Starting phenix.real_space_refine on Sat Mar 7 07:57:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z31_14470/03_2026/7z31_14470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z31_14470/03_2026/7z31_14470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z31_14470/03_2026/7z31_14470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z31_14470/03_2026/7z31_14470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z31_14470/03_2026/7z31_14470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z31_14470/03_2026/7z31_14470.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 212 5.16 5 C 25459 2.51 5 N 6922 2.21 5 O 7556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40156 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 11123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1419, 11123 Classifications: {'peptide': 1419} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1354} Chain breaks: 3 Chain: "B" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8701 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 41, 'TRANS': 1060} Chain breaks: 1 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1140 Classifications: {'peptide': 145} Incomplete info: {'backbone_only': 11} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 365 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 381 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1492 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 1 Chain: "N" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1169 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4558 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Chain: "P" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 829 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain breaks: 1 Chain: "W" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 141 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 100.210 116.738 89.570 1.00 81.71 S ATOM 510 SG CYS A 70 98.802 120.240 91.061 1.00 73.59 S ATOM 557 SG CYS A 77 97.995 117.435 91.961 1.00 58.88 S ATOM 795 SG CYS A 107 70.338 94.579 59.545 1.00 85.58 S ATOM 818 SG CYS A 110 70.485 96.680 57.505 1.00 79.06 S ATOM 1184 SG CYS A 154 67.406 95.753 58.253 1.00 80.78 S ATOM 1208 SG CYS A 157 70.392 94.395 55.268 1.00 90.24 S ATOM 19397 SG CYS B1095 84.688 124.704 81.619 1.00 49.19 S ATOM 19420 SG CYS B1098 84.558 121.141 80.560 1.00 50.73 S ATOM 19486 SG CYS B1107 86.984 122.879 80.780 1.00 59.22 S ATOM 19506 SG CYS B1110 85.485 123.485 77.659 1.00 67.66 S ATOM 28735 SG CYS I 5 57.289 37.446 88.472 1.00 68.49 S ATOM 28754 SG CYS I 8 61.092 39.022 88.587 1.00 72.34 S ATOM 28882 SG CYS I 26 57.758 40.036 86.526 1.00 70.98 S ATOM 28905 SG CYS I 29 59.094 37.797 85.919 1.00 77.27 S ATOM 29115 SG CYS J 7 86.168 99.824 157.940 1.00 17.39 S ATOM 29138 SG CYS J 10 85.859 101.756 160.595 1.00 20.72 S ATOM 29418 SG CYS J 45 82.735 99.641 159.349 1.00 16.56 S ATOM 29424 SG CYS J 46 86.001 99.144 161.769 1.00 24.36 S ATOM 30475 SG CYS L 31 120.126 86.143 135.016 1.00 51.23 S ATOM 30495 SG CYS L 34 122.405 85.003 137.721 1.00 47.08 S ATOM 30599 SG CYS L 48 124.020 86.325 134.696 1.00 53.16 S ATOM 30622 SG CYS L 51 122.150 83.086 134.956 1.00 53.88 S Time building chain proxies: 8.01, per 1000 atoms: 0.20 Number of scatterers: 40156 At special positions: 0 Unit cell: (137.8, 193.98, 199.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 212 16.00 Mg 1 11.99 O 7556 8.00 N 6922 7.00 C 25459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 29 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 33 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9534 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 51 sheets defined 41.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 133 through 151 Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.543A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.391A pdb=" N TYR A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.564A pdb=" N GLN A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 283 through 306 removed outlier: 4.297A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.659A pdb=" N VAL A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.629A pdb=" N LEU A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.921A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.026A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 566 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.757A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 720 through 748 removed outlier: 3.728A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 785 Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 857 through 881 Processing helix chain 'A' and resid 884 through 894 Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.658A pdb=" N MET A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.701A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 974 removed outlier: 3.824A pdb=" N LEU A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1026 Processing helix chain 'A' and resid 1037 through 1041 removed outlier: 3.682A pdb=" N GLN A1040 " --> pdb=" O LYS A1037 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY A1041 " --> pdb=" O GLU A1038 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1037 through 1041' Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1063 through 1082 removed outlier: 3.770A pdb=" N ARG A1082 " --> pdb=" O TYR A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1100 through 1104 removed outlier: 3.505A pdb=" N MET A1104 " --> pdb=" O GLY A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 Processing helix chain 'A' and resid 1153 through 1161 removed outlier: 4.167A pdb=" N VAL A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1171 removed outlier: 4.537A pdb=" N PHE A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 4.002A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1254 through 1267 Processing helix chain 'A' and resid 1299 through 1306 removed outlier: 3.708A pdb=" N VAL A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1345 Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 3.811A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 Processing helix chain 'A' and resid 1391 through 1402 removed outlier: 3.526A pdb=" N HIS A1395 " --> pdb=" O LYS A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1418 Processing helix chain 'A' and resid 1423 through 1427 Processing helix chain 'A' and resid 1447 through 1456 Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.835A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 80 removed outlier: 5.573A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 276 through 294 removed outlier: 4.610A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.693A pdb=" N LEU B 320 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 342 through 362 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 Processing helix chain 'B' and resid 419 through 426 Processing helix chain 'B' and resid 426 through 440 removed outlier: 3.836A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 525 through 536 removed outlier: 4.326A pdb=" N ILE B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 581 Processing helix chain 'B' and resid 624 through 633 Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.615A pdb=" N PHE B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.532A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.501A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 707 removed outlier: 3.628A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.625A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 927 through 931 Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.631A pdb=" N SER B 951 " --> pdb=" O