_start: 0.8002 (tt) cc_final: 0.7770 (tt) REVERT: D 1146 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6932 (tm-30) REVERT: D 1243 LEU cc_start: 0.8188 (tp) cc_final: 0.7977 (tp) REVERT: F 276 MET cc_start: 0.7472 (ppp) cc_final: 0.7185 (ppp) REVERT: P 87 TYR cc_start: 0.8795 (t80) cc_final: 0.8287 (t80) REVERT: Q 21 GLU cc_start: 0.7842 (tp30) cc_final: 0.7623 (mm-30) REVERT: Q 90 HIS cc_start: 0.8294 (t70) cc_final: 0.8066 (t-170) outliers start: 9 outliers final: 1 residues processed: 588 average time/residue: 0.2415 time to fit residues: 218.4220 Evaluate side-chains 396 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 150 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 93 GLN B 37 HIS B 128 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 447 HIS C 622 ASN C 673 HIS C1108 ASN C1313 HIS D 196 GLN D 232 ASN D 294 ASN D 300 GLN D 450 HIS D 504 GLN D 777 HIS D 875 ASN D1098 GLN D1108 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS D1259 GLN F 128 ASN F 258 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN P 68 GLN P 90 HIS ** Q 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.177068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141028 restraints weight = 41537.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135135 restraints weight = 59018.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131379 restraints weight = 48722.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132623 restraints weight = 46740.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132451 restraints weight = 35511.466| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33448 Z= 0.213 Angle : 0.670 19.222 45688 Z= 0.349 Chirality : 0.051 1.385 5175 Planarity : 0.005 0.067 5519 Dihedral : 16.085 89.662 5589 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.74 % Allowed : 12.44 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.30 (0.12), residues: 3802 helix: -0.34 (0.12), residues: 1584 sheet: -2.13 (0.23), residues: 401 loop : -2.50 (0.12), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 117 TYR 0.025 0.002 TYR C 70 PHE 0.024 0.002 PHE F 306 TRP 0.019 0.001 TRP F 326 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (33440) covalent geometry : angle 0.66472 / 0.35 (45676) hydrogen bonds : bond 0.04832 / 5.28 ( 1481) hydrogen bonds : angle 4.93219 / 6.38 ( 4166) metal coordination : bond 0.00959 / 0.90 ( 8) metal coordination : angle 5.29335 / 8.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 421 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 HIS cc_start: 0.7469 (p-80) cc_final: 0.7267 (p-80) REVERT: C 130 MET cc_start: 0.8670 (ttm) cc_final: 0.8440 (ttm) REVERT: C 158 ASP cc_start: 0.7073 (t70) cc_final: 0.6756 (t70) REVERT: C 239 MET cc_start: 0.7813 (tmm) cc_final: 0.7583 (tmm) REVERT: C 516 ASP cc_start: 0.7642 (t0) cc_final: 0.7310 (t0) REVERT: C 524 ILE cc_start: 0.8745 (tt) cc_final: 0.8455 (tt) REVERT: C 696 ASP cc_start: 0.8084 (t70) cc_final: 0.7748 (t70) REVERT: C 1108 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8400 (p0) REVERT: D 96 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8154 (ptpt) REVERT: D 136 GLU cc_start: 0.7899 (tp30) cc_final: 0.7666 (tp30) REVERT: D 140 TYR cc_start: 0.7250 (m-10) cc_final: 0.6904 (m-80) REVERT: D 697 MET cc_start: 0.7990 (tmm) cc_final: 0.7590 (tmm) REVERT: D 802 ASP cc_start: 0.7801 (m-30) cc_final: 0.7565 (m-30) REVERT: D 1146 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6936 (tm-30) REVERT: D 1208 ASP cc_start: 0.6035 (t0) cc_final: 0.5801 (t0) REVERT: F 276 MET cc_start: 0.7372 (ppp) cc_final: 0.7091 (ppp) REVERT: P 7 ASN cc_start: 0.7698 (m-40) cc_final: 0.7355 (t0) REVERT: P 12 GLN cc_start: 0.5416 (tp40) cc_final: 0.2951 (tp40) REVERT: P 132 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7433 (tm-30) REVERT: Q 21 GLU cc_start: 0.7972 (tp30) cc_final: 0.7612 (tm-30) REVERT: Q 90 HIS cc_start: 0.8277 (t70) cc_final: 0.8036 (t-170) outliers start: 57 outliers final: 35 residues processed: 453 average time/residue: 0.2282 time to fit residues: 163.6025 Evaluate side-chains 416 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 38 optimal weight: 9.9990 chunk 357 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 281 optimal weight: 30.0000 chunk 258 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C1008 GLN C1108 ASN D 157 GLN D 196 GLN D 341 ASN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.176224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145465 restraints weight = 41392.