Starting phenix.real_space_refine on Mon Jul 6 15:22:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei1_48073/07_2026/9ei1_48073.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei1_48073/07_2026/9ei1_48073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ei1_48073/07_2026/9ei1_48073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei1_48073/07_2026/9ei1_48073.map" model { file = "/net/cci-nas-00/data/ceres_data/9ei1_48073/07_2026/9ei1_48073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei1_48073/07_2026/9ei1_48073.cif" } resolution = 3.2 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= 0.002 sd= 0.034 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 8 6.06 5 P 57 5.49 5 Mg 1 5.21 5 S 225 5.16 5 C 22938 2.51 5 N 6438 2.21 5 O 6956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36623 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1442, 11431 Classifications: {'peptide': 1442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1371} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 11, 'TRANS': 197} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 455 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "T" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "U" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4235 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "A" 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} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 117.323 77.286 79.200 1.00 80.73 S ATOM 486 SG CYS A 74 117.050 73.565 79.395 1.00 61.40 S ATOM 533 SG CYS A 81 113.911 75.799 79.785 1.00 58.86 S ATOM 768 SG CYS A 111 103.415 66.494 124.872 1.00 82.39 S ATOM 796 SG CYS A 114 106.290 66.826 125.734 1.00 83.49 S ATOM 1109 SG CYS A 154 103.361 63.704 126.541 1.00 90.97 S ATOM 1142 SG CYS A 184 106.329 64.246 126.610 1.00 82.82 S ATOM 20063 SG CYS B1119 115.244 60.788 89.019 1.00 68.71 S ATOM 20085 SG CYS B1122 113.341 63.405 91.109 1.00 62.67 S ATOM 20200 SG CYS B1137 116.558 64.228 89.221 1.00 61.62 S ATOM 20221 SG CYS B1140 116.535 62.174 92.458 1.00 75.00 S ATOM 21188 SG CYS C 88 85.877 90.743 21.388 1.00 94.97 S ATOM 21201 SG CYS C 90 88.318 93.181 22.948 1.00 98.27 S ATOM 21236 SG CYS C 94 85.871 94.356 20.481 1.00 79.65 S ATOM 21258 SG CYS C 97 84.526 93.354 23.887 1.00 85.34 S ATOM 28494 SG CYS I 17 49.422 102.008 138.425 1.00 65.02 S ATOM 28518 SG CYS I 20 53.039 102.987 137.547 1.00 98.06 S ATOM 28679 SG CYS I 39 52.247 99.439 138.007 1.00 88.12 S ATOM 28704 SG CYS I 42 52.055 101.746 141.051 1.00100.69 S ATOM 29056 SG CYS I 86 20.854 99.726 105.625 1.00100.53 S ATOM 29080 SG CYS I 89 19.807 103.233 104.382 1.00105.70 S ATOM 29284 SG CYS I 114 22.800 101.326 102.845 1.00 92.62 S ATOM 29319 SG CYS I 119 23.000 102.826 106.247 1.00 81.13 S ATOM 29429 SG CYS J 7 58.369 94.648 41.418 1.00 49.94 S ATOM 29453 SG CYS J 10 57.674 92.947 37.980 1.00 49.71 S ATOM 29717 SG CYS J 44 55.358 92.507 40.989 1.00 48.05 S ATOM 29723 SG CYS J 45 55.565 95.708 38.945 1.00 59.24 S ATOM 30869 SG CYS L 19 87.581 122.764 57.485 1.00 72.86 S ATOM 30888 SG CYS L 22 87.312 125.992 55.509 1.00 48.96 S ATOM 31005 SG CYS L 36 90.753 124.231 55.958 1.00 81.45 S ATOM 31031 SG CYS L 39 89.063 125.891 58.835 1.00 81.37 S Time building chain proxies: 7.07, per 1000 atoms: 0.19 Number of scatterers: 36623 At special positions: 0 Unit cell: (177.45, 153.3, 200.55, 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 8 29.99 S 225 16.00 P 57 15.00 Mg 1 11.99 O 6956 8.00 N 6438 7.00 C 22938 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 Atom "ATOM 31600 O4' DA N 34 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 45 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8402 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 52 sheets defined 40.3% alpha, 17.7% beta 18 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.693A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.511A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 435 through 439 removed outlier: 3.691A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 439' Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.839A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.912A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.888A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.116A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.943A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.562A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 853 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.915A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.652A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 3.909A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.654A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.182A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1168 Processing helix chain 'A' and resid 1189 through 1197 removed outlier: 3.884A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.692A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1270 through 1277 removed outlier: 3.896A pdb=" N GLU A1273 " --> pdb=" O GLN A1270 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A1275 " --> pdb=" O GLU A1272 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A1276 " --> pdb=" O GLU A1273 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A1277 " --> pdb=" O GLU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1296 Processing helix chain 'A' and resid 1314 through 1318 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1362 through 1370 removed outlier: 3.676A pdb=" N GLY A1370 " --> pdb=" O PHE A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.811A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.908A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 4.028A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.675A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.867A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.598A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.551A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.655A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 450 removed outlier: 4.535A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.705A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.559A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.544A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.308A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.388A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.931A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.510A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1109 removed outlier: 3.534A pdb=" N LEU B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.620A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.581A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.743A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.061A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.155A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.554A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 28 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.567A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 60 removed outlier: 4.413A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.932A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'U' and resid 13 through 24 removed outlier: 3.911A pdb=" N LYS U 21 " --> pdb=" O ARG U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 44 removed outlier: 4.283A pdb=" N MET U 39 " --> pdb=" O GLU U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 68 removed outlier: 3.789A pdb=" N SER U 59 " --> pdb=" O GLY U 55 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR U 62 " --> pdb=" O LYS U 58 " (cutoff:3.500A) Proline residue: U 65 - end of helix removed outlier: 4.146A pdb=" N LEU U 68 " --> pdb=" O LEU U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 91 removed outlier: 3.529A pdb=" N LEU U 90 " --> pdb=" O GLN U 86 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU U 91 " --> pdb=" O VAL U 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 86 through 91' Processing helix chain 'U' and resid 105 through 118 removed outlier: 5.289A pdb=" N GLU U 111 " --> pdb=" O GLN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 149 removed outlier: 3.805A pdb=" N ASN U 143 " --> pdb=" O GLN U 139 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS U 149 " --> pdb=" O LEU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 206 Processing helix chain 'U' and resid 237 through 249 Processing helix chain 'U' and resid 268 through 282 Processing helix chain 'U' and resid 295 through 307 removed outlier: 4.518A pdb=" N LEU U 300 " --> pdb=" O SER U 296 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL U 301 " --> pdb=" O GLU U 297 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET U 306 " --> pdb=" O GLN U 302 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU U 307 " --> pdb=" O ASN U 303 " (cutoff:3.500A) Processing helix chain 'U' and resid 339 through 348 Processing helix chain 'U' and resid 364 through 385 Processing helix chain 'U' and resid 389 through 408 removed outlier: 4.042A pdb=" N LYS U 393 " --> pdb=" O LYS U 389 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE U 396 " --> pdb=" O ASP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 411 through 421 Processing helix chain 'U' and resid 431 through 436 removed outlier: 3.552A pdb=" N GLN U 435 " --> pdb=" O CYS U 431 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN U 436 " --> pdb=" O ASP U 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 431 through 436' Processing helix chain 'U' and resid 438 through 451 removed outlier: 3.502A pdb=" N GLU U 448 " --> pdb=" O LEU U 444 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER U 451 " --> pdb=" O LEU U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 499 through 517 removed outlier: 3.651A pdb=" N GLU U 503 " --> pdb=" O ALA U 499 " (cutoff:3.500A) Processing helix chain 'U' and resid 546 through 569 Processing helix chain 'U' and resid 573 through 591 removed outlier: 4.425A pdb=" N ALA U 578 " --> pdb=" O ALA U 574 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 615 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.515A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.196A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.505A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.687A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.472A pdb=" N LYS A 331 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.632A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1060 through 1061 removed outlier: 7.800A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.845A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.216A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.946A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.277A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 967 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.277A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.516A pdb=" N GLY A 789 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB8, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.814A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AC1, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.702A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.219A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC4, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.016A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS G 9 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR G 72 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.016A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.795A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AD1, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.604A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 225 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD3, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD4, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.282A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.546A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.546A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD8, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD9, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.646A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1127 through 1128 Processing sheet with id=AE2, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.513A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.541A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.377A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.512A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.683A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.789A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE9, first strand: chain 'G' and resid 84 through 92 removed outlier: 6.940A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 118 through 120 removed outlier: 4.300A pdb=" N GLU G 118 " --> pdb=" O LYS G 129 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS G 129 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP G 120 " --> pdb=" O CYS G 127 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF3, first strand: chain 'I' and resid 80 through 81 removed outlier: 4.640A pdb=" N LEU I 110 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU I 125 " --> pdb=" O LEU I 110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.620A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 189 through 192 removed outlier: 6.332A pdb=" N VAL U 48 " --> pdb=" O ALA U 190 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR U 192 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL U 50 " --> pdb=" O THR U 192 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE U 49 " --> pdb=" O PHE U 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'U' and resid 73 through 74 removed outlier: 6.577A pdb=" N THR U 73 " --> pdb=" O LEU U 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'U' and resid 228 through 231 removed outlier: 6.347A pdb=" N VAL U 331 " --> pdb=" O ARG U 360 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR U 362 " --> pdb=" O VAL U 331 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS U 333 " --> pdb=" O TYR U 362 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY U 262 " --> pdb=" O ILE U 313 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ALA U 315 " --> pdb=" O GLY U 262 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL U 264 " --> pdb=" O ALA U 315 " (cutoff:3.500A) 1544 hydrogen bonds defined for protein. 