HIS B 947 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.965A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1075 through 1084 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.749A pdb=" N LYS C 125 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.667A pdb=" N LEU C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 156' Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.632A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.653A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.849A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.957A pdb=" N ILE D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 removed outlier: 4.005A pdb=" N LEU D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'E' and resid 2 through 28 removed outlier: 4.092A pdb=" N TYR E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.727A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 188 removed outlier: 3.730A pdb=" N TYR E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 19 removed outlier: 4.171A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 162 through 173 Processing helix chain 'I' and resid 18 through 20 No H-bonds generated for 'chain 'I' and resid 18 through 20' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.638A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 4.166A pdb=" N LYS J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.650A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 183 through 195 Processing helix chain 'M' and resid 228 through 238 removed outlier: 3.518A pdb=" N LEU M 232 " --> pdb=" O THR M 228 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA M 233 " --> pdb=" O GLY M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 265 removed outlier: 4.013A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 279 removed outlier: 4.223A pdb=" N ASP M 279 " --> pdb=" O GLU M 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 219 removed outlier: 3.688A pdb=" N LYS N 216 " --> pdb=" O VAL N 212 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU N 218 " --> pdb=" O THR N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 296 Processing helix chain 'N' and resid 366 through 370 removed outlier: 4.034A pdb=" N GLY N 369 " --> pdb=" O HIS N 366 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS N 370 " --> pdb=" O LYS N 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 366 through 370' Processing helix chain 'O' and resid 38 through 42 removed outlier: 3.645A pdb=" N THR O 41 " --> pdb=" O GLU O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 57 Processing helix chain 'O' and resid 58 through 71 Processing helix chain 'O' and resid 75 through 83 Processing helix chain 'O' and resid 87 through 101 Processing helix chain 'O' and resid 124 through 143 removed outlier: 3.610A pdb=" N HIS O 128 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 167 removed outlier: 4.112A pdb=" N LYS O 153 " --> pdb=" O GLU O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 178 removed outlier: 3.598A pdb=" N SER O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 198 removed outlier: 4.601A pdb=" N THR O 186 " --> pdb=" O SER O 182 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE O 187 " --> pdb=" O MET O 183 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER O 189 " --> pdb=" O TYR O 185 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 Processing helix chain 'O' and resid 210 through 218 Processing helix chain 'O' and resid 233 through 258 Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 284 through 304 Processing helix chain 'O' and resid 305 through 318 removed outlier: 5.258A pdb=" N VAL O 311 " --> pdb=" O VAL O 307 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR O 312 " --> pdb=" O THR O 308 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS O 313 " --> pdb=" O ALA O 309 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 319 through 323 Processing helix chain 'O' and resid 343 through 356 Processing helix chain 'O' and resid 357 through 360 Processing helix chain 'O' and resid 364 through 370 removed outlier: 3.804A pdb=" N ARG O 368 " --> pdb=" O ASP O 365 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS O 369 " --> pdb=" O LEU O 366 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU O 370 " --> pdb=" O ALA O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 463 removed outlier: 3.751A pdb=" N SER O 455 " --> pdb=" O SER O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 500 Processing helix chain 'O' and resid 501 through 514 Processing helix chain 'O' and resid 520 through 527 Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.859A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 removed outlier: 4.023A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG O 578 " --> pdb=" O TYR O 574 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU O 581 " --> pdb=" O MET O 577 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 620 through 645 Processing helix chain 'O' and resid 647 through 652 removed outlier: 3.869A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 191 removed outlier: 3.815A pdb=" N ASN P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER P 177 " --> pdb=" O GLU P 173 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TRP P 183 " --> pdb=" O LEU P 179 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE P 185 " --> pdb=" O ILE P 181 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE P 186 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU P 188 " --> pdb=" O ARG P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 200 removed outlier: 3.726A pdb=" N LYS P 196 " --> pdb=" O ASN P 193 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN P 197 " --> pdb=" O GLY P 194 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN P 200 " --> pdb=" O ASN P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 229 removed outlier: 3.740A pdb=" N GLN P 229 " --> pdb=" O ILE P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 247 Processing helix chain 'P' and resid 248 through 252 removed outlier: 3.634A pdb=" N ASP P 251 " --> pdb=" O VAL P 248 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS P 252 " --> pdb=" O TYR P 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 248 through 252' Processing helix chain 'P' and resid 256 through 260 removed outlier: 3.725A pdb=" N CYS P 260 " --> pdb=" O THR P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 271 Processing helix chain 'Q' and resid 48 through 67 removed outlier: 4.714A pdb=" N GLY Q 62 " --> pdb=" O TYR Q 58 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 132 Processing helix chain 'Q' and resid 136 through 140 Processing helix chain 'W' and resid 612 through 617 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 20 removed outlier: 5.370A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 7.235A pdb=" N VAL A 32 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS A 85 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 180 removed outlier: 3.797A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.534A pdb=" N VAL A 373 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.566A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.560A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA8, first strand: chain 'A' and resid 597 through 599 removed outlier: 6.134A pdb=" N VAL H 96 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 629 removed outlier: 5.964A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 813 through 815 removed outlier: 4.267A pdb=" N GLY A 814 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 Processing sheet with id=AB3, first strand: chain 'A' and resid 1281 through 1285 