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147266 restraints weight = 110793.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147430 restraints weight = 46350.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147881 restraints weight = 32527.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147999 restraints weight = 28590.605| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33448 Z= 0.213 Angle : 0.637 15.427 45688 Z= 0.334 Chirality : 0.047 0.993 5175 Planarity : 0.004 0.062 5519 Dihedral : 16.037 89.895 5589 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.29 % Allowed : 14.40 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.66 (0.13), residues: 3802 helix: 0.32 (0.13), residues: 1591 sheet: -2.01 (0.24), residues: 398 loop : -2.23 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 285 TYR 0.030 0.002 TYR F 148 PHE 0.033 0.002 PHE F 306 TRP 0.018 0.001 TRP C 997 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (33440) covalent geometry : angle 0.63268 / 0.33 (45676) hydrogen bonds : bond 0.04457 / 4.86 ( 1481) hydrogen bonds : angle 4.65661 / 5.99 ( 4166) metal coordination : bond 0.00883 / 0.82 ( 8) metal coordination : angle 4.77922 / 7.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 399 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 352 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7167 (mtm-85) REVERT: C 516 ASP cc_start: 0.7399 (t0) cc_final: 0.6999 (t0) REVERT: C 524 ILE cc_start: 0.8733 (tt) cc_final: 0.8401 (tt) REVERT: C 696 ASP cc_start: 0.8243 (t70) cc_final: 0.7877 (t70) REVERT: C 1231 TYR cc_start: 0.9048 (t80) cc_final: 0.8177 (t80) REVERT: D 96 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8116 (ptpt) REVERT: D 140 TYR cc_start: 0.7276 (m-10) cc_final: 0.6928 (m-80) REVERT: D 802 ASP cc_start: 0.8006 (m-30) cc_final: 0.7804 (m-30) REVERT: D 1146 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6898 (tm-30) REVERT: E 55 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6103 (tp30) REVERT: P 12 GLN cc_start: 0.4335 (tp40) cc_final: 0.1839 (tp40) REVERT: P 87 TYR cc_start: 0.8664 (t80) cc_final: 0.8398 (t80) REVERT: Q 21 GLU cc_start: 0.7787 (tp30) cc_final: 0.7517 (tm-30) REVERT: Q 90 HIS cc_start: 0.8125 (t70) cc_final: 0.7909 (t-170) outliers start: 75 outliers final: 50 residues processed: 450 average time/residue: 0.2175 time to fit residues: 157.5396 Evaluate side-chains 420 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 367 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 167 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 chunk 279 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 373 optimal weight: 5.9990 chunk 335 optimal weight: 50.0000 chunk 285 optimal weight: 30.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN D 196 GLN D 962 ASN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.178034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144480 restraints weight = 41129.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147031 restraints weight = 101915.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147573 restraints weight = 40398.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147990 restraints weight = 30453.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148251 restraints weight = 25761.365| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33448 Z= 0.140 Angle : 0.579 15.393 45688 Z= 0.305 Chirality : 0.045 0.832 5175 Planarity : 0.004 0.057 5519 Dihedral : 15.945 89.375 5589 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.32 % Allowed : 15.77 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.20 (0.13), residues: 3802 helix: 0.75 (0.13), residues: 1593 sheet: -1.82 (0.25), residues: 391 loop : -2.02 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 54 TYR 0.052 0.002 TYR F 137 PHE 0.039 0.001 PHE F 302 TRP 0.017 0.001 TRP F 326 HIS 0.009 0.001 HIS F 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (33440) covalent geometry : angle 0.57539 / 0.30 (45676) hydrogen bonds : bond 0.03950 / 4.33 ( 1481) hydrogen bonds : angle 4.44888 / 5.71 ( 4166) metal coordination : bond 0.00578 / 0.52 ( 8) metal coordination : angle 3.85137 / 6.