4335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 8.79 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6674 1.32 - 1.45: 9202 1.45 - 1.57: 21089 1.57 - 1.69: 113 1.69 - 1.82: 350 Bond restraints: 37428 Sorted by residual: bond pdb=" N GLU U 158 " pdb=" CA GLU U 158 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.20e-02 6.94e+03 1.08e+01 bond pdb=" CA SER U 163 " pdb=" CB SER U 163 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.32e-02 5.74e+03 1.08e+01 bond pdb=" N TYR U 289 " pdb=" CA TYR U 289 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.27e-02 6.20e+03 1.04e+01 bond pdb=" N LEU U 100 " pdb=" CA LEU U 100 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" C3' DA T 4 " pdb=" C2' DA T 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 37423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 50563 4.20 - 8.40: 218 8.40 - 12.59: 21 12.59 - 16.79: 2 16.79 - 20.99: 2 Bond angle restraints: 50806 Sorted by residual: angle pdb=" CA PRO L 33 " pdb=" N PRO L 33 " pdb=" CD PRO L 33 " ideal model delta sigma weight residual 112.00 99.85 12.15 1.40e+00 5.10e-01 7.53e+01 angle pdb=" O3' A P 11 " pdb=" P A P 12 " pdb=" O5' A P 12 " ideal model delta sigma weight residual 104.00 116.71 -12.71 1.50e+00 4.44e-01 7.18e+01 angle pdb=" N VAL U 76 " pdb=" CA VAL U 76 " pdb=" C VAL U 76 " ideal model delta sigma weight residual 110.42 102.69 7.73 9.60e-01 1.09e+00 6.49e+01 angle pdb=" CA PRO E 80 " pdb=" N PRO E 80 " pdb=" CD PRO E 80 " ideal model delta sigma weight residual 112.00 101.09 10.91 1.40e+00 5.10e-01 6.07e+01 angle pdb=" C4' A P 11 " pdb=" C3' A P 11 " pdb=" C2' A P 11 " ideal model delta sigma weight residual 102.60 96.00 6.60 1.00e+00 1.00e+00 4.35e+01 ... (remaining 50801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 21879 34.25 - 68.50: 889 68.50 - 102.75: 58 102.75 - 137.00: 3 137.00 - 171.25: 3 Dihedral angle restraints: 22832 sinusoidal: 9854 harmonic: 12978 Sorted by residual: dihedral pdb=" CD ARG U 180 " pdb=" NE ARG U 180 " pdb=" CZ ARG U 180 " pdb=" NH1 ARG U 180 " ideal model delta sinusoidal sigma weight residual 0.00 81.90 -81.90 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CD ARG U 282 " pdb=" NE ARG U 282 " pdb=" CZ ARG U 282 " pdb=" NH1 ARG U 282 " ideal model delta sinusoidal sigma weight residual 0.00 -81.71 81.71 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CD ARG U 109 " pdb=" NE ARG U 109 " pdb=" CZ ARG U 109 " pdb=" NH1 ARG U 109 " ideal model delta sinusoidal sigma weight residual 0.00 61.48 -61.48 1 1.00e+01 1.00e-02 5.02e+01 ... (remaining 22829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 5610 0.132 - 0.264: 63 0.264 - 0.396: 3 0.396 - 0.528: 4 0.528 - 0.660: 9 Chirality restraints: 5689 Sorted by residual: chirality pdb=" P DC N 35 " pdb=" OP1 DC N 35 " pdb=" OP2 DC N 35 " pdb=" O5' DC N 35 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" P DA N 32 " pdb=" OP1 DA N 32 " pdb=" OP2 DA N 32 " pdb=" O5' DA N 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" P A P 11 " pdb=" OP1 A P 11 " pdb=" OP2 A P 11 " pdb=" O5' A P 11 " both_signs ideal model delta sigma weight residual True 2.41 -3.02 -0.61 2.00e-01 2.50e+01 9.39e+00 ... (remaining 5686 not shown) Planarity restraints: 6388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG U 282 " 1.089 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG U 282 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG U 282 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG U 282 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG U 282 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 180 " -1.087 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG U 180 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG U 180 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG U 180 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG U 180 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU U 131 " -0.059 2.00e-02 2.50e+03 1.17e-01 1.37e+02 pdb=" C GLU U 131 " 0.203 2.00e-02 2.50e+03 pdb=" O GLU U 131 " -0.076 2.00e-02 2.50e+03 pdb=" N MET U 132 " -0.068 2.00e-02 2.50e+03 ... (remaining 6385 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 16 2.16 - 2.85: 12594 2.85 - 3.53: 53813 3.53 - 4.22: 89568 4.22 - 4.90: 155337 Nonbonded interactions: 311328 Sorted by model distance: nonbonded pdb=" N6 DA N 27 " pdb=" O4 DT T 2 " model vdw 1.475 3.120 nonbonded pdb=" CG1 ILE U 80 " pdb=" OE2 GLU U 131 " model vdw 1.506 3.440 nonbonded pdb=" CD1 ILE U 80 " pdb=" OE2 GLU U 131 " model vdw 1.526 3.460 nonbonded pdb=" N1 DA N 27 " pdb=" N3 DT T 2 " model vdw 1.698 3.200 nonbonded pdb=" N6 DA N 27 " pdb=" C4 DT T 2 " model vdw 1.821 3.340 ... (remaining 311323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 38.720 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 0.146 37460 Z= 0.258 Angle : 0.858 37.660 50851 Z= 0.485 Chirality : 0.055 0.660 5689 Planarity : 0.015 0.488 6388 Dihedral : 17.040 171.249 14430 Min Nonbonded Distance : 1.475 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.08 % Favored : 93.36 % Rotamer: Outliers : 1.59 % Allowed : 18.61 % Favored : 79.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.97 % 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: 0.16 (0.13), residues: 4410 helix: 1.11 (0.14), residues: 1582 sheet: 0.25 (0.21), residues: 647 loop : -0.65 (0.14), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1396 TYR 0.019 0.001 TYR A 669 PHE 0.053 0.002 PHE E 73 TRP 0.018 0.001 TRP A 988 HIS 0.007 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.26 (37428) covalent geometry : angle 0.80018 / 0.48 (50806) hydrogen bonds : bond 0.17896 / 12.32 ( 1556) hydrogen bonds : angle 6.91888 / 5.02 ( 4427) metal coordination : bond 0.00823 / 0.50 ( 32) metal coordination : angle 10.44838 / 6.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 1042 time to evaluate : 1.405 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: A 16 ARG cc_start: 0.8195 (mmt90) cc_final: 0.7960 (mtt90) REVERT: A 117 LEU cc_start: 0.8737 (mt) cc_final: 0.8372 (mt) REVERT: A 123 ASN cc_start: 0.7985 (t0) cc_final: 0.7702 (t0) REVERT: A 125 LYS cc_start: 0.7901 (ptpp) cc_final: 0.7579 (ptpp) REVERT: A 145 TYR cc_start: 0.8404 (t80) cc_final: 0.8123 (t80) REVERT: A 151 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7589 (mmtm) REVERT: A 190 ARG cc_start: 0.6877 (mtm110) cc_final: 0.6542 (mtm110) REVERT: A 212 LYS cc_start: 0.8179 (mptt) cc_final: 0.7814 (mmtt) REVERT: A 232 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7682 (mm-30) REVERT: A 296 ASN cc_start: 0.7795 (m-40) cc_final: 0.7521 (m-40) REVERT: A 308 LYS cc_start: 0.8383 (ttmt) cc_final: 0.7936 (ttmm) REVERT: A 337 LYS cc_start: 0.7989 (ttmp) cc_final: 0.7764 (tttm) REVERT: A 417 LYS cc_start: 0.8313 (ttmm) cc_final: 0.8007 (ttmm) REVERT: A 418 TYR cc_start: 0.8537 (m-80) cc_final: 0.7872 (m-80) REVERT: A 430 ARG cc_start: 0.8044 (mtm180) cc_final: 0.7840 (mtm180) REVERT: A 461 GLN cc_start: 0.8091 (mt0) cc_final: 0.7881 (mt0) REVERT: A 501 MET cc_start: 0.8146 (mtp) cc_final: 0.7896 (mtp) REVERT: A 556 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7632 (mm-30) REVERT: A 607 SER cc_start: 0.8733 (m) cc_final: 0.8407 (p) REVERT: A 642 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8317 (ttpp) REVERT: A 742 ASN cc_start: 0.8344 (m-40) cc_final: 0.8106 (m-40) REVERT: A 862 ARG cc_start: 0.8177 (ttt90) cc_final: 0.7506 (ttt90) REVERT: A 928 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7183 (tpp80) REVERT: A 940 LYS cc_start: 0.8166 (pttt) cc_final: 0.7896 (pttt) REVERT: A 958 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7095 (ttp80) REVERT: A 962 ASP cc_start: 0.7457 (m-30) cc_final: 0.7241 (m-30) REVERT: A 1071 GLU cc_start: 0.7700 (tp30) cc_final: 0.7464 (tp30) REVERT: A 1093 GLN cc_start: 0.7835 (pt0) cc_final: 0.7624 (pt0) REVERT: A 1125 LYS cc_start: 0.8180 (mttt) cc_final: 0.7957 (mttt) REVERT: A 1149 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7874 (mtt90) REVERT: A 1155 LYS cc_start: 0.8314 (mmmm) cc_final: 0.8089 (mmmm) REVERT: A 1176 TYR cc_start: 0.8440 (m-80) cc_final: 0.8135 (m-80) REVERT: A 1189 ASP cc_start: 0.7934 (m-30) cc_final: 0.7705 (m-30) REVERT: A 1210 TRP cc_start: 0.8612 (m100) cc_final: 0.8321 (m100) REVERT: A 1215 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6694 (mt-10) REVERT: A 1281 ASP cc_start: 0.7399 (m-30) cc_final: 0.7196 (m-30) REVERT: A 1286 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7871 (mtp180) REVERT: A 1294 THR cc_start: 0.8090 (p) cc_final: 0.7723 (p) REVERT: A 1376 LYS cc_start: 0.8669 (tppt) cc_final: 0.8248 (tptm) REVERT: A 1408 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7705 (mmm160) REVERT: A 1441 GLU cc_start: 0.7603 (tt0) cc_final: 0.7386 (tt0) REVERT: A 1479 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7924 (mmmm) REVERT: B 35 ASP cc_start: 0.8249 (t0) cc_final: 0.7995 (t0) REVERT: B 109 MET cc_start: 0.8169 (mmm) cc_final: 0.7918 (mmt) REVERT: B 131 THR cc_start: 0.8440 (m) cc_final: 0.8111 (p) REVERT: B 160 TYR cc_start: 0.7900 (m-80) cc_final: 0.7662 (m-80) REVERT: B 169 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7527 (ttp80) REVERT: B 214 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8039 (ttpp) REVERT: B 218 THR cc_start: 0.8575 (m) cc_final: 0.8275 (t) REVERT: B 220 GLU cc_start: 0.8049 (pt0) cc_final: 0.7713 (pt0) REVERT: B 222 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7628 (mtt90) REVERT: B 297 MET cc_start: 0.8525 (tpp) cc_final: 0.7959 (tpp) REVERT: B 319 ASN cc_start: 0.8111 (t0) cc_final: 0.7873 (t0) REVERT: B 320 PHE cc_start: 0.8534 (t80) cc_final: 0.7935 (t80) REVERT: B 337 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8130 (ttpp) REVERT: B 347 MET cc_start: 0.8339 (ttp) cc_final: 0.8033 (ttp) REVERT: B 360 LYS cc_start: 0.8293 (mtmp) cc_final: 0.7929 (mttp) REVERT: B 385 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7762 (mtt180) REVERT: B 416 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7467 (ttm110) REVERT: B 497 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8473 (tppp) REVERT: B 525 ASN cc_start: 0.7967 (m110) cc_final: 0.7732 (m110) REVERT: B 547 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 552 ASN cc_start: 0.7635 (m110) cc_final: 0.7320 (m110) REVERT: B 645 GLU cc_start: 0.7985 (tp30) cc_final: 0.7722 (tp30) REVERT: B 646 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.8077 (ttp-110) REVERT: B 685 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7927 (mmmt) REVERT: B 689 TYR cc_start: 0.8454 (t80) cc_final: 0.8195 (t80) REVERT: B 744 MET cc_start: 0.8455 (mmm) cc_final: 0.8213 (mtp) REVERT: B 840 MET cc_start: 0.6851 (mmm) cc_final: 0.6549 (tpt) REVERT: B 908 MET cc_start: 0.8211 (tmm) cc_final: 0.7980 (tmm) REVERT: B 942 LYS cc_start: 0.8210 (pttm) cc_final: 0.7986 (pttp) REVERT: B 998 ASP cc_start: 0.8041 (t0) cc_final: 0.7666 (t0) REVERT: B 1004 ASP cc_start: 0.7537 (t70) cc_final: 0.7324 (t0) REVERT: B 1067 ILE cc_start: 0.8782 (pt) cc_final: 0.8486 (pt) REVERT: B 1075 MET cc_start: 0.8547 (mmt) cc_final: 0.7894 (mmt) REVERT: C 97 CYS cc_start: 0.6680 (p) cc_final: 0.6275 (p) REVERT: C 160 ARG cc_start: 0.8414 (mtm110) cc_final: 0.8088 (ttp-110) REVERT: E 30 GLN cc_start: 0.7730 (tp40) cc_final: 0.7429 (tp-100) REVERT: E 35 GLN cc_start: 0.8242 (tt0) cc_final: 0.7870 (tt0) REVERT: E 37 LEU cc_start: 0.8526 (tp) cc_final: 0.8311 (tp) REVERT: E 47 LYS cc_start: 0.7467 (pttm) cc_final: 0.7256 (pttm) REVERT: E 79 GLU cc_start: 0.7646 (mp0) cc_final: 0.7051 (mp0) REVERT: E 85 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7751 (mmmm) REVERT: E 92 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7612 (tp-100) REVERT: E 101 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7764 (mtp180) REVERT: E 131 LEU cc_start: 0.8808 (mt) cc_final: 0.8565 (mt) REVERT: E 153 LYS cc_start: 0.8341 (mttp) cc_final: 0.8115 (mttp) REVERT: E 155 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8067 (mt-10) REVERT: E 186 LYS cc_start: 0.8359 (ptmm) cc_final: 0.8135 (ptmm) REVERT: E 192 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8131 (ttpt) REVERT: G 66 VAL cc_start: 0.8852 (p) cc_final: 0.8634 (t) REVERT: G 117 MET cc_start: 0.5440 (tpp) cc_final: 0.5218 (tpp) REVERT: H 7 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: H 14 ASP cc_start: 0.7977 (m-30) cc_final: 0.7755 (t0) REVERT: H 88 PHE cc_start: 0.8814 (m-80) cc_final: 0.8603 (m-80) REVERT: I 60 HIS cc_start: 0.4920 (OUTLIER) cc_final: 0.4279 (p-80) REVERT: J 53 VAL cc_start: 0.8749 (p) cc_final: 0.8540 (m) REVERT: K 17 LYS cc_start: 0.8314 (mtpp) cc_final: 0.7986 (mtpp) REVERT: K 18 LYS cc_start: 0.8922 (tppt) cc_final: 0.8692 (tppt) REVERT: K 70 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8258 (ttmm) REVERT: U 35 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7556 (mt-10) REVERT: U 103 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.4569 (ttpt) REVERT: U 158 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: U 282 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6767 (tpp-160) REVERT: U 328 VAL cc_start: 0.7935 (t) cc_final: 0.7458 (t) REVERT: U 352 ARG cc_start: 0.3620 (tpt170) cc_final: 0.3254 (ttm-80) REVERT: U 370 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: U 373 PHE cc_start: 0.7101 (t80) cc_final: 0.6803 (t80) REVERT: U 418 LYS cc_start: 0.7857 (tptp) cc_final: 0.7591 (tptp) REVERT: U 438 THR cc_start: 0.8037 (t) cc_final: 0.7720 (m) REVERT: U 508 TYR cc_start: 0.7777 (t80) cc_final: 0.7458 (t80) REVERT: U 559 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6899 (mt-10) REVERT: U 598 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8631 (mtmm) REVERT: U 604 LYS cc_start: 0.8180 (tptm) cc_final: 0.7961 (tptm) outliers start: 62 outliers final: 23 residues processed: 1079 average time/residue: 0.2682 time to fit residues: 441.0652 Evaluate side-chains 970 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 941 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain I residue 60 HIS Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 158 GLU Chi-restraints excluded: chain U residue 160 HIS Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 284 VAL Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 370 GLN Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain U residue 377 LYS Chi-restraints excluded: chain U residue 385 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 HIS ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 576 GLN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 930 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN B1115 GLN C 265 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN E 19 GLN E 95 GLN I 41 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN U 89 HIS U 101 ASN U 107 GLN U 122 GLN U 200 GLN U 274 GLN U 302 GLN U 335 ASN U 370 GLN ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 435 GLN U 513 GLN U 595 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113808 restraints weight = 54036.394| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.67 r_work: 0.3361 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37460 Z= 0.175 Angle : 0.739 37.114 50851 Z= 0.356 Chirality : 0.047 0.393 5689 Planarity : 0.006 0.130 6388 Dihedral : 13.220 170.786 5604 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.94 % Favored : 93.85 % Rotamer: Outliers : 3.65 % Allowed : 18.53 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.03 (0.13), residues: 4410 helix: 1.04 (0.13), residues: 1608 sheet: 0.15 (0.20), residues: 616 loop : -0.76 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 360 TYR 0.016 0.002 TYR A 669 PHE 0.032 0.002 PHE E 73 TRP 0.015 0.001 TRP C 49 HIS 0.010 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (37428) covalent geometry : angle 0.66930 / 0.35 (50806) hydrogen bonds : bond 0.04791 / 3.20 ( 1556) hydrogen bonds : angle 5.46685 / 3.98 ( 4427) metal coordination : bond 0.00856 / 0.49 ( 32) metal coordination : angle 10.57250 / 6.