removed outlier: 8.049A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A1315 " --> pdb=" O ASN A1142 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1172 through 1173 removed outlier: 3.507A pdb=" N VAL A1173 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1222 through 1224 removed outlier: 3.567A pdb=" N ILE I 40 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AB7, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.842A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.593A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AC2, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AC3, first strand: chain 'B' and resid 442 through 444 removed outlier: 3.574A pdb=" N ARG B 451 " --> pdb=" O TRP B 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC5, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AC6, first strand: chain 'B' and resid 560 through 565 removed outlier: 5.522A pdb=" N LEU B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 557 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 563 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR B 553 " --> pdb=" O ILE B 565 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.886A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.886A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL B 884 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AD1, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 7.383A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 797 through 798 removed outlier: 3.694A pdb=" N THR B 802 " --> pdb=" O TYR B 798 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 841 through 843 removed outlier: 3.860A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id=AD6, first strand: chain 'C' and resid 12 through 13 removed outlier: 4.434A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.621A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.299A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LYS C 205 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE C 85 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS C 207 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL C 83 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 209 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU C 81 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY C 211 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA C 79 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE2, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE3, first strand: chain 'D' and resid 3 through 5 removed outlier: 7.115A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN G 69 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL G 54 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR G 71 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL G 75 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE G 48 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY G 43 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.730A pdb=" N PHE E 60 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP E 79 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.653A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'G' and resid 98 through 99 removed outlier: 4.373A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AE9, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.558A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 243 through 244 removed outlier: 4.087A pdb=" N ILE M 243 " --> pdb=" O TYR M 112 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR M 112 " --> pdb=" O ILE M 243 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA M 109 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP M 122 " --> pdb=" O ALA M 109 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR M 147 " --> pdb=" O PHE M 182 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL M 151 " --> pdb=" O GLN M 178 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN M 178 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL M 87 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU M 179 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN M 89 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU N 391 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLN N 392 " --> pdb=" O VAL N 412 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA N 396 " --> pdb=" O LEU N 408 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU N 408 " --> pdb=" O ALA N 396 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER N 398 " --> pdb=" O ALA N 406 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA N 406 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE N 304 " --> pdb=" O VAL N 412 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY N 414 " --> pdb=" O PHE N 304 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ARG N 303 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL M 163 " --> pdb=" O ARG N 303 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE M 162 " --> pdb=" O TYR M 169 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU M 170 " --> pdb=" O PRO M 75 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY N 361 " --> pdb=" O LEU M 76 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE M 78 " --> pdb=" O LYS N 359 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS N 359 " --> pdb=" O ILE M 78 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 246 through 248 Processing sheet with id=AF3, first strand: chain 'O' and resid 106 through 109 removed outlier: 3.590A pdb=" N THR O 117 " --> pdb=" O GLU O 109 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'O' and resid 469 through 472 removed outlier: 4.357A pdb=" N THR O 471 " --> pdb=" O VAL O 475 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL O 475 " --> pdb=" O THR O 471 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 547 through 548 1668 hydrogen bonds defined for protein. 4665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.29 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13121 1.34 - 1.46: 7051 1.46 - 1.58: 20355 1.58 - 1.70: 0 1.70 - 1.82: 346 Bond restraints: 40873 Sorted by residual: bond pdb=" N ASN B1136 " pdb=" CA ASN B1136 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.59e+00 bond pdb=" N VAL K 86 " pdb=" CA VAL K 86 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.55e+00 bond pdb=" N VAL A1207 " pdb=" CA VAL A1207 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.98e+00 bond pdb=" N ILE A1184 " pdb=" CA ILE A1184 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.15e-02 7.56e+03 8.77e+00 bond pdb=" N GLN A1185 " pdb=" CA GLN A1185 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.31e+00 ... (remaining 40868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 53597 1.80 - 3.60: 1386 3.60 - 5.40: 149 5.40 - 7.20: 37 7.20 - 9.00: 7 Bond angle restraints: 55176 Sorted by residual: angle pdb=" N ILE Q 43 " pdb=" CA ILE Q 43 " pdb=" C ILE Q 43 " ideal model delta sigma weight residual 111.91 107.20 4.71 8.90e-01 1.26e+00 2.81e+01 angle pdb=" C ASN Q 31 " pdb=" CA ASN Q 31 " pdb=" CB ASN Q 31 " ideal model delta sigma weight residual 116.54 110.84 5.70 1.15e+00 7.56e-01 2.45e+01 angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 113.71 109.39 4.32 9.50e-01 1.11e+00 2.07e+01 angle pdb=" C ILE E 116 " pdb=" N THR E 117 " pdb=" CA THR E 117 " ideal model delta sigma weight residual 120.68 127.16 -6.48 1.52e+00 4.33e-01 1.82e+01 angle pdb=" CA ILE A1217 " pdb=" C ILE A1217 " pdb=" O ILE A1217 " ideal model delta sigma weight residual 120.70 117.28 3.42 8.50e-01 1.38e+00 1.62e+01 ... (remaining 55171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 22345 17.88 - 35.76: 1970 35.76 - 53.65: 587 53.65 - 71.53: 145 71.53 - 89.41: 37 Dihedral angle restraints: 25084 sinusoidal: 10347 harmonic: 14737 Sorted by residual: dihedral pdb=" CD ARG A1211 " pdb=" NE ARG A1211 " pdb=" CZ ARG A1211 " pdb=" NH1 ARG A1211 " ideal model delta sinusoidal sigma weight residual 0.00 67.56 -67.56 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CA SER C 223 " pdb=" C SER C 223 " pdb=" N THR C 224 " pdb=" CA THR C 224 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA SER B 776 " pdb=" C SER B 776 " pdb=" N SER B 777 " pdb=" CA SER B 777 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 25081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4405 0.047 - 0.093: 1416 0.093 - 0.140: 361 0.140 - 0.186: 34 0.186 - 0.233: 5 Chirality restraints: 6221 Sorted by residual: chirality pdb=" CA LEU K 100 " pdb=" N LEU K 100 " pdb=" C LEU K 100 " pdb=" CB LEU K 100 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE A1184 " pdb=" N ILE A1184 " pdb=" C ILE A1184 " pdb=" CB ILE A1184 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE B1137 " pdb=" N ILE B1137 " pdb=" C ILE B1137 " pdb=" CB ILE B1137 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 6218 not shown) Planarity restraints: 7106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1211 " 1.007 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG A1211 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A1211 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A1211 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1211 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 48 " -0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO D 49 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 493 " 0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO A 494 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " 0.037 5.00e-02 4.00e+02 ... (remaining 7103 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 369 2.58 - 3.16: 34015 3.16 - 3.74: 64553 3.74 - 4.32: 90667 4.32 - 4.90: 147184 Nonbonded interactions: 336788 Sorted by model distance: nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A1503 " model vdw 1.998 2.170 nonbonded pdb=" OD2 ASP A 511 " pdb="MG MG A1503 " model vdw 2.010 2.170 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A1503 " model vdw 2.037 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A4001 " model vdw 2.067 2.170 nonbonded pdb=" CG ASP A 511 " pdb="MG MG A1503 " model vdw 2.088 2.400 ... (remaining 336783 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 41.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 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 : 0.006 0.126 40897 Z= 0.273 Angle : 0.845 37.565 55209 Z= 0.405 Chirality : 0.047 0.233 6221 Planarity : 0.008 0.451 7106 Dihedral : 15.672 89.410 15550 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 6.49 % Allowed : 13.71 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 4976 helix: 0.06 (0.12), residues: 1800 sheet: -0.62 (0.21), residues: 577 loop : -1.38 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 295 TYR 0.017 0.002 TYR E 112 PHE 0.028 0.002 PHE B 678 TRP 0.020 0.002 TRP C 31 HIS 0.013 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00573 (40873) covalent geometry : angle 0.70162 (55176) hydrogen bonds : bond 0.16032 ( 1636) hydrogen bonds : angle 6.76454 ( 4665) metal coordination : bond 0.06648 ( 24) metal coordination : angle 19.24826 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 289 poor density : 592 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.2923 (OUTLIER) cc_final: 0.2715 (t) REVERT: A 320 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: A 548 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 644 GLU cc_start: 0.8543 (pm20) cc_final: 0.8087 (pm20) REVERT: A 728 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 775 GLU cc_start: 0.6965 (tp30) cc_final: 0.6750 (tp30) REVERT: A 884 TYR cc_start: 0.6856 (t80) cc_final: 0.6555 (t80) REVERT: A 893 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8596 (mt) REVERT: A 909 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8222 (m-40) REVERT: A 951 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: A 1031 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8103 (mm) REVERT: A 1099 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6261 (tp30) REVERT: A 1107 LYS cc_start: 0.1321 (OUTLIER) cc_final: 0.1078 (mptm) REVERT: A 1161 VAL cc_start: 0.6584 (m) cc_final: 0.6373 (m) REVERT: A 1184 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6514 (mt) REVERT: A 1230 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7533 (mt) REVERT: A 1262 GLN cc_start: 0.6949 (pp30) cc_final: 0.6564 (pp30) REVERT: A 1267 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7869 (tm) REVERT: A 1301 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6817 (ttp80) REVERT: A 1379 MET cc_start: 0.3176 (ppp) cc_final: 0.2273 (ppp) REVERT: B 43 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: B 81 GLN cc_start: 0.6119 (tt0) cc_final: 0.5919 (tm-30) REVERT: B 168 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6427 (mt-10) REVERT: B 198 GLU cc_start: 0.8273 (tt0) cc_final: 0.8013 (tt0) REVERT: B 201 SER cc_start: 0.8153 (p) cc_final: 0.7899 (m) REVERT: B 263 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6429 (pp) REVERT: B 366 ILE cc_start: 0.8718 (pt) cc_final: 0.8505 (pp) REVERT: B 539 GLU cc_start: 0.7105 (pm20) cc_final: 0.6512 (pm20) REVERT: B 639 ASP cc_start: 0.7822 (m-30) cc_final: 0.7601 (m-30) REVERT: B 786 GLU cc_start: 0.8400 (pt0) cc_final: 0.8182 (pt0) REVERT: B 953 MET cc_start: 0.9058 (mtm) cc_final: 0.8817 (mtm) REVERT: B 1052 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.5199 (mm-30) REVERT: C 1 MET cc_start: 0.4258 (mmm) cc_final: 0.3890 (tmm) REVERT: C 35 LYS cc_start: 0.7643 (tmtt) cc_final: 0.7309 (tptm) REVERT: C 71 MET cc_start: 0.9429 (mtm) cc_final: 0.9212 (mtm) REVERT: C 82 TYR cc_start: 0.8652 (m-80) cc_final: 0.8278 (m-80) REVERT: C 152 ASP cc_start: 0.6390 (OUTLIER) cc_final: 0.6148 (t70) REVERT: D 21 THR cc_start: 0.7132 (OUTLIER) cc_final: 0.6794 (t) REVERT: E 41 ASP cc_start: 0.5689 (t0) cc_final: 0.5317 (t0) REVERT: E 67 GLU cc_start: 0.6654 (mp0) cc_final: 0.6440 (tp30) REVERT: E 79 TRP cc_start: 0.6329 (t-100) cc_final: 0.6001 (t-100) REVERT: E 101 GLN cc_start: 0.6831 (tt0) cc_final: 0.6621 (tt0) REVERT: F 116 ASP cc_start: 0.8643 (t70) cc_final: 0.8296 (t0) REVERT: F 122 MET cc_start: 0.8135 (mtt) cc_final: 0.7843 (mtp) REVERT: G 150 ILE cc_start: 0.2593 (OUTLIER) cc_final: 0.2254 (mp) REVERT: G 151 GLU cc_start: 0.3043 (OUTLIER) cc_final: 0.2122 (pm20) REVERT: G 205 MET cc_start: 0.3575 (mtm) cc_final: 0.3139 (mtp) REVERT: I 12 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7259 (mp) REVERT: K 45 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6915 (mt-10) REVERT: K 132 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7278 (mt-10) REVERT: L 38 LEU cc_start: 0.8219 (mt) cc_final: 0.7945 (mp) REVERT: M 268 LEU cc_start: 0.3253 (OUTLIER) cc_final: 0.2865 (mp) REVERT: N 298 ASN cc_start: 0.5485 (OUTLIER) cc_final: 0.5122 (m-40) REVERT: O 31 VAL cc_start: 0.3462 (t) cc_final: 0.3200 (p) REVERT: O 140 ILE cc_start: 0.2870 (OUTLIER) cc_final: 0.2641 (mm) REVERT: O 222 HIS cc_start: 0.2179 (OUTLIER) cc_final: 0.1394 (m90) REVERT: O 275 LYS cc_start: 0.3270 (OUTLIER) cc_final: 0.3058 (mtpt) REVERT: O 322 LYS cc_start: 0.3212 (OUTLIER) cc_final: 0.1881 (tttt) REVERT: O 523 ASN cc_start: 0.3199 (m110) cc_final: 0.2650 (OUTLIER) REVERT: O 567 ARG cc_start: 0.4108 (tpp80) cc_final: 0.3899 (tpp80) REVERT: O 585 MET cc_start: 0.4587 (mtm) cc_final: 0.4281 (mtm) REVERT: P 207 PHE cc_start: 0.2123 (OUTLIER) cc_final: 0.1729 (m-80) outliers start: 