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 389 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.8731 (ttm) cc_final: 0.8511 (ttm) REVERT: C 516 ASP cc_start: 0.7460 (t0) cc_final: 0.7014 (t0) REVERT: C 524 ILE cc_start: 0.8685 (tt) cc_final: 0.8426 (tt) REVERT: C 696 ASP cc_start: 0.8258 (t70) cc_final: 0.7862 (t70) REVERT: C 1230 MET cc_start: 0.8435 (ttm) cc_final: 0.8218 (ttt) REVERT: C 1231 TYR cc_start: 0.9054 (t80) cc_final: 0.8104 (t80) REVERT: D 96 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8247 (ptpt) REVERT: D 136 GLU cc_start: 0.7833 (tp30) cc_final: 0.7534 (tp30) REVERT: D 140 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: D 458 ASN cc_start: 0.8088 (t0) cc_final: 0.7862 (m-40) REVERT: D 526 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8635 (m) REVERT: D 822 MET cc_start: 0.8146 (mmm) cc_final: 0.7793 (tpt) REVERT: D 1215 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6163 (pt0) REVERT: E 55 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6194 (tp30) REVERT: F 362 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7579 (t0) REVERT: P 12 GLN cc_start: 0.4570 (tp40) cc_final: 0.2835 (tp40) REVERT: P 15 TRP cc_start: 0.6882 (t60) cc_final: 0.6488 (t60) REVERT: Q 21 GLU cc_start: 0.7917 (tp30) cc_final: 0.7614 (tm-30) REVERT: Q 90 HIS cc_start: 0.8225 (t70) cc_final: 0.8007 (t-170) outliers start: 76 outliers final: 49 residues processed: 444 average time/residue: 0.2204 time to fit residues: 156.0709 Evaluate side-chains 416 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 361 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 369 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 204 optimal weight: 8.9990 chunk 267 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 252 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN D 196 GLN D 651 HIS ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138987 restraints weight = 41318.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141386 restraints weight = 91182.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142951 restraints weight = 44628.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143348 restraints weight = 28042.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145847 restraints weight = 23870.143| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.004 0.054 33448 Z= 0.161 Angle : 0.584 14.810 45688 Z= 0.306 Chirality : 0.045 0.744 5175 Planarity : 0.004 0.057 5519 Dihedral : 15.934 89.621 5589 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.60 % Allowed : 16.69 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.00 (0.13), residues: 3802 helix: 0.91 (0.13), residues: 1599 sheet: -1.69 (0.25), residues: 390 loop : -1.92 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1345 TYR 0.047 0.002 TYR F 148 PHE 0.024 0.001 PHE F 221 TRP 0.016 0.001 TRP F 326 HIS 0.010 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (33440) covalent geometry : angle 0.58072 / 0.31 (45676) hydrogen bonds : bond 0.03944 / 4.32 ( 1481) hydrogen bonds : angle 4.37014 / 5.61 ( 4166) metal coordination : bond 0.00722 / 0.65 ( 8) metal coordination : angle 3.69480 / 5.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 378 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLN cc_start: 0.7443 (mm110) cc_final: 0.6867 (mm-40) REVERT: C 158 ASP cc_start: 0.7039 (t70) cc_final: 0.6721 (t70) REVERT: C 516 ASP cc_start: 0.7477 (t0) cc_final: 0.6977 (t0) REVERT: C 524 ILE cc_start: 0.8637 (tt) cc_final: 0.8376 (tt) REVERT: C 1230 MET cc_start: 0.8479 (ttm) cc_final: 0.8240 (ttt) REVERT: C 1231 TYR cc_start: 0.9087 (t80) cc_final: 0.8296 (t80) REVERT: D 140 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: D 221 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8999 (mm) REVERT: D 822 MET cc_start: 0.8212 (mmm) cc_final: 0.8007 (tpt) REVERT: D 1189 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7229 (tpp) REVERT: D 1215 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6121 (pt0) REVERT: E 55 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6404 (tp30) REVERT: F 277 MET cc_start: 0.5962 (OUTLIER) cc_final: 0.5734 (mmt) REVERT: F 362 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7894 (t0) REVERT: P 12 GLN cc_start: 0.4855 (tp40) cc_final: 0.4112 (tp40) REVERT: P 15 TRP cc_start: 0.7456 (t60) cc_final: 0.6926 (t60) REVERT: P 142 TYR cc_start: 0.6630 (t80) cc_final: 0.6198 (t80) REVERT: Q 21 GLU cc_start: 0.8107 (tp30) cc_final: 0.7740 (tm-30) outliers start: 85 outliers final: 63 residues processed: 439 average time/residue: 0.2137 time to fit residues: 151.3921 Evaluate side-chains 430 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 360 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 135 ASN Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 145 optimal weight: 7.9990 chunk 356 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 280 optimal weight: 0.1980 chunk 286 optimal weight: 30.0000 chunk 347 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 384 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.177604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146589 restraints weight = 41205.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148119 restraints weight = 109446.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148389 restraints weight = 50188.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148625 restraints weight = 32499.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149169 restraints weight = 27512.977| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33448 Z= 0.152 Angle : 0.575 14.388 45688 Z= 0.301 Chirality : 0.044 0.706 5175 Planarity : 0.004 0.055 5519 Dihedral : 15.910 89.506 5589 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.72 % Allowed : 17.12 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.87 (0.13), residues: 3802 helix: 1.00 (0.13), residues: 1604 sheet: -1.55 (0.25), residues: 402 loop : -1.85 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1345 TYR 0.046 0.002 TYR F 137 PHE 0.044 0.001 PHE F 221 TRP 0.016 0.001 TRP F 326 HIS 0.005 0.001 HIS Q 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (33440) covalent geometry : angle 0.57223 / 0.30 (45676) hydrogen bonds : bond 0.03842 / 4.22 ( 1481) hydrogen bonds : angle 4.31170 / 5.55 ( 4166) metal coordination : bond 0.00688 / 0.62 ( 8) metal coordination : angle 3.45124 / 5.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 373 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 ASP cc_start: 0.6828 (t70) cc_final: 0.6527 (t70) REVERT: C 284 LEU cc_start: 0.7720 (tp) cc_final: 0.7302 (tt) REVERT: C 516 ASP cc_start: 0.7466 (t0) cc_final: 0.6991 (t0) REVERT: C 524 ILE cc_start: 0.8749 (tt) cc_final: 0.8458 (tt) REVERT: C 696 ASP cc_start: 0.8293 (t70) cc_final: 0.8027 (t70) REVERT: C 817 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8689 (tt) REVERT: C 1230 MET cc_start: 0.8429 (ttm) cc_final: 0.8218 (ttt) REVERT: C 1231 TYR cc_start: 0.9009 (t80) cc_final: 0.8262 (t80) REVERT: D 136 GLU cc_start: 0.7874 (tp30) cc_final: 0.7599 (tp30) REVERT: D 140 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: D 214 ARG cc_start: 0.7300 (tpp80) cc_final: 0.7044 (mmm-85) REVERT: D 221 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8899 (mm) REVERT: D 724 MET cc_start: 0.7735 (mtm) cc_final: 0.7514 (mtm) REVERT: D 1189 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7078 (tpp) REVERT: D 1215 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5876 (pt0) REVERT: E 55 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6251 (tp30) REVERT: F 362 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7356 (t0) REVERT: P 12 GLN cc_start: 0.4040 (tp40) cc_final: 0.3214 (tp40) REVERT: Q 21 GLU cc_start: 0.7760 (tp30) cc_final: 0.7519 (tm-30) outliers start: 89 outliers final: 63 residues processed: 435 average time/residue: 0.2130 time to fit residues: 150.2106 Evaluate side-chains 427 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 357 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 147 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 281 optimal weight: 8.9990 chunk 8 optimal weight: 40.0000 chunk 96 optimal weight: 9.9990 chunk 302 optimal weight: 0.4980 chunk 225 optimal weight: 0.8980 chunk 220 optimal weight: 0.2980 chunk 172 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 651 HIS ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139756 restraints weight = 41134.