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 957 time to evaluate : 1.620 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 16 ARG cc_start: 0.8265 (mmt90) cc_final: 0.8060 (mtt90) REVERT: A 29 ASP cc_start: 0.8044 (t0) cc_final: 0.7763 (t70) REVERT: A 117 LEU cc_start: 0.8764 (mt) cc_final: 0.8416 (mt) REVERT: A 123 ASN cc_start: 0.7940 (t0) cc_final: 0.7700 (t0) REVERT: A 125 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7746 (ptpp) REVERT: A 148 CYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8542 (t) REVERT: A 151 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7790 (mmtm) REVERT: A 212 LYS cc_start: 0.8343 (mptt) cc_final: 0.8062 (mmtt) REVERT: A 232 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 308 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8055 (ttmm) REVERT: A 351 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7724 (mmm-85) REVERT: A 417 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8038 (ttmm) REVERT: A 418 TYR cc_start: 0.8623 (m-80) cc_final: 0.8020 (m-80) REVERT: A 430 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7923 (mtm180) REVERT: A 636 ILE cc_start: 0.8466 (mm) cc_final: 0.8243 (mt) REVERT: A 642 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8456 (ttpp) REVERT: A 703 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7797 (mm-40) REVERT: A 862 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7831 (ttt90) REVERT: A 868 MET cc_start: 0.8185 (mtp) cc_final: 0.7659 (mtm) REVERT: A 894 ASP cc_start: 0.8193 (p0) cc_final: 0.7992 (p0) REVERT: A 940 LYS cc_start: 0.8343 (pttt) cc_final: 0.8037 (pttt) REVERT: A 957 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 958 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7306 (ttp80) REVERT: A 1027 ASP cc_start: 0.7909 (t70) cc_final: 0.7692 (t70) REVERT: A 1167 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8266 (ttm-80) REVERT: A 1215 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6873 (mt-10) REVERT: A 1226 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8582 (tp) REVERT: A 1308 TYR cc_start: 0.8465 (m-80) cc_final: 0.8256 (m-80) REVERT: A 1344 MET cc_start: 0.8162 (tpt) cc_final: 0.7683 (tpt) REVERT: A 1376 LYS cc_start: 0.8671 (tppt) cc_final: 0.8268 (tptm) REVERT: A 1408 ARG cc_start: 0.8170 (mmm160) cc_final: 0.7805 (mmm160) REVERT: A 1441 GLU cc_start: 0.7895 (tt0) cc_final: 0.7677 (tt0) REVERT: A 1479 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8004 (mmmm) REVERT: B 21 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7781 (tt) REVERT: B 35 ASP cc_start: 0.8353 (t0) cc_final: 0.8086 (t0) REVERT: B 109 MET cc_start: 0.8104 (mmm) cc_final: 0.7701 (mmt) REVERT: B 169 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7767 (ttp80) REVERT: B 206 TYR cc_start: 0.8433 (m-80) cc_final: 0.7786 (m-80) REVERT: B 218 THR cc_start: 0.8318 (m) cc_final: 0.8031 (t) REVERT: B 220 GLU cc_start: 0.8169 (pt0) cc_final: 0.7785 (pt0) REVERT: B 222 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7806 (mtt-85) REVERT: B 297 MET cc_start: 0.8320 (tpp) cc_final: 0.7964 (ttm) REVERT: B 320 PHE cc_start: 0.8629 (t80) cc_final: 0.7838 (t80) REVERT: B 337 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8322 (ttpp) REVERT: B 347 MET cc_start: 0.8556 (ttp) cc_final: 0.8249 (ttp) REVERT: B 360 LYS cc_start: 0.8352 (mtmp) cc_final: 0.8103 (mtmm) REVERT: B 525 ASN cc_start: 0.7841 (m110) cc_final: 0.7641 (m110) REVERT: B 547 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 645 GLU cc_start: 0.8061 (tp30) cc_final: 0.7200 (tp30) REVERT: B 646 ARG cc_start: 0.8300 (ttp-110) cc_final: 0.7981 (ttp-110) REVERT: B 685 LYS cc_start: 0.8271 (mmmt) cc_final: 0.7946 (mmmt) REVERT: B 689 TYR cc_start: 0.8451 (t80) cc_final: 0.8162 (t80) REVERT: B 692 THR cc_start: 0.8500 (p) cc_final: 0.8189 (p) REVERT: B 721 ARG cc_start: 0.8553 (mmt180) cc_final: 0.8306 (mmt180) REVERT: B 744 MET cc_start: 0.8330 (mmm) cc_final: 0.8027 (mtp) REVERT: B 768 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8244 (mmm-85) REVERT: B 1004 ASP cc_start: 0.7584 (t70) cc_final: 0.7356 (t0) REVERT: B 1075 MET cc_start: 0.8291 (mmt) cc_final: 0.7784 (mmt) REVERT: B 1151 MET cc_start: 0.8413 (ttp) cc_final: 0.8195 (ptm) REVERT: C 10 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7349 (mtm110) REVERT: C 97 CYS cc_start: 0.7264 (p) cc_final: 0.6801 (p) REVERT: C 160 ARG cc_start: 0.8555 (mtm110) cc_final: 0.8297 (ttp-110) REVERT: C 188 PRO cc_start: 0.8808 (Cg_endo) cc_final: 0.8602 (Cg_exo) REVERT: C 246 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7847 (mp) REVERT: C 262 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8192 (mm110) REVERT: E 47 LYS cc_start: 0.7618 (pttm) cc_final: 0.7374 (pttm) REVERT: E 78 GLU cc_start: 0.8003 (pm20) cc_final: 0.7747 (pm20) REVERT: E 82 VAL cc_start: 0.8159 (t) cc_final: 0.7933 (m) REVERT: E 92 GLN cc_start: 0.8022 (tp-100) cc_final: 0.7792 (tp-100) REVERT: E 110 MET cc_start: 0.7050 (mtp) cc_final: 0.6724 (ttm) REVERT: E 131 LEU cc_start: 0.8893 (mt) cc_final: 0.8631 (mt) REVERT: E 155 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8302 (mt-10) REVERT: E 192 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8250 (ttpt) REVERT: H 7 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: H 14 ASP cc_start: 0.8127 (m-30) cc_final: 0.7908 (t0) REVERT: H 145 MET cc_start: 0.8386 (tpp) cc_final: 0.8128 (ttm) REVERT: I 122 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7762 (mtm-85) REVERT: J 53 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8565 (m) REVERT: K 17 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8327 (mtpp) REVERT: K 18 LYS cc_start: 0.8820 (tppt) cc_final: 0.8612 (tppt) REVERT: U 26 PHE cc_start: 0.6481 (t80) cc_final: 0.6192 (t80) REVERT: U 35 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7747 (mt-10) REVERT: U 39 MET cc_start: 0.7172 (tpt) cc_final: 0.6652 (tpt) REVERT: U 68 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6594 (tt) REVERT: U 82 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7294 (tt) REVERT: U 110 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8308 (mtmm) REVERT: U 117 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7235 (mm-30) REVERT: U 124 LYS cc_start: 0.4729 (tptt) cc_final: 0.3590 (pttt) REVERT: U 158 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: U 267 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6262 (pmt170) REVERT: U 270 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6547 (mm-30) REVERT: U 327 ASN cc_start: 0.6379 (p0) cc_final: 0.6155 (p0) REVERT: U 345 GLN cc_start: 0.6844 (tm-30) cc_final: 0.6528 (tm-30) REVERT: U 363 TYR cc_start: 0.7499 (t80) cc_final: 0.7001 (t80) REVERT: U 371 VAL cc_start: 0.8680 (t) cc_final: 0.8438 (p) REVERT: U 373 PHE cc_start: 0.7128 (t80) cc_final: 0.6919 (t80) REVERT: U 418 LYS cc_start: 0.7546 (tptp) cc_final: 0.7226 (tptp) REVERT: U 441 ARG cc_start: 0.7125 (mmt-90) cc_final: 0.6829 (mmt180) REVERT: U 509 GLN cc_start: 0.7902 (mt0) cc_final: 0.7611 (mt0) REVERT: U 513 GLN cc_start: 0.7240 (mt0) cc_final: 0.7014 (mt0) REVERT: U 518 LYS cc_start: 0.7757 (mmtp) cc_final: 0.7466 (mmtt) REVERT: U 530 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6604 (mp0) REVERT: U 544 ARG cc_start: 0.7101 (mmm-85) cc_final: 0.6822 (mmm-85) REVERT: U 556 LEU cc_start: 0.7499 (mm) cc_final: 0.6983 (tp) REVERT: U 559 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7038 (mt-10) REVERT: U 598 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7695 (mmtp) REVERT: U 602 LEU cc_start: 0.8089 (mp) cc_final: 0.7695 (mp) REVERT: U 604 LYS cc_start: 0.8167 (tptm) cc_final: 0.7896 (tptm) outliers start: 142 outliers final: 71 residues processed: 1031 average time/residue: 0.2925 time to fit residues: 458.1770 Evaluate side-chains 1021 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 936 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 725 GLN Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 89 HIS Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 158 GLU Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 284 VAL Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 301 VAL Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 377 LYS Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 12 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 257 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 418 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 GLN A1190 GLN A1332 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 350 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN C 260 GLN C 265 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 22 ASN U 89 HIS U 139 GLN ** U 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 274 GLN U 327 ASN U 370 GLN ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111611 restraints weight = 54065.817| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.69 r_work: 0.3349 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37460 Z= 0.169 Angle : 0.705 37.351 50851 Z= 0.335 Chirality : 0.046 0.346 5689 Planarity : 0.005 0.074 6388 Dihedral : 12.982 171.147 5573 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.01 % Rotamer: Outliers : 3.70 % Allowed : 19.43 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.04 (0.13), residues: 4410 helix: 1.07 (0.13), residues: 1619 sheet: -0.06 (0.20), residues: 626 loop : -0.84 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1396 TYR 0.018 0.001 TYR A 669 PHE 0.024 0.002 PHE E 73 TRP 0.017 0.001 TRP C 49 HIS 0.020 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (37428) covalent geometry : angle 0.63077 / 0.33 (50806) hydrogen bonds : bond 0.04173 / 2.80 ( 1556) hydrogen bonds : angle 5.12730 / 3.75 ( 4427) metal coordination : bond 0.00907 / 0.52 ( 32) metal coordination : angle 10.58305 / 6.85 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 979 time to evaluate : 1.459 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 29 ASP cc_start: 0.8057 (t0) cc_final: 0.7737 (t70) REVERT: A 117 LEU cc_start: 0.8789 (mt) cc_final: 0.8296 (mt) REVERT: A 123 ASN cc_start: 0.7967 (t0) cc_final: 0.7677 (t0) REVERT: A 125 LYS cc_start: 0.8087 (ptpp) cc_final: 0.7778 (ptpp) REVERT: A 148 CYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8547 (t) REVERT: A 151 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7819 (mmtm) REVERT: A 212 LYS cc_start: 0.8391 (mptt) cc_final: 0.8060 (mmtt) REVERT: A 232 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 308 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8071 (ttmm) REVERT: A 351 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7692 (mmm-85) REVERT: A 417 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7991 (ttmm) REVERT: A 418 TYR cc_start: 0.8668 (m-80) cc_final: 0.8173 (m-80) REVERT: A 512 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7950 (ttm170) REVERT: A 636 ILE cc_start: 0.8457 (mm) cc_final: 0.8254 (mt) REVERT: A 642 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8442 (ttpp) REVERT: A 703 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7845 (mm-40) REVERT: A 835 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7220 (mt-10) REVERT: A 860 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8336 (mt) REVERT: A 862 ARG cc_start: 0.8157 (ttt90) cc_final: 0.7765 (ttt90) REVERT: A 868 MET cc_start: 0.8136 (mtp) cc_final: 0.7858 (mtt) REVERT: A 940 LYS cc_start: 0.8304 (pttt) cc_final: 0.7997 (pttt) REVERT: A 957 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 958 ARG cc_start: 0.7567 (ttp80) cc_final: 0.7254 (ttp80) REVERT: A 1125 LYS cc_start: 0.8268 (mttt) cc_final: 0.7953 (mttt) REVERT: A 1167 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8314 (ttm-80) REVERT: A 1215 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: A 1254 LYS cc_start: 0.7681 (ptmm) cc_final: 0.7116 (ptmm) REVERT: A 1308 TYR cc_start: 0.8519 (m-80) cc_final: 0.8190 (m-80) REVERT: A 1344 MET cc_start: 0.8154 (tpt) cc_final: 0.7679 (tpt) REVERT: A 1376 LYS cc_start: 0.8640 (tppt) cc_final: 0.8252 (tptm) REVERT: A 1408 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7358 (mmm160) REVERT: A 1441 GLU cc_start: 0.7917 (tt0) cc_final: 0.7706 (tt0) REVERT: A 1451 MET cc_start: 0.8498 (mmm) cc_final: 0.8095 (tpp) REVERT: A 1479 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7983 (mmmm) REVERT: B 35 ASP cc_start: 0.8368 (t0) cc_final: 0.8116 (t0) REVERT: B 40 VAL cc_start: 0.8418 (t) cc_final: 0.8082 (t) REVERT: B 109 MET cc_start: 0.8074 (mmm) cc_final: 0.7659 (mmt) REVERT: B 131 THR cc_start: 0.8313 (m) cc_final: 0.7845 (p) REVERT: B 214 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8008 (ttpp) REVERT: B 218 THR cc_start: 0.8397 (m) cc_final: 0.8099 (t) REVERT: B 220 GLU cc_start: 0.8175 (pt0) cc_final: 0.7884 (pt0) REVERT: B 222 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7875 (mtt-85) REVERT: B 262 TYR cc_start: 0.6892 (m-80) cc_final: 0.6690 (m-80) REVERT: B 285 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8078 (mm) REVERT: B 320 PHE cc_start: 0.8648 (t80) cc_final: 0.7867 (t80) REVERT: B 337 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8339 (ttpp) REVERT: B 346 GLU cc_start: 0.8256 (tt0) cc_final: 0.7636 (tt0) REVERT: B 347 MET cc_start: 0.8554 (ttp) cc_final: 0.8258 (ttp) REVERT: B 360 LYS cc_start: 0.8364 (mtmp) cc_final: 0.8066 (mttp) REVERT: B 525 ASN cc_start: 0.7826 (m110) cc_final: 0.7578 (m110) REVERT: B 547 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7378 (tm-30) REVERT: B 645 GLU cc_start: 0.8103 (tp30) cc_final: 0.7880 (tp30) REVERT: B 646 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.8081 (ttp-110) REVERT: B 685 LYS cc_start: 0.8329 (mmmt) cc_final: 0.8004 (mmmt) REVERT: B 689 TYR cc_start: 0.8420 (t80) cc_final: 0.8146 (t80) REVERT: B 692 THR cc_start: 0.8543 (p) cc_final: 0.8216 (p) REVERT: B 721 ARG cc_start: 0.8587 (mmt180) cc_final: 0.8309 (mmt180) REVERT: B 744 MET cc_start: 0.8407 (mmm) cc_final: 0.8046 (mtt) REVERT: B 768 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8272 (mmm-85) REVERT: B 914 GLU cc_start: 0.8118 (mp0) cc_final: 0.7807 (mp0) REVERT: B 942 LYS cc_start: 0.8225 (pttm) cc_final: 0.8022 (pttp) REVERT: B 1004 ASP cc_start: 0.7612 (t70) cc_final: 0.7356 (t0) REVERT: B 1071 ASN cc_start: 0.7981 (m110) cc_final: 0.7750 (m110) REVERT: B 1075 MET cc_start: 0.8253 (mmt) cc_final: 0.7626 (mmt) REVERT: B 1151 MET cc_start: 0.8432 (ttp) cc_final: 0.8231 (ptm) REVERT: C 62 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: C 97 CYS cc_start: 0.7185 (p) cc_final: 0.6763 (p) REVERT: C 118 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7858 (ttm110) REVERT: C 162 ARG cc_start: 0.8024 (ttp-110) cc_final: 0.7799 (ttt-90) REVERT: C 215 GLU cc_start: 0.8110 (pt0) cc_final: 0.7835 (pt0) REVERT: C 238 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7811 (t) REVERT: C 246 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7918 (mp) REVERT: E 47 LYS cc_start: 0.7623 (pttm) cc_final: 0.7405 (pttm) REVERT: E 78 GLU cc_start: 0.8031 (pm20) cc_final: 0.7751 (pm20) REVERT: E 82 VAL cc_start: 0.8190 (t) cc_final: 0.7943 (m) REVERT: E 92 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7810 (tp-100) REVERT: E 110 MET cc_start: 0.7259 (mtp) cc_final: 0.6879 (ttm) REVERT: E 131 LEU cc_start: 0.8873 (mt) cc_final: 0.8668 (mt) REVERT: E 155 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8335 (mt-10) REVERT: E 172 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7121 (mtm-85) REVERT: E 192 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8281 (ttpt) REVERT: H 7 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: I 122 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7827 (mtm-85) REVERT: J 53 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8627 (m) REVERT: K 17 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8319 (mtpp) REVERT: U 26 PHE cc_start: 0.6605 (t80) cc_final: 0.6221 (t80) REVERT: U 35 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7724 (mt-10) REVERT: U 39 MET cc_start: 0.7170 (tpt) cc_final: 0.6676 (tpt) REVERT: U 68 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6723 (tt) REVERT: U 109 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7385 (ttm110) REVERT: U 117 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7346 (mm-30) REVERT: U 124 LYS cc_start: 0.4578 (tptt) cc_final: 0.3510 (pttt) REVERT: U 158 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: U 161 CYS cc_start: 0.8536 (p) cc_final: 0.8289 (p) REVERT: U 270 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6544 (mm-30) REVERT: U 307 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: U 327 ASN cc_start: 0.6160 (p0) cc_final: 0.5925 (p0) REVERT: U 345 GLN cc_start: 0.6716 (tm-30) cc_final: 0.6310 (tm-30) REVERT: U 360 ARG cc_start: 0.7721 (ttm170) cc_final: 0.6621 (ttm-80) REVERT: U 371 VAL cc_start: 0.8675 (t) cc_final: 0.8410 (p) REVERT: U 373 PHE cc_start: 0.7096 (t80) cc_final: 0.6855 (t80) REVERT: U 397 MET cc_start: 0.6818 (ptt) cc_final: 0.6583 (ptt) REVERT: U 418 LYS cc_start: 0.7539 (tptp) cc_final: 0.7225 (tptp) REVERT: U 441 ARG cc_start: 0.6998 (mmt-90) cc_final: 0.6625 (mmt180) REVERT: U 509 GLN cc_start: 0.7959 (mt0) cc_final: 0.7622 (mt0) REVERT: U 518 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7411 (mmtt) REVERT: U 530 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6553 (mp0) REVERT: U 544 ARG cc_start: 0.7104 (mmm-85) cc_final: 0.6766 (mmm-85) REVERT: U 556 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7063 (tp) REVERT: U 559 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7125 (mt-10) REVERT: U 598 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7561 (mmtp) REVERT: U 602 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7560 (mp) REVERT: U 604 LYS cc_start: 0.8166 (tptm) cc_final: 0.7906 (tptm) outliers start: 144 outliers final: 85 residues processed: 1048 average time/residue: 0.2887 time to fit residues: 461.6735 Evaluate side-chains 1041 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 939 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 89 HIS Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 158 GLU Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 307 GLU Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 355 LYS Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 501 LYS Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 556 LEU Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 76 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 157 optimal weight: 0.1980 chunk 282 optimal weight: 0.0000 chunk 198 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 861 GLN A1236 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 649 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 265 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 174 GLN I 100 HIS K 2 ASN K 22 ASN U 89 HIS U 274 GLN ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112451 restraints weight = 53752.377| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.69 r_work: 0.3353 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37460 Z= 0.151 Angle : 0.685 36.426 50851 Z= 0.323 Chirality : 0.045 0.255 5689 Planarity : 0.005 0.062 6388 Dihedral : 12.877 171.464 5567 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 3.93 % Allowed : 19.99 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.04 (0.13), residues: 4410 helix: 1.10 (0.13), residues: 1636 sheet: -0.13 (0.20), residues: 606 loop : -0.85 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 405 TYR 0.018 0.001 TYR A 669 PHE 0.036 0.001 PHE U 420 TRP 0.016 0.001 TRP C 49 HIS 0.009 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (37428) covalent geometry : angle 0.60929 / 0.32 (50806) hydrogen bonds : bond 0.03787 / 2.53 ( 1556) hydrogen bonds : angle 4.96438 / 3.64 ( 4427) metal coordination : bond 0.00765 / 0.44 ( 32) metal coordination : angle 10.53129 / 6.77 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 964 time to evaluate : 1.424 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: A 29 ASP cc_start: 0.8070 (t0) cc_final: 0.7697 (t70) REVERT: A 117 LEU cc_start: 0.8806 (mt) cc_final: 0.7514 (mt) REVERT: A 123 ASN cc_start: 0.8021 (t0) cc_final: 0.7812 (t0) REVERT: A 125 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7781 (ptpp) REVERT: A 148 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8533 (t) REVERT: A 151 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7883 (mmtm) REVERT: A 212 LYS cc_start: 0.8398 (mptt) cc_final: 0.8052 (mmtt) REVERT: A 232 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 250 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8435 (m) REVERT: A 266 MET cc_start: 0.3427 (mmp) cc_final: 0.3053 (mmm) REVERT: A 308 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8092 (ttmm) REVERT: A 417 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7947 (ttmm) REVERT: A 418 TYR cc_start: 0.8703 (m-80) cc_final: 0.8236 (m-80) REVERT: A 426 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5983 (mpp80) REVERT: A 512 ARG cc_start: 0.8260 (ttm170) cc_final: 0.7976 (ttm170) REVERT: A 703 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7799 (mm-40) REVERT: A 835 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7237 (mt-10) REVERT: A 862 ARG cc_start: 0.8122 (ttt90) cc_final: 0.7861 (ttt90) REVERT: A 863 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8378 (mtm-85) REVERT: A 868 MET cc_start: 0.8213 (mtp) cc_final: 0.7782 (mtm) REVERT: A 940 LYS cc_start: 0.8315 (pttt) cc_final: 0.8001 (pttt) REVERT: A 1125 LYS cc_start: 0.8253 (mttt) cc_final: 0.7953 (mttt) REVERT: A 1167 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8330 (ttm-80) REVERT: A 1215 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: A 1254 LYS cc_start: 0.7833 (ptmm) cc_final: 0.7182 (ptmm) REVERT: A 1308 TYR cc_start: 0.8526 (m-80) cc_final: 0.8290 (m-80) REVERT: A 1311 LEU cc_start: 0.8564 (mt) cc_final: 0.8272 (tp) REVERT: A 1344 MET cc_start: 0.8120 (tpt) cc_final: 0.7663 (tpt) REVERT: A 1374 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8143 (t) REVERT: A 1376 LYS cc_start: 0.8645 (tppt) cc_final: 0.8243 (tptm) REVERT: A 1441 GLU cc_start: 0.7907 (tt0) cc_final: 0.7697 (tt0) REVERT: A 1451 MET cc_start: 0.8499 (mmm) cc_final: 0.8074 (tpp) REVERT: A 1479 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7973 (mmmm) REVERT: B 35 ASP cc_start: 0.8368 (t0) cc_final: 0.8115 (t0) REVERT: B 109 MET cc_start: 0.8017 (mmm) cc_final: 0.7612 (mmt) REVERT: B 131 THR cc_start: 0.8279 (m) cc_final: 0.7797 (p) REVERT: B 157 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8308 (mtt90) REVERT: B 169 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7677 (tmm160) REVERT: B 206 TYR cc_start: 0.8466 (m-80) cc_final: 0.7826 (m-80) REVERT: B 214 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7987 (ttpp) REVERT: B 218 THR cc_start: 0.8397 (m) cc_final: 0.8139 (t) REVERT: B 220 GLU cc_start: 0.8157 (pt0) cc_final: 0.7825 (pt0) REVERT: B 222 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7821 (mtt-85) REVERT: B 262 TYR cc_start: 0.7022 (m-80) cc_final: 0.6717 (m-80) REVERT: B 285 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8077 (mm) REVERT: B 320 PHE cc_start: 0.8626 (t80) cc_final: 0.7875 (t80) REVERT: B 337 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8354 (ttpp) REVERT: B 346 GLU cc_start: 0.8281 (tt0) cc_final: 0.7596 (tt0) REVERT: B 360 LYS cc_start: 0.8419 (mtmp) cc_final: 0.8101 (mtmm) REVERT: B 525 ASN cc_start: 0.7837 (m110) cc_final: 0.7588 (m110) REVERT: B 547 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7359 (tm-30) REVERT: B 555 GLU cc_start: 0.7812 (mp0) cc_final: 0.7582 (mp0) REVERT: B 646 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8015 (ttp-110) REVERT: B 685 LYS cc_start: 0.8337 (mmmt) cc_final: 0.7996 (mmmt) REVERT: B 689 TYR cc_start: 0.8387 (t80) cc_final: 0.8106 (t80) REVERT: B 692 THR cc_start: 0.8558 (p) cc_final: 0.8209 (p) REVERT: B 721 ARG cc_start: 0.8564 (mmt180) cc_final: 0.8306 (mmt180) REVERT: B 744 MET cc_start: 0.8414 (mmm) cc_final: 0.8022 (mtt) REVERT: B 768 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8248 (mmm-85) REVERT: B 914 GLU cc_start: 0.8083 (mp0) cc_final: 0.7772 (mp0) REVERT: B 1004 ASP cc_start: 0.7627 (t70) cc_final: 0.7370 (t0) REVERT: B 1071 ASN cc_start: 0.7964 (m110) cc_final: 0.7719 (m110) REVERT: B 1151 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8084 (ptm) REVERT: C 97 CYS cc_start: 0.7147 (p) cc_final: 0.6765 (p) REVERT: C 246 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7826 (mp) REVERT: D 36 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7432 (mt-10) REVERT: E 30 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7479 (tp-100) REVERT: E 47 LYS cc_start: 0.7613 (pttm) cc_final: 0.7393 (pttm) REVERT: E 78 GLU cc_start: 0.8047 (pm20) cc_final: 0.7765 (pm20) REVERT: E 82 VAL cc_start: 0.8281 (t) cc_final: 0.8028 (m) REVERT: E 92 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7815 (tp-100) REVERT: E 96 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7633 (tm-30) REVERT: E 110 MET cc_start: 0.7268 (mtp) cc_final: 0.6876 (ttm) REVERT: E 151 MET cc_start: 0.8377 (mtp) cc_final: 0.8142 (mtm) REVERT: H 7 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: H 124 ARG cc_start: 0.8786 (ttp80) cc_final: 0.8444 (ttp80) REVERT: I 122 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7834 (mtm-85) REVERT: J 53 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8625 (m) REVERT: K 17 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8295 (mtpp) REVERT: U 26 PHE cc_start: 0.6744 (t80) cc_final: 0.6346 (t80) REVERT: U 31 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7622 (p) REVERT: U 35 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7699 (mt-10) REVERT: U 39 MET cc_start: 0.7163 (tpt) cc_final: 0.6680 (tpt) REVERT: U 63 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6639 (mm-40) REVERT: U 68 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6681 (tt) REVERT: U 105 SER cc_start: 0.5218 (OUTLIER) cc_final: 0.4301 (m) REVERT: U 117 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7368 (mm-30) REVERT: U 124 LYS cc_start: 0.4734 (tptt) cc_final: 0.3652 (pttm) REVERT: U 138 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: U 158 GLU cc_start: 0.7911 (tp30) cc_final: 0.7385 (mm-30) REVERT: U 161 CYS cc_start: 0.8541 (p) cc_final: 0.8285 (p) REVERT: U 228 ASP cc_start: 0.7166 (p0) cc_final: 0.6941 (p0) REVERT: U 270 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6546 (mm-30) REVERT: U 319 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: U 345 GLN cc_start: 0.6725 (tm-30) cc_final: 0.6279 (tm-30) REVERT: U 360 ARG cc_start: 0.7809 (ttm170) cc_final: 0.6765 (ttm-80) REVERT: U 363 TYR cc_start: 0.7664 (t80) cc_final: 0.6893 (t80) REVERT: U 371 VAL cc_start: 0.8651 (t) cc_final: 0.8402 (p) REVERT: U 418 LYS cc_start: 0.7578 (tptp) cc_final: 0.7264 (tptp) REVERT: U 441 ARG cc_start: 0.6945 (mmt-90) cc_final: 0.6617 (mmt180) REVERT: U 509 GLN cc_start: 0.7941 (mt0) cc_final: 0.7726 (mt0) REVERT: U 518 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7546 (mmtt) REVERT: U 530 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6543 (mp0) REVERT: U 595 ASN cc_start: 0.7800 (m-40) cc_final: 0.7404 (m-40) REVERT: U 602 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7519 (mp) REVERT: U 604 LYS cc_start: 0.8167 (tptm) cc_final: 