289 outliers final: 146 residues processed: 823 average time/residue: 0.7041 time to fit residues: 705.7331 Evaluate side-chains 688 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 516 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1301 ARG Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 43 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 235 LYS Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 83 ILE Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 222 HIS Chi-restraints excluded: chain O residue 261 GLN Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 323 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 377 ARG Chi-restraints excluded: chain O residue 477 TYR Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 558 SER Chi-restraints excluded: chain O residue 561 ARG Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 620 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 THR Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 617 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 275 GLN A 310 ASN A 455 ASN A 675 HIS A 746 ASN A 753 GLN A 789 ASN A 808 GLN A 815 GLN A 950 GLN A 964 ASN A1058 GLN A1131 ASN A1233 ASN A1284 ASN A1317 ASN ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN B 197 GLN B 203 ASN B 217 GLN B 244 HIS B 275 ASN B 280 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 513 ASN ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 774 ASN B 837 GLN B 893 GLN B 928 GLN B 945 ASN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 88 ASN C 158 ASN C 248 GLN D 61 ASN D 71 ASN E 99 HIS E 106 GLN G 29 GLN G 31 ASN G 32 ASN H 35 GLN H 64 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS L 66 GLN M 92 ASN M 167 GLN M 234 HIS N 287 HIS N 298 ASN N 308 GLN O 100 GLN O 143 GLN ** O 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 448 HIS O 549 GLN ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 607 ASN P 219 GLN P 239 ASN Q 31 ASN W 615 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.199498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138388 restraints weight = 47735.420| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.76 r_work: 0.3258 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 40897 Z= 0.135 Angle : 0.628 24.126 55209 Z= 0.313 Chirality : 0.044 0.193 6221 Planarity : 0.005 0.094 7106 Dihedral : 9.026 91.965 5810 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 5.69 % Allowed : 16.85 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.85 (0.12), residues: 4976 helix: 0.46 (0.12), residues: 1826 sheet: -0.59 (0.21), residues: 580 loop : -1.31 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 578 TYR 0.020 0.001 TYR E 112 PHE 0.025 0.001 PHE B 678 TRP 0.018 0.002 TRP C 31 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00300 (40873) covalent geometry : angle 0.59400 (55176) hydrogen bonds : bond 0.04456 ( 1636) hydrogen bonds : angle 5.33025 ( 4665) metal coordination : bond 0.01854 ( 24) metal coordination : angle 8.34394 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 591 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.5901 (p-80) cc_final: 0.5607 (p-80) REVERT: A 312 MET cc_start: 0.3628 (tmm) cc_final: 0.3417 (tmm) REVERT: A 446 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7137 (p90) REVERT: A 725 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6533 (tm-30) REVERT: A 728 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 736 HIS cc_start: 0.6762 (t70) cc_final: 0.5957 (m-70) REVERT: A 775 GLU cc_start: 0.7201 (tp30) cc_final: 0.6881 (tp30) REVERT: A 828 GLN cc_start: 0.7662 (tp40) cc_final: 0.7344 (mm110) REVERT: A 884 TYR cc_start: 0.6901 (t80) cc_final: 0.6597 (t80) REVERT: A 909 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8213 (m-40) REVERT: A 1099 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6539 (tp30) REVERT: A 1230 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7529 (mt) REVERT: A 1260 MET cc_start: 0.7210 (mmm) cc_final: 0.6968 (mmm) REVERT: A 1267 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7774 (tm) REVERT: A 1301 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6629 (ttp80) REVERT: B 43 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: B 90 GLU cc_start: 0.5228 (OUTLIER) cc_final: 0.4951 (pm20) REVERT: B 132 ASP cc_start: 0.6573 (m-30) cc_final: 0.6365 (m-30) REVERT: B 198 GLU cc_start: 0.8271 (tt0) cc_final: 0.8012 (tt0) REVERT: B 277 SER cc_start: 0.7479 (t) cc_final: 0.6756 (m) REVERT: B 296 TYR cc_start: 0.6930 (m-80) cc_final: 0.6599 (m-80) REVERT: B 366 ILE cc_start: 0.8593 (pt) cc_final: 0.8315 (pp) REVERT: B 378 GLU cc_start: 0.7658 (pt0) cc_final: 0.7231 (tt0) REVERT: B 539 GLU cc_start: 0.7414 (pm20) cc_final: 0.6894 (mt-10) REVERT: B 639 ASP cc_start: 0.7847 (m-30) cc_final: 0.7577 (m-30) REVERT: B 656 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: B 953 MET cc_start: 0.8863 (mtm) cc_final: 0.8657 (mtm) REVERT: B 1114 GLU cc_start: 0.6688 (tp30) cc_final: 0.6397 (tt0) REVERT: C 1 MET cc_start: 0.4646 (mmm) cc_final: 0.3972 (tmm) REVERT: C 35 LYS cc_start: 0.7745 (tmtt) cc_final: 0.6775 (ttpt) REVERT: C 82 TYR cc_start: 0.8639 (m-80) cc_final: 0.8183 (m-80) REVERT: C 277 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8223 (pmt170) REVERT: E 41 ASP cc_start: 0.5776 (t0) cc_final: 0.5489 (t0) REVERT: E 50 MET cc_start: 0.3775 (tpp) cc_final: 0.3568 (mmt) REVERT: E 67 GLU cc_start: 0.7140 (mp0) cc_final: 0.6569 (tp30) REVERT: E 79 TRP cc_start: 0.6279 (t-100) cc_final: 0.5655 (t-100) REVERT: E 99 HIS cc_start: 0.5869 (OUTLIER) cc_final: 0.5631 (t-170) REVERT: E 101 GLN cc_start: 0.7437 (tt0) cc_final: 0.6598 (tm130) REVERT: E 106 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5805 (tp40) REVERT: E 148 GLU cc_start: 0.7721 (pt0) cc_final: 0.7413 (pp20) REVERT: F 76 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7620 (ttpt) REVERT: F 116 ASP cc_start: 0.8564 (t70) cc_final: 0.8265 (t0) REVERT: G 73 ARG cc_start: 0.6623 (mtm180) cc_final: 0.6371 (mtm-85) REVERT: G 205 MET cc_start: 0.3869 (mtm) cc_final: 0.3376 (mtp) REVERT: H 64 ASN cc_start: 0.7142 (m-40) cc_final: 0.6652 (t0) REVERT: H 86 ASP cc_start: 0.7344 (m-30) cc_final: 0.7092 (m-30) REVERT: H 105 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: K 45 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7253 (mt-10) REVERT: K 48 LYS cc_start: 0.8283 (mttm) cc_final: 0.8032 (mttm) REVERT: L 36 SER cc_start: 0.8077 (m) cc_final: 0.7864 (p) REVERT: L 38 LEU cc_start: 0.8177 (mt) cc_final: 0.7846 (mp) REVERT: L 54 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7714 (mtt-85) REVERT: L 68 GLU cc_start: 0.8013 (tt0) cc_final: 0.7747 (tp30) REVERT: M 156 ASN cc_start: 0.7541 (m-40) cc_final: 0.7312 (m-40) REVERT: N 298 ASN cc_start: 0.5570 (OUTLIER) cc_final: 0.5020 (m110) REVERT: N 312 ARG cc_start: 0.5587 (tpt90) cc_final: 0.4943 (ttm110) REVERT: N 392 GLN cc_start: 0.6870 (mt0) cc_final: 0.6574 (mt0) REVERT: N 407 GLU cc_start: 0.5245 (tt0) cc_final: 0.4933 (tp30) REVERT: O 31 VAL cc_start: 0.2723 (t) cc_final: 0.2414 (p) REVERT: O 86 MET cc_start: 0.3400 (tmm) cc_final: 0.3005 (tmm) REVERT: O 275 LYS cc_start: 0.3514 (OUTLIER) cc_final: 0.3060 (mtpt) REVERT: O 288 MET cc_start: 0.4129 (tmm) cc_final: 0.3878 (mtp) REVERT: O 511 ILE cc_start: 0.3638 (mp) cc_final: 0.3220 (tp) REVERT: O 585 MET cc_start: 0.5322 (mtm) cc_final: 0.4744 (mtp) REVERT: O 588 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.6189 (mt) REVERT: O 592 LYS cc_start: 0.5940 (ptmt) cc_final: 0.5593 (tppt) REVERT: P 207 PHE cc_start: 0.2055 (OUTLIER) cc_final: 0.1690 (m-80) REVERT: W 617 LYS cc_start: 0.4068 (OUTLIER) cc_final: 0.3682 (ttpp) REVERT: W 619 MET cc_start: 0.4480 (OUTLIER) cc_final: 0.4273 (mpp) outliers start: 253 outliers final: 111 residues processed: 789 average time/residue: 0.7132 time to fit residues: 683.4831 Evaluate side-chains 651 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 519 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1301 ARG Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 477 TYR Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 558 SER Chi-restraints excluded: chain O residue 561 ARG Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 620 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 617 LYS Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 47 optimal weight: 1.9990 chunk 458 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 746 ASN A 753 GLN A 805 ASN A 950 GLN A 964 ASN A1284 ASN A1317 ASN A1345 ASN ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 HIS ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 88 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN E 5 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 69 ASN H 137 GLN J 53 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN O 161 GLN ** O 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 599 ASN ** O 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.196606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136591 restraints weight = 47760.097| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.72 r_work: 0.3199 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 40897 Z= 0.295 Angle : 0.760 26.092 55209 Z= 0.382 Chirality : 0.049 0.227 6221 Planarity : 0.006 0.098 7106 Dihedral : 8.336 58.923 5672 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 6.65 % Allowed : 18.61 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -1.20 (0.12), residues: 4976 helix: 0.05 (0.12), residues: 1819 sheet: -0.80 (0.20), residues: 600 loop : -1.41 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 952 TYR 0.023 0.002 TYR O 132 PHE 0.027 0.003 PHE B 678 TRP 0.020 0.003 TRP A 201 HIS 0.015 0.002 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00690 (40873) covalent geometry : angle 0.73282 (55176) hydrogen bonds : bond 0.05192 ( 1636) hydrogen bonds : angle 5.46596 ( 4665) metal coordination : bond 0.01748 ( 24) metal coordination : angle 8.28190 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 536 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 VAL cc_start: 0.6652 (OUTLIER) cc_final: 0.6438 (m) REVERT: A 83 HIS cc_start: 0.5923 (p-80) cc_final: 0.5672 (p-80) REVERT: A 455 ASN cc_start: 0.8007 (m-40) cc_final: 0.7770 (m110) REVERT: A 725 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: A 728 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7308 (tm-30) REVERT: A 736 HIS cc_start: 0.6923 (t70) cc_final: 0.6077 (m-70) REVERT: A 775 GLU cc_start: 0.7204 (tp30) cc_final: 0.6880 (tp30) REVERT: A 828 GLN cc_start: 0.7732 (tp40) cc_final: 0.7484 (mm110) REVERT: A 884 TYR cc_start: 0.6950 (t80) cc_final: 0.6651 (t80) REVERT: A 893 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 1099 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6496 (tp30) REVERT: A 1230 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7545 (mt) REVERT: A 1262 GLN cc_start: 0.6819 (pp30) cc_final: 0.6546 (pp30) REVERT: A 1267 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7729 (tm) REVERT: A 1301 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6714 (ttp80) REVERT: A 1379 MET cc_start: 0.2675 (ppp) cc_final: 0.1940 (ppp) REVERT: B 43 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: B 198 GLU cc_start: 0.8462 (tt0) cc_final: 0.8193 (tt0) REVERT: B 201 SER cc_start: 0.8182 (p) cc_final: 0.7970 (m) REVERT: B 263 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6545 (pp) REVERT: B 296 TYR cc_start: 0.6810 (m-80) cc_final: 0.6553 (m-80) REVERT: B 378 GLU cc_start: 0.7716 (pt0) cc_final: 0.7293 (tt0) REVERT: B 504 GLU cc_start: 0.5672 (OUTLIER) cc_final: 0.5070 (pm20) REVERT: B 527 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: B 539 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: B 639 ASP cc_start: 0.7878 (m-30) cc_final: 0.7623 (m-30) REVERT: B 656 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: B 705 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8147 (mpp) REVERT: B 1114 GLU cc_start: 0.7074 (tp30) cc_final: 0.6759 (tt0) REVERT: C 1 MET cc_start: 0.4480 (mmm) cc_final: 0.3894 (tmm) REVERT: C 35 LYS cc_start: 0.7729 (tmtt) cc_final: 0.7484 (tptm) REVERT: C 71 MET cc_start: 0.9357 (mtm) cc_final: 0.9127 (mtm) REVERT: C 201 GLU cc_start: 0.8209 (tt0) cc_final: 0.7934 (tt0) REVERT: E 41 ASP cc_start: 0.5785 (t0) cc_final: 0.5441 (t0) REVERT: E 67 GLU cc_start: 0.7055 (mp0) cc_final: 0.6443 (tp30) REVERT: E 82 PHE cc_start: 0.4909 (m-80) cc_final: 0.4673 (m-80) REVERT: E 101 GLN cc_start: 0.7410 (tt0) cc_final: 0.7201 (tt0) REVERT: E 106 GLN cc_start: 0.6173 (OUTLIER) cc_final: 0.5841 (tt0) REVERT: E 200 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7627 (ptp-170) REVERT: F 76 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7544 (ttpt) REVERT: F 116 ASP cc_start: 0.8650 (t70) cc_final: 0.8337 (t0) REVERT: G 73 ARG cc_start: 0.6625 (mtm180) cc_final: 0.6323 (mtm180) REVERT: G 106 ASP cc_start: 0.1669 (OUTLIER) cc_final: 0.1008 (p0) REVERT: G 205 MET cc_start: 0.3899 (mtm) cc_final: 0.3406 (mtp) REVERT: H 22 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8459 (mtmt) REVERT: H 86 ASP cc_start: 0.7487 (m-30) cc_final: 0.7225 (m-30) REVERT: H 105 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7636 (pt0) REVERT: H 126 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: I 27 ARG cc_start: 0.6568 (ttm110) cc_final: 0.6137 (mtp-110) REVERT: K 45 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7233 (mt-10) REVERT: L 33 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7677 (tp30) REVERT: L 38 LEU cc_start: 0.8192 (mt) cc_final: 0.7946 (mp) REVERT: L 63 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7333 (ptp-170) REVERT: L 68 GLU cc_start: 0.8058 (tt0) cc_final: 0.7683 (tp30) REVERT: M 81 GLU cc_start: 0.3980 (tt0) cc_final: 0.3651 (tt0) REVERT: M 166 MET cc_start: 0.4220 (OUTLIER) cc_final: 0.3574 (tpp) REVERT: M 195 GLN cc_start: 0.3709 (OUTLIER) cc_final: 0.3493 (pp30) REVERT: M 231 LEU cc_start: 0.6533 (mt) cc_final: 0.6301 (mt) REVERT: N 298 ASN cc_start: 0.5474 (OUTLIER) cc_final: 0.4871 (m110) REVERT: N 407 GLU cc_start: 0.5316 (tt0) cc_final: 0.4956 (tp30) REVERT: O 31 VAL cc_start: 0.2759 (t) cc_final: 0.2499 (p) REVERT: O 86 MET cc_start: 0.3655 (tmm) cc_final: 0.3288 (tmm) REVERT: O 125 GLU cc_start: 0.5607 (tp30) cc_final: 0.4900 (tp30) REVERT: O 275 LYS cc_start: 0.3605 (OUTLIER) cc_final: 0.2817 (tttt) REVERT: O 585 MET cc_start: 0.5281 (mtm) cc_final: 0.4684 (mtp) REVERT: P 207 PHE cc_start: 0.2088 (OUTLIER) cc_final: 0.1600 (m-80) REVERT: P 299 MET cc_start: 0.1994 (OUTLIER) cc_final: 0.1294 (mmt) REVERT: Q 116 ARG cc_start: 0.3522 (OUTLIER) cc_final: 0.3311 (mtp180) outliers start: 296 outliers final: 178 residues processed: 763 average time/residue: 0.7174 time to fit residues: 667.1733 Evaluate side-chains 719 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 511 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1301 ARG Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 166 MET Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 399 ILE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 83 ILE Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 477 TYR Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 558 SER Chi-restraints excluded: chain O residue 561 ARG Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 588 LEU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 620 