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141611 restraints weight = 95396.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143444 restraints weight = 48548.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144197 restraints weight = 28774.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146685 restraints weight = 24077.903| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33448 Z= 0.131 Angle : 0.565 13.636 45688 Z= 0.297 Chirality : 0.043 0.650 5175 Planarity : 0.004 0.057 5519 Dihedral : 15.872 89.172 5589 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.48 % Allowed : 18.43 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.73 (0.14), residues: 3802 helix: 1.11 (0.13), residues: 1603 sheet: -1.55 (0.25), residues: 422 loop : -1.74 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1345 TYR 0.048 0.001 TYR F 137 PHE 0.047 0.001 PHE F 221 TRP 0.016 0.001 TRP F 326 HIS 0.009 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (33440) covalent geometry : angle 0.56303 / 0.30 (45676) hydrogen bonds : bond 0.03712 / 4.07 ( 1481) hydrogen bonds : angle 4.25448 / 5.45 ( 4166) metal coordination : bond 0.00552 / 0.50 ( 8) metal coordination : angle 3.12932 / 4.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 379 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7461 (mtm110) REVERT: C 429 MET cc_start: 0.7805 (mmm) cc_final: 0.7455 (mtt) REVERT: C 516 ASP cc_start: 0.7532 (t0) cc_final: 0.7041 (t0) REVERT: C 524 ILE cc_start: 0.8676 (tt) cc_final: 0.8415 (tt) REVERT: C 1108 ASN cc_start: 0.8819 (p0) cc_final: 0.8437 (p0) REVERT: C 1230 MET cc_start: 0.8434 (ttm) cc_final: 0.8206 (ttt) REVERT: C 1231 TYR cc_start: 0.9046 (t80) cc_final: 0.8260 (t80) REVERT: D 136 GLU cc_start: 0.7911 (tp30) cc_final: 0.7529 (tp30) REVERT: D 140 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: D 724 MET cc_start: 0.7762 (mtm) cc_final: 0.7545 (mtm) REVERT: D 1189 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7435 (tpp) REVERT: E 55 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6361 (tp30) REVERT: Q 21 GLU cc_start: 0.8014 (tp30) cc_final: 0.7678 (tm-30) outliers start: 81 outliers final: 62 residues processed: 437 average time/residue: 0.2156 time to fit residues: 152.2441 Evaluate side-chains 436 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 371 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 6 optimal weight: 9.9990 chunk 240 optimal weight: 3.9990 chunk 340 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 360 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.146593 restraints weight = 41522.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147497 restraints weight = 117512.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146781 restraints weight = 51205.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146182 restraints weight = 43371.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146779 restraints weight = 30212.097| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33448 Z= 0.221 Angle : 0.631 13.315 45688 Z= 0.328 Chirality : 0.045 0.652 5175 Planarity : 0.004 0.056 5519 Dihedral : 15.944 89.806 5589 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.81 % Allowed : 18.34 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.80 (0.13), residues: 3802 helix: 1.00 (0.13), residues: 1602 sheet: -1.58 (0.25), residues: 395 loop : -1.74 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1345 TYR 0.038 0.002 TYR F 137 PHE 0.037 0.002 PHE F 221 TRP 0.016 0.001 TRP F 326 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (33440) covalent geometry : angle 0.62905 / 0.33 (45676) hydrogen bonds : bond 0.04148 / 4.55 ( 1481) hydrogen bonds : angle 4.35492 / 5.59 ( 4166) metal coordination : bond 0.01039 / 0.94 ( 8) metal coordination : angle 3.48492 / 5.