0.7950 (tptm) outliers start: 153 outliers final: 91 residues processed: 1042 average time/residue: 0.2848 time to fit residues: 452.8437 Evaluate side-chains 1043 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 929 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 89 HIS Chi-restraints excluded: chain U residue 105 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 138 PHE Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 319 PHE Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 355 LYS Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 388 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 393 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 406 optimal weight: 0.0060 chunk 214 optimal weight: 0.8980 chunk 398 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 392 optimal weight: 0.7980 chunk 354 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A1093 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 683 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 265 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 35 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 HIS U 274 GLN ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115966 restraints weight = 53318.101| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.78 r_work: 0.3353 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37460 Z= 0.130 Angle : 0.675 35.736 50851 Z= 0.316 Chirality : 0.045 0.237 5689 Planarity : 0.005 0.063 6388 Dihedral : 12.700 171.259 5564 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.83 % Favored : 94.06 % Rotamer: Outliers : 4.19 % Allowed : 20.97 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.01 (0.13), residues: 4410 helix: 1.14 (0.13), residues: 1636 sheet: -0.15 (0.20), residues: 609 loop : -0.83 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 109 TYR 0.018 0.001 TYR A 669 PHE 0.040 0.001 PHE U 420 TRP 0.019 0.001 TRP C 49 HIS 0.026 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (37428) covalent geometry : angle 0.59963 / 0.31 (50806) hydrogen bonds : bond 0.03598 / 2.40 ( 1556) hydrogen bonds : angle 4.86796 / 3.58 ( 4427) metal coordination : bond 0.00647 / 0.37 ( 32) metal coordination : angle 10.45056 / 6.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 966 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8097 (t0) cc_final: 0.7790 (t70) REVERT: A 117 LEU cc_start: 0.8782 (mt) cc_final: 0.8168 (mt) REVERT: A 123 ASN cc_start: 0.8069 (t0) cc_final: 0.7824 (t0) REVERT: A 125 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7738 (ptpp) REVERT: A 148 CYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8536 (t) REVERT: A 151 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7897 (mmtm) REVERT: A 212 LYS cc_start: 0.8426 (mptt) cc_final: 0.8126 (mttp) REVERT: A 232 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 250 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8435 (m) REVERT: A 266 MET cc_start: 0.3328 (mmp) cc_final: 0.3003 (mmm) REVERT: A 308 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8085 (ttmm) REVERT: A 407 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7760 (ttm-80) REVERT: A 417 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7962 (ttmm) REVERT: A 418 TYR cc_start: 0.8690 (m-80) cc_final: 0.8258 (m-80) REVERT: A 426 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.5974 (mpp80) REVERT: A 430 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7741 (mtm180) REVERT: A 512 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7915 (ttm170) REVERT: A 703 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7803 (mm-40) REVERT: A 835 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7217 (mt-10) REVERT: A 862 ARG cc_start: 0.8153 (ttt90) cc_final: 0.7879 (ttt90) REVERT: A 863 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8376 (mtm-85) REVERT: A 940 LYS cc_start: 0.8323 (pttt) cc_final: 0.8014 (pttt) REVERT: A 1097 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 1215 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: A 1254 LYS cc_start: 0.7850 (ptmm) cc_final: 0.7293 (ptmm) REVERT: A 1308 TYR cc_start: 0.8500 (m-80) cc_final: 0.8218 (m-80) REVERT: A 1311 LEU cc_start: 0.8540 (mt) cc_final: 0.8196 (tp) REVERT: A 1344 MET cc_start: 0.8151 (tpt) cc_final: 0.7720 (tpt) REVERT: A 1374 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8140 (t) REVERT: A 1376 LYS cc_start: 0.8653 (tppt) cc_final: 0.8250 (tptm) REVERT: A 1441 GLU cc_start: 0.7914 (tt0) cc_final: 0.7692 (tt0) REVERT: A 1451 MET cc_start: 0.8475 (mmm) cc_final: 0.8179 (mmt) REVERT: A 1479 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7988 (mmmm) REVERT: B 20 ASP cc_start: 0.5409 (p0) cc_final: 0.4910 (p0) REVERT: B 35 ASP cc_start: 0.8390 (t0) cc_final: 0.8136 (t0) REVERT: B 131 THR cc_start: 0.8276 (m) cc_final: 0.7795 (p) REVERT: B 157 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8267 (mtt90) REVERT: B 169 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7755 (tmm160) REVERT: B 206 TYR cc_start: 0.8459 (m-80) cc_final: 0.7824 (m-80) REVERT: B 214 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7982 (ttpp) REVERT: B 218 THR cc_start: 0.8425 (m) cc_final: 0.8175 (t) REVERT: B 220 GLU cc_start: 0.8204 (pt0) cc_final: 0.7858 (pt0) REVERT: B 222 ARG cc_start: 0.8160 (mtt-85) cc_final: 0.7783 (mtt-85) REVERT: B 285 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8058 (mm) REVERT: B 320 PHE cc_start: 0.8630 (t80) cc_final: 0.7875 (t80) REVERT: B 337 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8377 (ttpp) REVERT: B 346 GLU cc_start: 0.8360 (tt0) cc_final: 0.7840 (tt0) REVERT: B 347 MET cc_start: 0.8468 (ttp) cc_final: 0.8255 (ttp) REVERT: B 360 LYS cc_start: 0.8419 (mtmp) cc_final: 0.8121 (mtmm) REVERT: B 508 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7864 (mtt) REVERT: B 525 ASN cc_start: 0.7839 (m110) cc_final: 0.7587 (m110) REVERT: B 547 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7332 (tm-30) REVERT: B 646 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.8138 (ttp-110) REVERT: B 689 TYR cc_start: 0.8355 (t80) cc_final: 0.8084 (t80) REVERT: B 692 THR cc_start: 0.8611 (p) cc_final: 0.8265 (p) REVERT: B 721 ARG cc_start: 0.8520 (mmt180) cc_final: 0.8271 (mmt180) REVERT: B 744 MET cc_start: 0.8380 (mmm) cc_final: 0.8168 (mtt) REVERT: B 768 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8254 (mmm-85) REVERT: B 840 MET cc_start: 0.7257 (tpt) cc_final: 0.6812 (tpt) REVERT: B 914 GLU cc_start: 0.8118 (mp0) cc_final: 0.7800 (mp0) REVERT: B 1004 ASP cc_start: 0.7615 (t70) cc_final: 0.7356 (t0) REVERT: B 1071 ASN cc_start: 0.7979 (m110) cc_final: 0.7710 (m110) REVERT: C 97 CYS cc_start: 0.7156 (p) cc_final: 0.6799 (p) REVERT: C 160 ARG cc_start: 0.8628 (mtm110) cc_final: 0.8406 (ttp-110) REVERT: C 238 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7734 (t) REVERT: C 246 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7777 (mp) REVERT: D 36 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7605 (mt-10) REVERT: E 47 LYS cc_start: 0.7605 (pttm) cc_final: 0.7389 (pttm) REVERT: E 78 GLU cc_start: 0.8042 (pm20) cc_final: 0.7767 (pm20) REVERT: E 82 VAL cc_start: 0.8333 (t) cc_final: 0.8056 (m) REVERT: E 92 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7814 (tp-100) REVERT: E 96 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7635 (tm-30) REVERT: E 107 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7523 (mm-40) REVERT: E 110 MET cc_start: 0.7273 (mtp) cc_final: 0.6860 (ttm) REVERT: E 154 GLU cc_start: 0.8106 (mp0) cc_final: 0.7875 (mp0) REVERT: G 101 ILE cc_start: 0.4454 (OUTLIER) cc_final: 0.4210 (pt) REVERT: H 7 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: H 124 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8466 (ttp80) REVERT: J 53 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8645 (m) REVERT: K 17 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8317 (mtpp) REVERT: U 26 PHE cc_start: 0.6721 (t80) cc_final: 0.6366 (t80) REVERT: U 31 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7629 (p) REVERT: U 35 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7689 (mt-10) REVERT: U 39 MET cc_start: 0.7264 (tpt) cc_final: 0.6750 (tpt) REVERT: U 68 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6684 (tt) REVERT: U 84 GLN cc_start: 0.8628 (mp10) cc_final: 0.8151 (pm20) REVERT: U 109 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7168 (ttm170) REVERT: U 117 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7403 (mm-30) REVERT: U 124 LYS cc_start: 0.4690 (tptt) cc_final: 0.3620 (pttm) REVERT: U 138 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7151 (m-10) REVERT: U 158 GLU cc_start: 0.7888 (tp30) cc_final: 0.7404 (mm-30) REVERT: U 161 CYS cc_start: 0.8546 (p) cc_final: 0.8284 (p) REVERT: U 164 GLN cc_start: 0.7050 (pp30) cc_final: 0.6763 (pp30) REVERT: U 200 GLN cc_start: 0.7103 (pp30) cc_final: 0.6597 (pp30) REVERT: U 230 GLN cc_start: 0.7729 (mp10) cc_final: 0.7320 (mp10) REVERT: U 270 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6546 (mm-30) REVERT: U 302 GLN cc_start: 0.7276 (tm130) cc_final: 0.6916 (tm-30) REVERT: U 319 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: U 345 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6194 (tm-30) REVERT: U 360 ARG cc_start: 0.7836 (ttm170) cc_final: 0.6042 (ptm-80) REVERT: U 363 TYR cc_start: 0.7703 (t80) cc_final: 0.7069 (t80) REVERT: U 371 VAL cc_start: 0.8644 (t) cc_final: 0.8385 (p) REVERT: U 418 LYS cc_start: 0.7596 (tptp) cc_final: 0.7286 (tptp) REVERT: U 441 ARG cc_start: 0.6962 (mmt-90) cc_final: 0.6670 (mmt180) REVERT: U 518 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7633 (mmtt) REVERT: U 530 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6538 (mp0) REVERT: U 559 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7144 (mt-10) REVERT: U 595 ASN cc_start: 0.7794 (m-40) cc_final: 0.7433 (m-40) REVERT: U 602 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7555 (mp) REVERT: U 603 LYS cc_start: 0.8253 (tppt) cc_final: 0.7962 (tppt) REVERT: U 604 LYS cc_start: 0.8142 (tptm) cc_final: 0.7922 (tptm) outliers start: 163 outliers final: 106 residues processed: 1054 average time/residue: 0.2837 time to fit residues: 457.7036 Evaluate side-chains 1057 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 931 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 89 HIS Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 138 PHE Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 319 PHE Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 556 LEU Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 365 optimal weight: 0.8980 chunk 428 optimal weight: 0.8980 chunk 435 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 348 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 265 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 43 GLN I 46 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN U 89 HIS U 274 GLN ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114262 restraints weight = 53586.658| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.80 r_work: 0.3333 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37460 Z= 0.163 Angle : 0.682 35.762 50851 Z= 0.319 Chirality : 0.045 0.249 5689 Planarity : 0.004 0.061 6388 Dihedral : 12.666 171.257 5562 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 3.98 % Allowed : 21.05 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.02 (0.13), residues: 4410 helix: 1.14 (0.13), residues: 1635 sheet: -0.15 (0.20), residues: 616 loop : -0.85 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 292 TYR 0.015 0.001 TYR A 669 PHE 0.032 0.001 PHE U 420 TRP 0.020 0.001 TRP C 49 HIS 0.008 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (37428) covalent geometry : angle 0.60706 / 0.31 (50806) hydrogen bonds : bond 0.03601 / 2.40 ( 1556) hydrogen bonds : angle 4.81674 / 3.53 ( 4427) metal coordination : bond 0.00837 / 0.47 ( 32) metal coordination : angle 10.49641 / 6.70 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 952 time to evaluate : 1.437 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: A 29 ASP cc_start: 0.8090 (t0) cc_final: 0.7563 (t0) REVERT: A 117 LEU cc_start: 0.8829 (mt) cc_final: 0.8240 (mt) REVERT: A 125 LYS cc_start: 0.8037 (ptpp) cc_final: 0.7822 (ptpp) REVERT: A 148 CYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8521 (t) REVERT: A 151 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7952 (mmtm) REVERT: A 212 LYS cc_start: 0.8447 (mptt) cc_final: 0.8186 (mttp) REVERT: A 213 LYS cc_start: 0.8200 (mmmm) cc_final: 0.7996 (tptt) REVERT: A 232 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 250 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8472 (m) REVERT: A 266 MET cc_start: 0.3199 (mmp) cc_final: 0.2971 (mmm) REVERT: A 308 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8124 (ttmm) REVERT: A 347 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7376 (mp0) REVERT: A 407 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7782 (ttm-80) REVERT: A 417 LYS cc_start: 0.8273 (ttmm) cc_final: 0.7935 (ttmm) REVERT: A 418 TYR cc_start: 0.8692 (m-80) cc_final: 0.8179 (m-80) REVERT: A 426 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6102 (mpp80) REVERT: A 512 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7921 (ttm170) REVERT: A 703 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7840 (mm-40) REVERT: A 835 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7230 (mt-10) REVERT: A 862 ARG cc_start: 0.8161 (ttt90) cc_final: 0.7807 (ttt90) REVERT: A 863 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8440 (mtm-85) REVERT: A 940 LYS cc_start: 0.8356 (pttt) cc_final: 0.8040 (pttt) REVERT: A 1015 GLU cc_start: 0.8241 (tp30) cc_final: 0.8019 (tp30) REVERT: A 1125 LYS cc_start: 0.8234 (mttt) cc_final: 0.7938 (mttt) REVERT: A 1167 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8423 (ttm-80) REVERT: A 1215 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: A 1254 LYS cc_start: 0.7912 (ptmm) cc_final: 0.7390 (ptmm) REVERT: A 1265 ASP cc_start: 0.5808 (OUTLIER) cc_final: 0.5330 (p0) REVERT: A 1308 TYR cc_start: 0.8495 (m-80) cc_final: 0.8274 (m-80) REVERT: A 1311 LEU cc_start: 0.8559 (mt) cc_final: 0.8206 (tp) REVERT: A 1344 MET cc_start: 0.8111 (tpt) cc_final: 0.7688 (tpt) REVERT: A 1374 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8159 (t) REVERT: A 1376 LYS cc_start: 0.8662 (tppt) cc_final: 0.8254 (tptm) REVERT: A 1441 GLU cc_start: 0.7918 (tt0) cc_final: 0.7681 (tt0) REVERT: A 1451 MET cc_start: 0.8491 (mmm) cc_final: 0.8157 (mmt) REVERT: A 1479 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7888 (mmmm) REVERT: B 20 ASP cc_start: 0.5363 (OUTLIER) cc_final: 0.4919 (p0) REVERT: B 35 ASP cc_start: 0.8400 (t0) cc_final: 0.8135 (t0) REVERT: B 131 THR cc_start: 0.8318 (m) cc_final: 0.7847 (p) REVERT: B 157 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8318 (mtt90) REVERT: B 169 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7734 (tmm160) REVERT: B 206 TYR cc_start: 0.8476 (m-80) cc_final: 0.7869 (m-80) REVERT: B 214 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8013 (ttpp) REVERT: B 218 THR cc_start: 0.8444 (m) cc_final: 0.8175 (t) REVERT: B 220 GLU cc_start: 0.8221 (pt0) cc_final: 0.7966 (pt0) REVERT: B 222 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7722 (mtt90) REVERT: B 285 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8108 (mm) REVERT: B 320 PHE cc_start: 0.8602 (t80) cc_final: 0.7839 (t80) REVERT: B 337 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8380 (ttpp) REVERT: B 360 LYS cc_start: 0.8437 (mtmp) cc_final: 0.8123 (mtmm) REVERT: B 508 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7846 (mtt) REVERT: B 525 ASN cc_start: 0.7879 (m110) cc_final: 0.7674 (m110) REVERT: B 547 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 646 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.8062 (ttp-110) REVERT: B 682 LEU cc_start: 0.7302 (mt) cc_final: 0.7070 (mp) REVERT: B 689 TYR cc_start: 0.8371 (t80) cc_final: 0.8066 (t80) REVERT: B 692 THR cc_start: 0.8631 (p) cc_final: 0.8269 (p) REVERT: B 721 ARG cc_start: 0.8556 (mmt180) cc_final: 0.8298 (mmt180) REVERT: B 744 MET cc_start: 0.8414 (mmm) cc_final: 0.8138 (mtt) REVERT: B 768 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8300 (mmm-85) REVERT: B 871 VAL cc_start: 0.8264 (t) cc_final: 0.7896 (m) REVERT: B 914 GLU cc_start: 0.8125 (mp0) cc_final: 0.7785 (mp0) REVERT: B 919 CYS cc_start: 0.8410 (t) cc_final: 0.7831 (p) REVERT: B 1004 ASP cc_start: 0.7690 (t70) cc_final: 0.7421 (t0) REVERT: B 1071 ASN cc_start: 0.8005 (m110) cc_final: 0.7747 (m110) REVERT: C 97 CYS cc_start: 0.7300 (p) cc_final: 0.6904 (p) REVERT: C 160 ARG cc_start: 0.8652 (mtm110) cc_final: 0.8408 (ttp-110) REVERT: C 238 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7758 (t) REVERT: C 246 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7817 (mp) REVERT: D 36 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7591 (mt-10) REVERT: E 47 LYS cc_start: 0.7634 (pttm) cc_final: 0.7424 (pttm) REVERT: E 78 GLU cc_start: 0.8068 (pm20) cc_final: 0.7814 (pm20) REVERT: E 82 VAL cc_start: 0.8331 (t) cc_final: 0.8014 (m) REVERT: E 92 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7824 (tp-100) REVERT: E 96 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 107 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7596 (mm110) REVERT: E 110 MET cc_start: 0.7440 (mtp) cc_final: 0.7044 (ttm) REVERT: E 154 GLU cc_start: 0.8124 (mp0) cc_final: 0.7896 (mp0) REVERT: H 7 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: H 124 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8572 (ttp80) REVERT: K 17 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8307 (mtpp) REVERT: U 26 PHE cc_start: 0.6814 (t80) cc_final: 0.6446 (t80) REVERT: U 31 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7665 (p) REVERT: U 35 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7676 (mt-10) REVERT: U 39 MET cc_start: 0.7278 (tpt) cc_final: 0.6758 (tpt) REVERT: U 68 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6689 (tt) REVERT: U 105 SER cc_start: 0.4294 (OUTLIER) cc_final: 0.3651 (t) REVERT: U 109 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7165 (ttm170) REVERT: U 117 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7363 (mm-30) REVERT: U 124 LYS cc_start: 0.4739 (tptt) cc_final: 0.3688 (pttm) REVERT: U 138 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7182 (m-10) REVERT: U 158 GLU cc_start: 0.7903 (tp30) cc_final: 0.7240 (mm-30) REVERT: U 161 CYS cc_start: 0.8541 (p) cc_final: 0.8257 (p) REVERT: U 270 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6535 (mm-30) REVERT: U 319 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: U 345 GLN cc_start: 0.6816 (tm-30) cc_final: 0.6298 (tm-30) REVERT: U 360 ARG cc_start: 0.7826 (ttm170) cc_final: 0.6578 (ttm-80) REVERT: U 363 TYR cc_start: 0.7760 (t80) cc_final: 0.7067 (t80) REVERT: U 371 VAL cc_start: 0.8653 (t) cc_final: 0.8444 (p) REVERT: U 418 LYS cc_start: 0.7597 (tptp) cc_final: 0.7300 (tptp) REVERT: U 441 ARG cc_start: 0.6961 (mmt-90) cc_final: 0.6760 (mmt180) REVERT: U 518 LYS cc_start: 0.8005 (mmtp) cc_final: 0.7565 (mmtt) REVERT: U 530 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6502 (mp0) REVERT: U 559 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7160 (mt-10) REVERT: U 595 ASN cc_start: 0.7787 (m-40) cc_final: 0.7396 (m-40) REVERT: U 598 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7639 (mmtp) REVERT: U 602 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7600 (mp) REVERT: U 603 LYS cc_start: 0.8272 (tppt) cc_final: 0.7962 (tppt) REVERT: U 604 LYS cc_start: 0.8148 (tptm) cc_final: 0.7929 (tptm) outliers start: 155 outliers final: 105 residues processed: 1029 average time/residue: 0.2841 time to fit residues: 446.8180 Evaluate side-chains 1056 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 929 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1265 ASP Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 105 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 138 PHE Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 319 PHE Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 113 optimal weight: 0.8980 chunk 436 optimal weight: 6.9990 chunk 319 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 408 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 286 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A1236 ASN A1310 HIS ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 43 GLN E 95 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 513 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114277 restraints weight = 53334.620| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.75 r_work: 0.3334 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37460 Z= 0.160 Angle : 0.685 35.425 50851 Z= 0.320 Chirality : 0.045 0.250 5689 Planarity : 0.004 0.059 6388 Dihedral : 12.641 171.665 5562 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 4.14 % Allowed : 21.18 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.02 (0.13), residues: 4410 helix: 1.14 (0.13), residues: 1637 sheet: -0.17 (0.20), residues: 612 loop : -0.84 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 292 TYR 0.016 0.001 TYR A 669 PHE 0.048 0.001 PHE U 420 TRP 0.020 0.001 TRP C 49 HIS 0.007 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (37428) covalent geometry : angle 0.60931 / 0.31 (50806) hydrogen bonds : bond 0.03582 / 2.39 ( 1556) hydrogen bonds : angle 4.78792 / 3.51 ( 4427) metal coordination : bond 0.00823 / 0.47 ( 32) metal coordination : angle 10.50507 / 6.69 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 944 time to evaluate : 1.433 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: A 29 ASP cc_start: 0.8085 (t0) cc_final: 0.7753 (t0) REVERT: A 117 LEU cc_start: 0.8832 (mt) cc_final: 0.8259 (mt) REVERT: A 148 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8490 (t) REVERT: A 151 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7971 (mmtm) REVERT: A 212 LYS cc_start: 0.8467 (mptt) cc_final: 0.8217 (mttp) REVERT: A 232 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 250 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8494 (m) REVERT: A 308 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8143 (ttmm) REVERT: A 347 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7352 (mp0) REVERT: A 407 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7805 (ttm-80) REVERT: A 417 LYS cc_start: 0.8259 (ttmm) cc_final: 0.8009 (ttmm) REVERT: A 418 TYR cc_start: 0.8710 (m-80) cc_final: 0.8216 (m-80) REVERT: A 426 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6120 (mpp80) REVERT: A 430 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7382 (mtm180) REVERT: A 512 ARG cc_start: 0.8281 (ttm170) cc_final: 0.7910 (ttm170) REVERT: A 583 ARG cc_start: 0.8308 (ptm160) cc_final: 0.8092 (ptm-80) REVERT: A 703 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7797 (mm-40) REVERT: A 777 SER cc_start: 0.8382 (p) cc_final: 0.8169 (m) REVERT: A 835 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 862 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7827 (ttt90) REVERT: A 863 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8403 (mtm-85) REVERT: A 940 LYS cc_start: 0.8349 (pttt) cc_final: 0.8037 (pttt) REVERT: A 1125 LYS cc_start: 0.8222 (mttt) cc_final: 0.7932 (mttt) REVERT: A 1215 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: A 1254 LYS cc_start: 0.7950 (ptmm) cc_final: 0.7368 (ptmm) REVERT: A 1265 ASP cc_start: 0.5777 (OUTLIER) cc_final: 0.5288 (p0) REVERT: A 1308 TYR cc_start: 0.8461 (m-80) cc_final: 0.8191 (m-80) REVERT: A 1344 MET cc_start: 0.8106 (tpt) cc_final: 0.7828 (tpt) REVERT: A 1374 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8130 (t) REVERT: A 1376 LYS cc_start: 0.8649 (tppt) cc_final: 0.8254 (tptm) REVERT: A 1441 GLU cc_start: 0.7909 (tt0) cc_final: 0.7682 (tt0) REVERT: B 20 ASP cc_start: 0.5448 (OUTLIER) cc_final: 0.4999 (p0) REVERT: B 35 ASP cc_start: 0.8391 (t0) cc_final: 0.7982 (t0) REVERT: B 131 THR cc_start: 0.8332 (m) cc_final: 0.7880 (p) REVERT: B 157 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8341 (mtt90) REVERT: B 169 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7691 (tmm160) REVERT: B 206 TYR cc_start: 0.8477 (m-80) cc_final: 0.7864 (m-80) REVERT: B 214 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8019 (ttpp) REVERT: B 218 THR cc_start: 0.8449 (m) cc_final: 0.8161 (t) REVERT: B 220 GLU cc_start: 0.8187 (pt0) cc_final: 0.7939 (pt0) REVERT: B 222 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7745 (mtt90) REVERT: B 285 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8136 (mm) REVERT: B 320 PHE cc_start: 0.8594 (t80) cc_final: 0.7918 (t80) REVERT: B 337 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8304 (ttpt) REVERT: B 360 LYS cc_start: 0.8402 (mtmp) cc_final: 0.8105 (mtmm) REVERT: B 547 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 552 ASN cc_start: 0.8450 (m110) cc_final: 0.8216 (m-40) REVERT: B 646 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.8075 (ttp-110) REVERT: B 689 TYR cc_start: 0.8360 (t80) cc_final: 0.8046 (t80) REVERT: B 692 THR cc_start: 0.8640 (p) cc_final: 0.8282 (p) REVERT: B 721 ARG cc_start: 0.8546 (mmt180) cc_final: 0.8289 (mmt180) REVERT: B 768 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8318 (mmm-85) REVERT: B 914 GLU cc_start: 0.8109 (mp0) cc_final: 0.7763 (mp0) REVERT: B 919 CYS cc_start: 0.8383 (t) cc_final: 0.7883 (p) REVERT: B 1004 ASP cc_start: 0.7620 (t70) cc_final: 0.7318 (t0) REVERT: B 1071 ASN cc_start: 0.7997 (m110) cc_final: 0.7697 (m110) REVERT: C 97 CYS cc_start: 0.7375 (p) cc_final: 0.7045 (p) REVERT: C 162 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7739 (ttt-90) REVERT: C 238 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7755 (t) REVERT: C 246 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7875 (mp) REVERT: D 36 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7756 (mt-10) REVERT: E 19 GLN cc_start: 0.7984 (mt0) cc_final: 0.7778 (mt0) REVERT: E 47 LYS cc_start: 0.7616 (pttm) cc_final: 0.7415 (pttm) REVERT: E 67 ASP cc_start: 0.7983 (p0) cc_final: 0.7627 (p0) REVERT: E 78 GLU cc_start: 0.8056 (pm20) cc_final: 0.7809 (pm20) REVERT: E 82 VAL cc_start: 0.8333 (t) cc_final: 0.8021 (m) REVERT: E 92 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7815 (tp-100) REVERT: E 96 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7578 (tm-30) REVERT: E 107 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7601 (mm110) REVERT: E 110 MET cc_start: 0.7472 (mtp) cc_final: 0.7089 (ttm) REVERT: E 120 ASP cc_start: 0.6561 (m-30) cc_final: 0.6033 (m-30) REVERT: E 154 GLU cc_start: 0.8100 (mp0) cc_final: 0.7876 (mp0) REVERT: H 7 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: H 124 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8571 (ttp80) REVERT: K 17 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8346 (mtpp) REVERT: U 26 PHE cc_start: 0.6796 (t80) cc_final: 0.6440 (t80) REVERT: U 31 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7692 (p) REVERT: U 35 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7684 (mt-10) REVERT: U 39 MET cc_start: 0.7252 (tpt) cc_final: 0.6744 (tpt) REVERT: U 68 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6673 (tt) REVERT: U 84 GLN cc_start: 0.8620 (mp10) cc_final: 0.8240 (pm20) REVERT: U 109 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7222 (ttm170) REVERT: U 117 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7337 (mm-30) REVERT: U 124 LYS cc_start: 0.4735 (tptt) cc_final: 0.3687 (pttm) REVERT: U 138 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: U 158 GLU cc_start: 0.7937 (tp30) cc_final: 0.7286 (mm-30) REVERT: U 161 CYS cc_start: 0.8527 (p) cc_final: 0.8252 (p) REVERT: U 270 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6525 (mm-30) REVERT: U 319 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: U 345 GLN cc_start: 0.6803 (tm-30) cc_final: 0.6353 (tm-30) REVERT: U 360 ARG cc_start: 0.7883 (ttm170) cc_final: 0.6682 (ttm-80) REVERT: U 363 TYR cc_start: 0.7761 (t80) cc_final: 0.7012 (t80) REVERT: U 371 VAL cc_start: 0.8636 (t) cc_final: 0.8389 (p) REVERT: U 418 LYS cc_start: 0.7543 (tptp) cc_final: 0.7250 (tptp) REVERT: U 559 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7163 (mt-10) REVERT: U 602 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7617 (mp) REVERT: U 603 LYS cc_start: 0.8258 (tppt) cc_final: 0.7927 (tppt) REVERT: U 604 LYS cc_start: 0.8162 (tptm) cc_final: 0.7959 (tptm) outliers start: 161 outliers final: 114 residues processed: 1027 average time/residue: 0.2804 time to fit residues: 442.2912 Evaluate side-chains 1065 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 933 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1265 ASP Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 138 PHE Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 319 PHE Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 513 GLN Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 183 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 347 optimal weight: 0.0170 chunk 175 optimal weight: 3.9990 chunk 411 optimal weight: 0.9990 chunk 421 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 423 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1457 ASN B 350 HIS B 649 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 265 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 43 GLN E 174 GLN I 74 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN U 274 GLN ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 513 GLN U 595 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114764 restraints weight = 53392.069| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.79 r_work: 0.3338 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37460 Z= 0.147 Angle : 0.688 35.279 50851 Z= 0.322 Chirality : 0.045 0.244 5689 Planarity : 0.004 0.062 6388 Dihedral : 12.593 171.782 5557 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 3.91 % Allowed : 21.56 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.00 (0.13), residues: 4410 helix: 1.14 (0.13), residues: 1639 sheet: -0.17 (0.20), residues: 612 loop : -0.81 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 192 TYR 0.022 0.001 TYR B 262 PHE 0.042 0.001 PHE U 420 TRP 0.018 0.001 TRP C 49 HIS 0.007 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (37428) covalent geometry : angle 0.61394 / 0.32 (50806) hydrogen bonds : bond 0.03518 / 2.35 ( 1556) hydrogen bonds : angle 4.77450 / 3.50 ( 4427) metal coordination : bond 0.00726 / 0.41 ( 32) metal coordination : angle 10.48509 / 6.