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 299 MET Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 116 ARG Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 617 LYS Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 444 optimal weight: 30.0000 chunk 211 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 424 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 168 optimal weight: 0.1980 chunk 497 optimal weight: 30.0000 chunk 469 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 386 optimal weight: 0.7980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN A 753 GLN A 950 GLN A 964 ASN A1317 ASN ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 ASN C 3 ASN C 88 ASN C 172 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 32 ASN H 64 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN N 198 GLN ** O 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.198825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138686 restraints weight = 47723.688| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.81 r_work: 0.3228 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 40897 Z= 0.164 Angle : 0.634 22.173 55209 Z= 0.318 Chirality : 0.044 0.193 6221 Planarity : 0.005 0.094 7106 Dihedral : 7.861 59.575 5668 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 5.84 % Allowed : 19.75 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.99 (0.12), residues: 4976 helix: 0.36 (0.12), residues: 1814 sheet: -0.79 (0.20), residues: 586 loop : -1.37 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 797 TYR 0.021 0.002 TYR O 132 PHE 0.024 0.002 PHE B 678 TRP 0.018 0.002 TRP C 31 HIS 0.012 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00374 (40873) covalent geometry : angle 0.61052 (55176) hydrogen bonds : bond 0.04183 ( 1636) hydrogen bonds : angle 5.16421 ( 4665) metal coordination : bond 0.01142 ( 24) metal coordination : angle 6.96024 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 551 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7820 (ptt180) REVERT: A 32 VAL cc_start: 0.6650 (OUTLIER) cc_final: 0.6443 (m) REVERT: A 83 HIS cc_start: 0.5962 (p-80) cc_final: 0.5749 (p-80) REVERT: A 351 ARG cc_start: 0.4714 (OUTLIER) cc_final: 0.3649 (ttm-80) REVERT: A 446 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.7114 (p90) REVERT: A 457 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7249 (mm-40) REVERT: A 725 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: A 728 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 736 HIS cc_start: 0.6900 (t70) cc_final: 0.6039 (m-70) REVERT: A 775 GLU cc_start: 0.7240 (tp30) cc_final: 0.6942 (tp30) REVERT: A 828 GLN cc_start: 0.7687 (tp40) cc_final: 0.7458 (mm110) REVERT: A 884 TYR cc_start: 0.6956 (t80) cc_final: 0.6724 (t80) REVERT: A 1099 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6611 (tp30) REVERT: A 1121 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6995 (tm) REVERT: A 1230 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7640 (mt) REVERT: A 1262 GLN cc_start: 0.6769 (pp30) cc_final: 0.6505 (pp30) REVERT: A 1267 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7666 (tm) REVERT: A 1301 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6639 (ttp80) REVERT: A 1379 MET cc_start: 0.2495 (ppp) cc_final: 0.1822 (ppp) REVERT: B 43 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: B 198 GLU cc_start: 0.8374 (tt0) cc_final: 0.8122 (tt0) REVERT: B 201 SER cc_start: 0.8171 (p) cc_final: 0.7936 (m) REVERT: B 263 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6429 (pp) REVERT: B 296 TYR cc_start: 0.6846 (m-80) cc_final: 0.6553 (m-80) REVERT: B 378 GLU cc_start: 0.7670 (pt0) cc_final: 0.7321 (tt0) REVERT: B 435 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7506 (ttp-170) REVERT: B 469 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7494 (tpp) REVERT: B 527 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B 539 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: B 639 ASP cc_start: 0.7897 (m-30) cc_final: 0.7647 (m-30) REVERT: B 904 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7752 (mmm-85) REVERT: B 1114 GLU cc_start: 0.6798 (tp30) cc_final: 0.6447 (tt0) REVERT: C 1 MET cc_start: 0.4721 (mmm) cc_final: 0.3940 (tmm) REVERT: C 35 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7470 (tptm) REVERT: C 71 MET cc_start: 0.9336 (mtm) cc_final: 0.9037 (mtm) REVERT: C 82 TYR cc_start: 0.8585 (m-80) cc_final: 0.8179 (m-80) REVERT: C 172 GLN cc_start: 0.7608 (mm110) cc_final: 0.7229 (mm110) REVERT: C 335 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6054 (tp40) REVERT: D 2 LYS cc_start: 0.6415 (pttp) cc_final: 0.5902 (pptt) REVERT: D 8 ASN cc_start: 0.5130 (t0) cc_final: 0.4682 (m110) REVERT: E 41 ASP cc_start: 0.5966 (t0) cc_final: 0.5680 (t0) REVERT: E 67 GLU cc_start: 0.7135 (mp0) cc_final: 0.6485 (tp30) REVERT: E 79 TRP cc_start: 0.6430 (t-100) cc_final: 0.5819 (t-100) REVERT: E 101 GLN cc_start: 0.7291 (tt0) cc_final: 0.6582 (tm130) REVERT: E 106 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.5722 (tt0) REVERT: E 148 GLU cc_start: 0.7791 (pt0) cc_final: 0.7466 (pp20) REVERT: E 200 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7138 (ptp-170) REVERT: F 76 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7463 (ttpt) REVERT: F 116 ASP cc_start: 0.8622 (t70) cc_final: 0.8274 (t0) REVERT: G 73 ARG cc_start: 0.6672 (mtm180) cc_final: 0.6408 (mtm-85) REVERT: G 106 ASP cc_start: 0.2143 (OUTLIER) cc_final: 0.1445 (p0) REVERT: G 205 MET cc_start: 0.3824 (mtm) cc_final: 0.3344 (mtp) REVERT: H 86 ASP cc_start: 0.7444 (m-30) cc_final: 0.7173 (m-30) REVERT: H 105 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: H 129 TYR cc_start: 0.4177 (m-10) cc_final: 0.3970 (m-10) REVERT: I 12 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6735 (mp) REVERT: I 27 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.6084 (mtp-110) REVERT: I 43 ARG cc_start: 0.6089 (OUTLIER) cc_final: 0.5820 (ptp-170) REVERT: K 45 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7234 (mt-10) REVERT: L 33 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: L 36 SER cc_start: 0.8111 (m) cc_final: 0.7891 (p) REVERT: L 38 LEU cc_start: 0.8193 (mt) cc_final: 0.7895 (mp) REVERT: L 68 GLU cc_start: 0.8062 (tt0) cc_final: 0.7712 (tp30) REVERT: M 81 GLU cc_start: 0.4050 (tt0) cc_final: 0.3770 (tt0) REVERT: N 297 MET cc_start: 0.4031 (OUTLIER) cc_final: 0.3410 (tpt) REVERT: N 298 ASN cc_start: 0.5440 (OUTLIER) cc_final: 0.4881 (m110) REVERT: O 31 VAL cc_start: 0.2704 (t) cc_final: 0.2420 (p) REVERT: O 86 MET cc_start: 0.3594 (tmm) cc_final: 0.3178 (tmm) REVERT: O 125 GLU cc_start: 0.5604 (tp30) cc_final: 0.4913 (tp30) REVERT: O 275 LYS cc_start: 0.3580 (OUTLIER) cc_final: 0.2800 (tttt) REVERT: O 288 MET cc_start: 0.4191 (tmm) cc_final: 0.3881 (mtp) REVERT: O 312 TYR cc_start: 0.1596 (m-80) cc_final: 0.1013 (m-10) REVERT: O 511 ILE cc_start: 0.3447 (OUTLIER) cc_final: 0.3088 (tp) REVERT: O 585 MET cc_start: 0.5266 (mtm) cc_final: 0.4753 (mtp) REVERT: P 207 PHE cc_start: 0.2233 (OUTLIER) cc_final: 0.1691 (m-80) REVERT: P 299 MET cc_start: 0.1902 (OUTLIER) cc_final: 0.1247 (mmt) outliers start: 260 outliers final: 143 residues processed: 752 average time/residue: 0.7143 time to fit residues: 654.5718 Evaluate side-chains 690 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 514 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1301 ARG Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 43 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain N residue 297 MET Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 399 ILE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 323 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 