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 376 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 ASP cc_start: 0.6860 (t70) cc_final: 0.6525 (t70) REVERT: C 239 MET cc_start: 0.7985 (tmm) cc_final: 0.7617 (tmm) REVERT: C 516 ASP cc_start: 0.7536 (t0) cc_final: 0.7140 (t0) REVERT: C 524 ILE cc_start: 0.8777 (tt) cc_final: 0.8552 (tt) REVERT: C 800 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: D 52 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6575 (mm-30) REVERT: D 214 ARG cc_start: 0.7348 (tpp80) cc_final: 0.7116 (mmm-85) REVERT: D 1189 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7150 (tpp) REVERT: E 55 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6315 (tp30) REVERT: P 12 GLN cc_start: 0.4214 (tp40) cc_final: 0.2457 (tp40) REVERT: Q 21 GLU cc_start: 0.7781 (tp30) cc_final: 0.7535 (tm-30) outliers start: 92 outliers final: 79 residues processed: 441 average time/residue: 0.2145 time to fit residues: 153.0553 Evaluate side-chains 442 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 360 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 384 optimal weight: 6.9990 chunk 249 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 40.0000 chunk 65 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.176350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142810 restraints weight = 41147.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144988 restraints weight = 103255.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145644 restraints weight = 48194.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145045 restraints weight = 40041.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145781 restraints weight = 30390.649| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33448 Z= 0.185 Angle : 0.613 12.741 45688 Z= 0.319 Chirality : 0.044 0.612 5175 Planarity : 0.004 0.061 5519 Dihedral : 15.933 89.072 5589 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.35 % Allowed : 19.23 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.71 (0.14), residues: 3802 helix: 1.06 (0.13), residues: 1601 sheet: -1.52 (0.25), residues: 420 loop : -1.66 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1345 TYR 0.030 0.002 TYR P 142 PHE 0.038 0.001 PHE F 302 TRP 0.043 0.002 TRP D1193 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (33440) covalent geometry : angle 0.61070 / 0.32 (45676) hydrogen bonds : bond 0.03995 / 4.38 ( 1481) hydrogen bonds : angle 4.32825 / 5.55 ( 4166) metal coordination : bond 0.00869 / 0.80 ( 8) metal coordination : angle 3.29416 / 5.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 370 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 ASP cc_start: 0.6859 (t70) cc_final: 0.6550 (t70) REVERT: C 516 ASP cc_start: 0.7548 (t0) cc_final: 0.7182 (t0) REVERT: C 524 ILE cc_start: 0.8755 (tt) cc_final: 0.8523 (tt) REVERT: C 696 ASP cc_start: 0.8240 (t70) cc_final: 0.7989 (t70) REVERT: C 800 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8019 (mtm) REVERT: C 922 ASN cc_start: 0.7945 (m-40) cc_final: 0.7683 (m-40) REVERT: C 1230 MET cc_start: 0.8410 (ttm) cc_final: 0.8161 (ttt) REVERT: D 140 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: D 1189 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7200 (tpp) REVERT: D 1215 GLU cc_start: 0.6739 (pm20) cc_final: 0.6486 (pt0) REVERT: E 55 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6364 (tp30) REVERT: Q 21 GLU cc_start: 0.7833 (tp30) cc_final: 0.7566 (tm-30) outliers start: 77 outliers final: 70 residues processed: 426 average time/residue: 0.2141 time to fit residues: 147.1320 Evaluate side-chains 437 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 363 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 380 optimal weight: 2.9990 chunk 365 optimal weight: 0.0170 chunk 312 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 194 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 346 optimal weight: 5.9990 chunk 1 optimal weight: 40.0000 chunk 371 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 273 HIS C 490 GLN C 517 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.178298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147653 restraints weight = 41446.