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 948 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7945 (tp40) REVERT: A 29 ASP cc_start: 0.8040 (t0) cc_final: 0.7539 (t0) REVERT: A 148 CYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8510 (t) REVERT: A 151 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7981 (mmtm) REVERT: A 212 LYS cc_start: 0.8439 (mptt) cc_final: 0.8195 (mttp) REVERT: A 232 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 250 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8527 (m) REVERT: A 329 MET cc_start: 0.5778 (mmm) cc_final: 0.5406 (mmm) REVERT: A 347 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7322 (mp0) REVERT: A 407 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7830 (ttm-80) REVERT: A 417 LYS cc_start: 0.8275 (ttmm) cc_final: 0.8028 (ttmm) REVERT: A 418 TYR cc_start: 0.8699 (m-80) cc_final: 0.8195 (m-80) REVERT: A 426 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6146 (mpp80) REVERT: A 430 ARG cc_start: 0.8054 (mtm180) cc_final: 0.7486 (mtm180) REVERT: A 512 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7891 (ttm170) REVERT: A 703 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7792 (mm-40) REVERT: A 835 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7233 (mt-10) REVERT: A 862 ARG cc_start: 0.8186 (ttt90) cc_final: 0.7850 (ttt90) REVERT: A 863 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8300 (mtm-85) REVERT: A 940 LYS cc_start: 0.8329 (pttt) cc_final: 0.8021 (pttt) REVERT: A 1125 LYS cc_start: 0.8221 (mttt) cc_final: 0.7927 (mttt) REVERT: A 1215 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: A 1254 LYS cc_start: 0.7951 (ptmm) cc_final: 0.7423 (ptmm) REVERT: A 1265 ASP cc_start: 0.5832 (OUTLIER) cc_final: 0.5319 (p0) REVERT: A 1308 TYR cc_start: 0.8473 (m-80) cc_final: 0.8232 (m-80) REVERT: A 1344 MET cc_start: 0.8129 (tpt) cc_final: 0.7873 (tpt) REVERT: A 1374 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8146 (t) REVERT: A 1376 LYS cc_start: 0.8630 (tppt) cc_final: 0.8402 (tppt) REVERT: A 1441 GLU cc_start: 0.7933 (tt0) cc_final: 0.7705 (tt0) REVERT: B 20 ASP cc_start: 0.5516 (OUTLIER) cc_final: 0.5097 (p0) REVERT: B 35 ASP cc_start: 0.8414 (t0) cc_final: 0.8003 (t0) REVERT: B 131 THR cc_start: 0.8338 (m) cc_final: 0.7870 (p) REVERT: B 157 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8348 (mtt90) REVERT: B 169 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7653 (tmm160) REVERT: B 200 MET cc_start: 0.8332 (mmt) cc_final: 0.8115 (mmt) REVERT: B 206 TYR cc_start: 0.8474 (m-80) cc_final: 0.7853 (m-80) REVERT: B 214 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8070 (ttpp) REVERT: B 218 THR cc_start: 0.8446 (m) cc_final: 0.8158 (t) REVERT: B 220 GLU cc_start: 0.8218 (pt0) cc_final: 0.7910 (pt0) REVERT: B 222 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7789 (mtt-85) REVERT: B 285 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8124 (mm) REVERT: B 320 PHE cc_start: 0.8585 (t80) cc_final: 0.7840 (t80) REVERT: B 337 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8367 (ttpp) REVERT: B 346 GLU cc_start: 0.8362 (tt0) cc_final: 0.8098 (tt0) REVERT: B 360 LYS cc_start: 0.8440 (mtmp) cc_final: 0.8105 (mtmm) REVERT: B 542 LEU cc_start: 0.8484 (mp) cc_final: 0.8257 (mp) REVERT: B 547 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 552 ASN cc_start: 0.8432 (m110) cc_final: 0.8206 (m-40) REVERT: B 646 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.8073 (ttp-110) REVERT: B 677 MET cc_start: 0.8475 (mmm) cc_final: 0.8161 (tpp) REVERT: B 689 TYR cc_start: 0.8343 (t80) cc_final: 0.8029 (t80) REVERT: B 692 THR cc_start: 0.8649 (p) cc_final: 0.8280 (p) REVERT: B 721 ARG cc_start: 0.8541 (mmt180) cc_final: 0.8286 (mmt180) REVERT: B 768 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8328 (mmm-85) REVERT: B 914 GLU cc_start: 0.8120 (mp0) cc_final: 0.7758 (mp0) REVERT: B 919 CYS cc_start: 0.8410 (t) cc_final: 0.7934 (p) REVERT: B 1004 ASP cc_start: 0.7598 (t70) cc_final: 0.7288 (t0) REVERT: B 1071 ASN cc_start: 0.7974 (m110) cc_final: 0.7706 (m110) REVERT: C 97 CYS cc_start: 0.7237 (p) cc_final: 0.6955 (p) REVERT: C 162 ARG cc_start: 0.8133 (ttt-90) cc_final: 0.7718 (ttt-90) REVERT: C 238 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7728 (t) REVERT: C 246 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7865 (mp) REVERT: D 36 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7780 (mt-10) REVERT: E 23 ASP cc_start: 0.7745 (m-30) cc_final: 0.7483 (m-30) REVERT: E 35 GLN cc_start: 0.8418 (tt0) cc_final: 0.8203 (tt0) REVERT: E 47 LYS cc_start: 0.7523 (pttm) cc_final: 0.7309 (pttm) REVERT: E 67 ASP cc_start: 0.7966 (p0) cc_final: 0.7613 (p0) REVERT: E 78 GLU cc_start: 0.8066 (pm20) cc_final: 0.7822 (pm20) REVERT: E 82 VAL cc_start: 0.8335 (t) cc_final: 0.8017 (m) REVERT: E 92 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7835 (tp-100) REVERT: E 96 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7533 (tm-30) REVERT: E 107 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7633 (mm110) REVERT: E 110 MET cc_start: 0.7492 (mtp) cc_final: 0.7084 (ttm) REVERT: E 120 ASP cc_start: 0.6582 (m-30) cc_final: 0.6054 (m-30) REVERT: E 154 GLU cc_start: 0.8099 (mp0) cc_final: 0.7868 (mp0) REVERT: H 7 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: H 124 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8588 (ttp80) REVERT: K 17 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8352 (mtpp) REVERT: U 26 PHE cc_start: 0.6819 (t80) cc_final: 0.6524 (t80) REVERT: U 31 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7694 (p) REVERT: U 35 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7663 (mt-10) REVERT: U 39 MET cc_start: 0.7257 (tpt) cc_final: 0.6743 (tpt) REVERT: U 68 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6664 (tt) REVERT: U 84 GLN cc_start: 0.8609 (mp10) cc_final: 0.8255 (pm20) REVERT: U 109 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7269 (ttm170) REVERT: U 132 MET cc_start: 0.6807 (mmt) cc_final: 0.6385 (mmp) REVERT: U 138 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: U 158 GLU cc_start: 0.7945 (tp30) cc_final: 0.7320 (mm-30) REVERT: U 161 CYS cc_start: 0.8547 (p) cc_final: 0.8267 (p) REVERT: U 270 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6526 (mm-30) REVERT: U 319 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: U 345 GLN cc_start: 0.6857 (tm-30) cc_final: 0.6446 (tm-30) REVERT: U 360 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7144 (ttm-80) REVERT: U 363 TYR cc_start: 0.7772 (t80) cc_final: 0.7034 (t80) REVERT: U 371 VAL cc_start: 0.8636 (t) cc_final: 0.8391 (p) REVERT: U 418 LYS cc_start: 0.7541 (tptp) cc_final: 0.7244 (tptp) REVERT: U 515 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7622 (mpt-90) REVERT: U 518 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7514 (mmtt) REVERT: U 559 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7138 (mt-10) REVERT: U 602 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7605 (mp) REVERT: U 603 LYS cc_start: 0.8241 (tppt) cc_final: 0.7921 (tppt) outliers start: 152 outliers final: 111 residues processed: 1023 average time/residue: 0.2727 time to fit residues: 427.0916 Evaluate side-chains 1075 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 946 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1265 ASP Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 138 PHE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 319 PHE Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 513 GLN Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 317 optimal weight: 0.3980 chunk 348 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 275 optimal weight: 0.5980 chunk 333 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 430 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 265 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 174 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 513 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112264 restraints weight = 53289.219| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.69 r_work: 0.3345 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37460 Z= 0.157 Angle : 0.692 35.264 50851 Z= 0.323 Chirality : 0.045 0.246 5689 Planarity : 0.005 0.069 6388 Dihedral : 12.576 171.988 5557 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 3.75 % Allowed : 22.00 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.00 (0.13), residues: 4410 helix: 1.13 (0.13), residues: 1639 sheet: -0.15 (0.20), residues: 612 loop : -0.82 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 292 TYR 0.022 0.001 TYR B 262 PHE 0.039 0.001 PHE U 420 TRP 0.019 0.001 TRP C 49 HIS 0.034 0.001 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (37428) covalent geometry : angle 0.61767 / 0.32 (50806) hydrogen bonds : bond 0.03546 / 2.37 ( 1556) hydrogen bonds : angle 4.75794 / 3.49 ( 4427) metal coordination : bond 0.00771 / 0.43 ( 32) metal coordination : angle 10.49220 / 6.67 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 942 time to evaluate : 1.515 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: A 22 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7978 (tp40) REVERT: A 29 ASP cc_start: 0.8020 (t0) cc_final: 0.7508 (t0) REVERT: A 148 CYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8505 (t) REVERT: A 151 LYS cc_start: 0.8237 (mmtm) cc_final: 0.7956 (mmtm) REVERT: A 212 LYS cc_start: 0.8436 (mptt) cc_final: 0.8182 (mttp) REVERT: A 232 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 250 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8524 (m) REVERT: A 329 MET cc_start: 0.5786 (mmm) cc_final: 0.5477 (mmm) REVERT: A 347 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7320 (mp0) REVERT: A 407 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7821 (ttm-80) REVERT: A 417 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7887 (ttmm) REVERT: A 418 TYR cc_start: 0.8688 (m-80) cc_final: 0.8172 (m-80) REVERT: A 426 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6111 (mpp80) REVERT: A 430 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7436 (mtm180) REVERT: A 512 ARG cc_start: 0.8262 (ttm170) cc_final: 0.7901 (ttm170) REVERT: A 703 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7818 (mm-40) REVERT: A 835 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 862 ARG cc_start: 0.8219 (ttt90) cc_final: 0.7558 (ttt90) REVERT: A 940 LYS cc_start: 0.8306 (pttt) cc_final: 0.8014 (pttt) REVERT: A 1125 LYS cc_start: 0.8217 (mttt) cc_final: 0.7928 (mttt) REVERT: A 1215 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6717 (mt-10) REVERT: A 1254 LYS cc_start: 0.7973 (ptmm) cc_final: 0.7420 (ptmm) REVERT: A 1265 ASP cc_start: 0.5760 (OUTLIER) cc_final: 0.5301 (p0) REVERT: A 1308 TYR cc_start: 0.8437 (m-80) cc_final: 0.8219 (m-80) REVERT: A 1344 MET cc_start: 0.8102 (tpt) cc_final: 0.7701 (tpt) REVERT: A 1374 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8130 (t) REVERT: A 1376 LYS cc_start: 0.8623 (tppt) cc_final: 0.8393 (tppt) REVERT: A 1441 GLU cc_start: 0.7841 (tt0) cc_final: 0.7611 (tt0) REVERT: B 20 ASP cc_start: 0.5878 (OUTLIER) cc_final: 0.5440 (p0) REVERT: B 35 ASP cc_start: 0.8361 (t0) cc_final: 0.7951 (t0) REVERT: B 131 THR cc_start: 0.8353 (m) cc_final: 0.7889 (p) REVERT: B 157 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8318 (mtt90) REVERT: B 169 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7631 (tmm160) REVERT: B 200 MET cc_start: 0.8292 (mmt) cc_final: 0.7945 (mmt) REVERT: B 206 TYR cc_start: 0.8479 (m-80) cc_final: 0.7800 (m-80) REVERT: B 214 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8071 (ttpp) REVERT: B 218 THR cc_start: 0.8453 (m) cc_final: 0.8172 (t) REVERT: B 222 ARG cc_start: 0.8135 (mtt-85) cc_final: 0.7727 (mtt90) REVERT: B 285 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 320 PHE cc_start: 0.8588 (t80) cc_final: 0.7839 (t80) REVERT: B 337 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8340 (ttpp) REVERT: B 360 LYS cc_start: 0.8405 (mtmp) cc_final: 0.8069 (mtmm) REVERT: B 542 LEU cc_start: 0.8461 (mp) cc_final: 0.8251 (mp) REVERT: B 547 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 552 ASN cc_start: 0.8401 (m110) cc_final: 0.8169 (m-40) REVERT: B 646 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.8074 (ttp-110) REVERT: B 677 MET cc_start: 0.8444 (mmm) cc_final: 0.8145 (tpp) REVERT: B 689 TYR cc_start: 0.8354 (t80) cc_final: 0.8026 (t80) REVERT: B 692 THR cc_start: 0.8649 (p) cc_final: 0.8287 (p) REVERT: B 721 ARG cc_start: 0.8521 (mmt180) cc_final: 0.8262 (mmt180) REVERT: B 768 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8293 (mmm-85) REVERT: B 914 GLU cc_start: 0.8116 (mp0) cc_final: 0.7760 (mp0) REVERT: B 919 CYS cc_start: 0.8383 (t) cc_final: 0.7915 (p) REVERT: B 1004 ASP cc_start: 