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149047 restraints weight = 107620.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147681 restraints weight = 42460.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148125 restraints weight = 29866.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148361 restraints weight = 23700.519| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33448 Z= 0.137 Angle : 0.592 12.584 45688 Z= 0.310 Chirality : 0.043 0.551 5175 Planarity : 0.004 0.062 5519 Dihedral : 15.872 88.349 5589 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.26 % Allowed : 19.63 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.56 (0.14), residues: 3802 helix: 1.17 (0.13), residues: 1603 sheet: -1.41 (0.25), residues: 419 loop : -1.58 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1345 TYR 0.030 0.001 TYR P 142 PHE 0.038 0.001 PHE F 221 TRP 0.036 0.001 TRP D1193 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (33440) covalent geometry : angle 0.58970 / 0.31 (45676) hydrogen bonds : bond 0.03736 / 4.10 ( 1481) hydrogen bonds : angle 4.25751 / 5.45 ( 4166) metal coordination : bond 0.00599 / 0.54 ( 8) metal coordination : angle 3.00463 / 4.80 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 380 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8411 (ptp) cc_final: 0.8128 (mtt) REVERT: C 158 ASP cc_start: 0.6857 (t70) cc_final: 0.6548 (t70) REVERT: C 239 MET cc_start: 0.8000 (tmm) cc_final: 0.7614 (tmm) REVERT: C 516 ASP cc_start: 0.7555 (t0) cc_final: 0.7198 (t0) REVERT: C 696 ASP cc_start: 0.8231 (t70) cc_final: 0.7939 (t70) REVERT: C 922 ASN cc_start: 0.7965 (m-40) cc_final: 0.7708 (m-40) REVERT: C 1230 MET cc_start: 0.8398 (ttm) cc_final: 0.8196 (ttt) REVERT: C 1231 TYR cc_start: 0.8918 (t80) cc_final: 0.8510 (t80) REVERT: D 1189 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7189 (tpp) REVERT: D 1215 GLU cc_start: 0.6820 (pm20) cc_final: 0.6543 (pt0) REVERT: E 55 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6349 (tp30) REVERT: F 376 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7992 (ttmt) REVERT: Q 21 GLU cc_start: 0.7853 (tp30) cc_final: 0.7589 (tm-30) outliers start: 74 outliers final: 64 residues processed: 431 average time/residue: 0.2098 time to fit residues: 146.4986 Evaluate side-chains 426 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 359 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 148 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 8 optimal weight: 40.0000 chunk 338 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 378 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 235 ASN C 517 GLN C 686 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142660 restraints weight = 41622.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144596 restraints weight = 113764.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145494 restraints weight = 49026.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144853 restraints weight = 41254.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145648 restraints weight = 29665.504| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33448 Z= 0.218 Angle : 0.642 13.907 45688 Z= 0.333 Chirality : 0.045 0.557 5175 Planarity : 0.004 0.059 5519 Dihedral : 15.949 89.284 5589 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.26 % Allowed : 19.96 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.62 (0.14), residues: 3802 helix: 1.05 (0.13), residues: 1611 sheet: -1.39 (0.26), residues: 407 loop : -1.57 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1345 TYR 0.028 0.002 TYR D 140 PHE 0.038 0.002 PHE F 221 TRP 0.036 0.002 TRP D1193 HIS 0.007 0.001 HIS F 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (33440) covalent geometry : angle 0.64016 / 0.33 (45676) hydrogen bonds : bond 0.04144 / 4.55 ( 1481) hydrogen bonds : angle 4.32681 / 5.53 ( 4166) metal coordination : bond 0.01072 / 0.97 ( 8) metal coordination : angle 3.38292 / 5.24 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5325.54 seconds wall clock time: 93 minutes 1.13 seconds (5581.13 seconds total)