0.7579 (t70) cc_final: 0.7244 (t0) REVERT: B 1071 ASN cc_start: 0.7969 (m110) cc_final: 0.7715 (m110) REVERT: C 97 CYS cc_start: 0.7243 (p) cc_final: 0.6957 (p) REVERT: C 162 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7649 (ttt-90) REVERT: C 215 GLU cc_start: 0.8155 (pt0) cc_final: 0.7835 (pt0) REVERT: C 238 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7696 (t) REVERT: C 246 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7856 (mp) REVERT: D 36 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7738 (mt-10) REVERT: E 23 ASP cc_start: 0.7763 (m-30) cc_final: 0.7491 (m-30) REVERT: E 35 GLN cc_start: 0.8433 (tt0) cc_final: 0.8232 (tt0) REVERT: E 67 ASP cc_start: 0.7954 (p0) cc_final: 0.7595 (p0) REVERT: E 78 GLU cc_start: 0.8024 (pm20) cc_final: 0.7795 (pm20) REVERT: E 82 VAL cc_start: 0.8341 (t) cc_final: 0.8014 (m) REVERT: E 92 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7773 (tp-100) REVERT: E 96 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7502 (tm-30) REVERT: E 107 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7623 (mm110) REVERT: E 110 MET cc_start: 0.7530 (mtp) cc_final: 0.7086 (ttm) REVERT: E 120 ASP cc_start: 0.6538 (m-30) cc_final: 0.6009 (m-30) REVERT: E 154 GLU cc_start: 0.8068 (mp0) cc_final: 0.7849 (mp0) REVERT: H 7 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: H 124 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8571 (ttp80) REVERT: H 132 LEU cc_start: 0.8188 (tp) cc_final: 0.7513 (tt) REVERT: U 26 PHE cc_start: 0.6805 (t80) cc_final: 0.6513 (t80) REVERT: U 31 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7712 (p) REVERT: U 35 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7681 (mt-10) REVERT: U 39 MET cc_start: 0.7222 (tpt) cc_final: 0.6716 (tpt) REVERT: U 68 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6634 (tt) REVERT: U 84 GLN cc_start: 0.8624 (mp10) cc_final: 0.8270 (pm20) REVERT: U 109 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7288 (ttm170) REVERT: U 124 LYS cc_start: 0.4302 (tptt) cc_final: 0.3135 (pttm) REVERT: U 138 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: U 158 GLU cc_start: 0.7962 (tp30) cc_final: 0.7558 (mm-30) REVERT: U 161 CYS cc_start: 0.8525 (p) cc_final: 0.8243 (p) REVERT: U 270 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6544 (mm-30) REVERT: U 319 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: U 345 GLN cc_start: 0.7026 (tm-30) cc_final: 0.6646 (tm-30) REVERT: U 360 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7136 (ttm-80) REVERT: U 363 TYR cc_start: 0.7789 (t80) cc_final: 0.7039 (t80) REVERT: U 371 VAL cc_start: 0.8608 (t) cc_final: 0.8368 (p) REVERT: U 418 LYS cc_start: 0.7568 (tptp) cc_final: 0.7280 (tptp) REVERT: U 515 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7567 (mpt-90) REVERT: U 559 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7134 (mt-10) REVERT: U 602 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7607 (mp) REVERT: U 603 LYS cc_start: 0.8156 (tppt) cc_final: 0.7818 (tppt) REVERT: U 604 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7626 (tptm) outliers start: 146 outliers final: 113 residues processed: 1020 average time/residue: 0.2641 time to fit residues: 412.8971 Evaluate side-chains 1059 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 928 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1265 ASP Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 138 PHE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 319 PHE Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 253 optimal weight: 2.9990 chunk 204 optimal weight: 0.0980 chunk 180 optimal weight: 0.9980 chunk 397 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 410 optimal weight: 1.9990 chunk 412 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN B 350 HIS ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN I 74 GLN I 84 HIS ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN ** U 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112466 restraints weight = 53191.876| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.66 r_work: 0.3347 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37460 Z= 0.157 Angle : 0.701 35.106 50851 Z= 0.329 Chirality : 0.045 0.245 5689 Planarity : 0.005 0.070 6388 Dihedral : 12.556 172.375 5555 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 3.65 % Allowed : 22.18 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.02 (0.13), residues: 4410 helix: 1.11 (0.13), residues: 1639 sheet: -0.16 (0.20), residues: 612 loop : -0.83 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 292 TYR 0.024 0.001 TYR C 186 PHE 0.038 0.001 PHE U 420 TRP 0.019 0.001 TRP C 49 HIS 0.038 0.001 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (37428) covalent geometry : angle 0.62765 / 0.32 (50806) hydrogen bonds : bond 0.03550 / 2.37 ( 1556) hydrogen bonds : angle 4.74924 / 3.48 ( 4427) metal coordination : bond 0.00755 / 0.42 ( 32) metal coordination : angle 10.49464 / 6.66 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 927 time to evaluate : 1.355 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: A 22 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7972 (tp40) REVERT: A 29 ASP cc_start: 0.7951 (t0) cc_final: 0.7441 (t0) REVERT: A 148 CYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8477 (t) REVERT: A 151 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7944 (mmtm) REVERT: A 201 GLU cc_start: 0.7911 (tt0) cc_final: 0.7567 (tt0) REVERT: A 212 LYS cc_start: 0.8394 (mptt) cc_final: 0.8182 (mttp) REVERT: A 232 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 250 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8530 (m) REVERT: A 329 MET cc_start: 0.5986 (mmm) cc_final: 0.5702 (mmm) REVERT: A 347 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7301 (mp0) REVERT: A 407 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7814 (ttm-80) REVERT: A 417 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7883 (ttmm) REVERT: A 418 TYR cc_start: 0.8684 (m-80) cc_final: 0.8256 (m-80) REVERT: A 426 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6155 (mpp80) REVERT: A 512 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7909 (ttm170) REVERT: A 703 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7785 (mm-40) REVERT: A 940 LYS cc_start: 0.8294 (pttt) cc_final: 0.8003 (pttt) REVERT: A 957 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 1125 LYS cc_start: 0.8220 (mttt) cc_final: 0.7934 (mttt) REVERT: A 1215 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6735 (mt-10) REVERT: A 1254 LYS cc_start: 0.7957 (ptmm) cc_final: 0.7360 (ptmm) REVERT: A 1265 ASP cc_start: 0.5725 (OUTLIER) cc_final: 0.5279 (p0) REVERT: A 1308 TYR cc_start: 0.8435 (m-80) cc_final: 0.8215 (m-80) REVERT: A 1344 MET cc_start: 0.8117 (tpt) cc_final: 0.7709 (tpt) REVERT: A 1374 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8112 (t) REVERT: A 1376 LYS cc_start: 0.8616 (tppt) cc_final: 0.8370 (tppt) REVERT: A 1441 GLU cc_start: 0.7837 (tt0) cc_final: 0.7612 (tt0) REVERT: B 20 ASP cc_start: 0.5859 (OUTLIER) cc_final: 0.5411 (p0) REVERT: B 35 ASP cc_start: 0.8353 (t0) cc_final: 0.7945 (t0) REVERT: B 131 THR cc_start: 0.8356 (m) cc_final: 0.7897 (p) REVERT: B 169 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7628 (tmm160) REVERT: B 200 MET cc_start: 0.8303 (mmt) cc_final: 0.8058 (mmt) REVERT: B 206 TYR cc_start: 0.8477 (m-80) cc_final: 0.7781 (m-80) REVERT: B 214 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8057 (ttpp) REVERT: B 218 THR cc_start: 0.8468 (m) cc_final: 0.8172 (t) REVERT: B 220 GLU cc_start: 0.8062 (pt0) cc_final: 0.7752 (pt0) REVERT: B 285 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8096 (mm) REVERT: B 320 PHE cc_start: 0.8581 (t80) cc_final: 0.7843 (t80) REVERT: B 337 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8331 (ttpp) REVERT: B 346 GLU cc_start: 0.8479 (tt0) cc_final: 0.8276 (tt0) REVERT: B 360 LYS cc_start: 0.8387 (mtmp) cc_final: 0.8074 (mtmm) REVERT: B 542 LEU cc_start: 0.8447 (mp) cc_final: 0.8225 (mp) REVERT: B 547 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7338 (tm-30) REVERT: B 552 ASN cc_start: 0.8398 (m110) cc_final: 0.8173 (m-40) REVERT: B 646 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.8085 (ttp-110) REVERT: B 677 MET cc_start: 0.8451 (mmm) cc_final: 0.8193 (tpp) REVERT: B 689 TYR cc_start: 0.8344 (t80) cc_final: 0.8021 (t80) REVERT: B 692 THR cc_start: 0.8648 (p) cc_final: 0.8290 (p) REVERT: B 721 ARG cc_start: 0.8515 (mmt180) cc_final: 0.8269 (mmt180) REVERT: B 744 MET cc_start: 0.8364 (mmm) cc_final: 0.8102 (mtt) REVERT: B 768 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8297 (mmm-85) REVERT: B 778 SER cc_start: 0.8462 (p) cc_final: 0.8243 (p) REVERT: B 914 GLU cc_start: 0.8085 (mp0) cc_final: 0.7716 (mp0) REVERT: B 919 CYS cc_start: 0.8388 (t) cc_final: 0.7898 (p) REVERT: B 1004 ASP cc_start: 0.7610 (t70) cc_final: 0.7271 (t0) REVERT: B 1071 ASN cc_start: 0.7950 (m110) cc_final: 0.7695 (m110) REVERT: B 1088 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6945 (mt-10) REVERT: C 97 CYS cc_start: 0.7233 (p) cc_final: 0.6914 (p) REVERT: C 162 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7659 (ttt-90) REVERT: C 246 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7849 (mp) REVERT: C 262 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8032 (mm110) REVERT: D 36 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 23 ASP cc_start: 0.7734 (m-30) cc_final: 0.7478 (m-30) REVERT: E 67 ASP cc_start: 0.7949 (p0) cc_final: 0.7588 (p0) REVERT: E 78 GLU cc_start: 0.8029 (pm20) cc_final: 0.7809 (pm20) REVERT: E 82 VAL cc_start: 0.8340 (t) cc_final: 0.8010 (m) REVERT: E 92 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7774 (tp-100) REVERT: E 96 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7479 (tm-30) REVERT: E 107 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7633 (mm110) REVERT: E 110 MET cc_start: 0.7505 (mtp) cc_final: 0.7070 (ttm) REVERT: E 120 ASP cc_start: 0.6527 (m-30) cc_final: 0.6007 (m-30) REVERT: E 154 GLU cc_start: 0.8077 (mp0) cc_final: 0.7850 (mp0) REVERT: H 7 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: H 124 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8577 (ttp80) REVERT: H 132 LEU cc_start: 0.8199 (tp) cc_final: 0.7537 (tt) REVERT: J 25 LEU cc_start: 0.8814 (mm) cc_final: 0.8610 (mm) REVERT: U 26 PHE cc_start: 0.6793 (t80) cc_final: 0.6487 (t80) REVERT: U 31 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7721 (p) REVERT: U 35 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7687 (mt-10) REVERT: U 39 MET cc_start: 0.7192 (tpt) cc_final: 0.6670 (tpt) REVERT: U 68 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6635 (tt) REVERT: U 84 GLN cc_start: 0.8616 (mp10) cc_final: 0.8263 (pm20) REVERT: U 109 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7262 (ttm170) REVERT: U 124 LYS cc_start: 0.4232 (tptt) cc_final: 0.3074 (pttm) REVERT: U 138 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: U 158 GLU cc_start: 0.7976 (tp30) cc_final: 0.7577 (mm-30) REVERT: U 161 CYS cc_start: 0.8540 (p) cc_final: 0.8259 (p) REVERT: U 270 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6539 (mm-30) REVERT: U 319 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: U 345 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6627 (tm-30) REVERT: U 360 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7155 (ttm-80) REVERT: U 363 TYR cc_start: 0.7800 (t80) cc_final: 0.7022 (t80) REVERT: U 371 VAL cc_start: 0.8558 (t) cc_final: 0.8324 (p) REVERT: U 418 LYS cc_start: 0.7595 (tptp) cc_final: 0.7310 (tptp) REVERT: U 515 ARG cc_start: 0.8027 (tpp80) cc_final: 0.7558 (mpt-90) REVERT: U 530 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6321 (mp0) REVERT: U 559 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7137 (mt-10) REVERT: U 602 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7601 (mp) REVERT: U 603 LYS cc_start: 0.8155 (tppt) cc_final: 0.7792 (tppt) REVERT: U 604 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7657 (tptm) outliers start: 142 outliers final: 116 residues processed: 1004 average time/residue: 0.2578 time to fit residues: 396.5882 Evaluate side-chains 1046 residues out of total 3925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 914 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1265 ASP Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 138 PHE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 220 CYS Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 299 THR Chi-restraints excluded: chain U residue 319 PHE Chi-restraints excluded: chain U residue 336 ILE Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 385 LYS Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 604 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 98 optimal weight: 0.4980 chunk 120 optimal weight: 0.4980 chunk 256 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 441 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 274 optimal weight: 0.5980 chunk 343 optimal weight: 0.9990 chunk 408 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN B 350 HIS ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 383 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 = 0.3793 r_free = 0.3793 target = 0.139206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112730 restraints weight = 52771.877| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.65 r_work: 0.3345 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 37460 Z= 0.206 Angle : 0.784 59.198 50851 Z= 0.398 Chirality : 0.046 0.355 5689 Planarity : 0.005 0.127 6388 Dihedral : 12.556 172.385 5555 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.81 % Rotamer: Outliers : 3.44 % Allowed : 22.51 % Favored : 74.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.03 (0.13), residues: 4410 helix: 1.10 (0.13), residues: 1639 sheet: -0.16 (0.20), residues: 612 loop : -0.83 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 862 TYR 0.021 0.001 TYR C 186 PHE 0.036 0.001 PHE U 420 TRP 0.019 0.001 TRP C 49 HIS 0.183 0.002 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (37428) covalent geometry : angle 0.71953 / 0.39 (50806) hydrogen bonds : bond 0.03551 / 2.37 ( 1556) hydrogen bonds : angle 4.74645 / 3.48 ( 4427) metal coordination : bond 0.00766 / 0.42 ( 32) metal coordination : angle 10.49370 / 6.66 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13235.82 seconds wall clock time: 226 minutes 26.38 seconds (13586.38 seconds total)