477 TYR Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 561 ARG Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 620 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 299 MET Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 617 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 277 optimal weight: 9.9990 chunk 288 optimal weight: 0.2980 chunk 162 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 317 optimal weight: 7.9990 chunk 456 optimal weight: 8.9990 chunk 278 optimal weight: 0.9980 chunk 417 optimal weight: 0.9990 chunk 332 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 325 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 630 ASN A 746 ASN A 753 GLN A 950 GLN A 964 ASN A1317 ASN B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 32 ASN H 64 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 607 ASN P 193 ASN Q 31 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.200891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143859 restraints weight = 47686.310| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.61 r_work: 0.3286 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40897 Z= 0.113 Angle : 0.578 19.035 55209 Z= 0.290 Chirality : 0.043 0.193 6221 Planarity : 0.004 0.093 7106 Dihedral : 7.128 59.854 5652 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 4.90 % Allowed : 21.26 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.70 (0.12), residues: 4976 helix: 0.66 (0.12), residues: 1815 sheet: -0.69 (0.20), residues: 599 loop : -1.24 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 364 TYR 0.020 0.001 TYR O 132 PHE 0.029 0.001 PHE O 576 TRP 0.017 0.001 TRP C 31 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00251 (40873) covalent geometry : angle 0.56058 (55176) hydrogen bonds : bond 0.03557 ( 1636) hydrogen bonds : angle 4.89846 ( 4665) metal coordination : bond 0.00815 ( 24) metal coordination : angle 5.75475 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 570 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.6069 (p-80) cc_final: 0.5868 (p-80) REVERT: A 101 GLN cc_start: 0.7446 (mt0) cc_final: 0.7173 (mt0) REVERT: A 446 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7245 (p90) REVERT: A 728 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 736 HIS cc_start: 0.6836 (t70) cc_final: 0.6022 (m90) REVERT: A 884 TYR cc_start: 0.6849 (t80) cc_final: 0.6606 (t80) REVERT: A 909 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8196 (m-40) REVERT: A 1099 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6585 (tp30) REVERT: A 1142 ASN cc_start: 0.7860 (t0) cc_final: 0.7485 (m-40) REVERT: A 1230 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7610 (mt) REVERT: B 43 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7535 (m-30) REVERT: B 132 ASP cc_start: 0.6498 (m-30) cc_final: 0.6208 (m-30) REVERT: B 199 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: B 230 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7520 (mtpp) REVERT: B 263 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6331 (pp) REVERT: B 338 GLU cc_start: 0.5816 (pm20) cc_final: 0.5272 (pm20) REVERT: B 369 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7335 (mmm160) REVERT: B 378 GLU cc_start: 0.7592 (pt0) cc_final: 0.7228 (tt0) REVERT: B 435 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7462 (ttp-170) REVERT: B 527 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: B 539 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: B 636 ASP cc_start: 0.7504 (p0) cc_final: 0.7302 (p0) REVERT: B 639 ASP cc_start: 0.7826 (m-30) cc_final: 0.7578 (m-30) REVERT: B 653 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8240 (mm-30) REVERT: B 886 MET cc_start: 0.8629 (mtp) cc_final: 0.8415 (mmm) REVERT: B 904 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7720 (mmm-85) REVERT: B 1097 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7675 (mmtt) REVERT: B 1114 GLU cc_start: 0.6787 (tp30) cc_final: 0.6497 (tt0) REVERT: C 1 MET cc_start: 0.4638 (mmm) cc_final: 0.4002 (tmm) REVERT: C 32 ASN cc_start: 0.7927 (p0) cc_final: 0.7663 (t0) REVERT: C 35 LYS cc_start: 0.7637 (tmtt) cc_final: 0.7158 (tppt) REVERT: C 71 MET cc_start: 0.9246 (mtm) cc_final: 0.8930 (mtm) REVERT: C 82 TYR cc_start: 0.8560 (m-80) cc_final: 0.8101 (m-80) REVERT: C 172 GLN cc_start: 0.7576 (mm110) cc_final: 0.7312 (mm-40) REVERT: C 277 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8258 (pmt170) REVERT: C 326 GLU cc_start: 0.8255 (tt0) cc_final: 0.7944 (tt0) REVERT: C 335 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.6046 (tp40) REVERT: D 2 LYS cc_start: 0.6200 (pttp) cc_final: 0.5610 (pptt) REVERT: D 5 GLU cc_start: 0.5167 (pp20) cc_final: 0.4199 (pp20) REVERT: D 8 ASN cc_start: 0.5465 (t0) cc_final: 0.5018 (m110) REVERT: D 95 ILE cc_start: 0.3614 (OUTLIER) cc_final: 0.3306 (mp) REVERT: E 1 MET cc_start: 0.2461 (OUTLIER) cc_final: 0.0763 (pmm) REVERT: E 67 GLU cc_start: 0.7106 (mp0) cc_final: 0.6450 (tp30) REVERT: E 79 TRP cc_start: 0.6532 (t-100) cc_final: 0.5910 (t-100) REVERT: E 101 GLN cc_start: 0.7344 (tt0) cc_final: 0.6608 (tm130) REVERT: E 106 GLN cc_start: 0.6183 (mm-40) cc_final: 0.5813 (tt0) REVERT: E 148 GLU cc_start: 0.7806 (pt0) cc_final: 0.7541 (pp20) REVERT: E 191 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7169 (mmmm) REVERT: F 76 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7409 (ttpt) REVERT: F 116 ASP cc_start: 0.8538 (t70) cc_final: 0.8191 (t0) REVERT: G 46 ILE cc_start: 0.7376 (mm) cc_final: 0.7159 (mm) REVERT: G 73 ARG cc_start: 0.6776 (mtm180) cc_final: 0.6443 (mtm180) REVERT: G 106 ASP cc_start: 0.2531 (OUTLIER) cc_final: 0.1727 (p0) REVERT: H 86 ASP cc_start: 0.7412 (m-30) cc_final: 0.7148 (m-30) REVERT: H 129 TYR cc_start: 0.4225 (m-10) cc_final: 0.4008 (m-10) REVERT: I 12 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6798 (mp) REVERT: I 27 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.6038 (mtp-110) REVERT: K 45 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7311 (mt-10) REVERT: L 33 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: L 38 LEU cc_start: 0.8193 (mt) cc_final: 0.7822 (mp) REVERT: L 68 GLU cc_start: 0.7969 (tt0) cc_final: 0.7634 (tp30) REVERT: M 81 GLU cc_start: 0.4158 (tt0) cc_final: 0.3842 (tt0) REVERT: M 156 ASN cc_start: 0.7524 (m-40) cc_final: 0.7290 (m-40) REVERT: M 158 GLN cc_start: 0.6468 (tp40) cc_final: 0.6252 (tp-100) REVERT: M 167 GLN cc_start: 0.5518 (mt0) cc_final: 0.4993 (mp10) REVERT: N 297 MET cc_start: 0.3939 (OUTLIER) cc_final: 0.3542 (tpt) REVERT: N 298 ASN cc_start: 0.5402 (OUTLIER) cc_final: 0.4893 (m110) REVERT: N 303 ARG cc_start: 0.5348 (mmm160) cc_final: 0.5135 (mmm160) REVERT: N 399 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.5267 (tp) REVERT: O 31 VAL cc_start: 0.2783 (t) cc_final: 0.2390 (p) REVERT: O 86 MET cc_start: 0.3493 (tmm) cc_final: 0.3064 (tmm) REVERT: O 109 GLU cc_start: 0.2697 (mm-30) cc_final: 0.2184 (mt-10) REVERT: O 125 GLU cc_start: 0.5679 (tp30) cc_final: 0.4934 (tp30) REVERT: O 275 LYS cc_start: 0.3466 (OUTLIER) cc_final: 0.2737 (tttt) REVERT: O 288 MET cc_start: 0.4200 (tmm) cc_final: 0.3887 (mtp) REVERT: O 312 TYR cc_start: 0.1716 (m-80) cc_final: 0.1172 (m-10) REVERT: O 574 TYR cc_start: 0.5196 (m-80) cc_final: 0.4980 (m-80) REVERT: O 585 MET cc_start: 0.5282 (mtm) cc_final: 0.4773 (mtp) REVERT: O 589 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5581 (mt) REVERT: P 207 PHE cc_start: 0.2040 (OUTLIER) cc_final: 0.1534 (m-80) REVERT: W 619 MET cc_start: 0.4447 (mtt) cc_final: 0.4205 (mpp) outliers start: 218 outliers final: 104 residues processed: 741 average time/residue: 0.7176 time to fit residues: 647.7980 Evaluate side-chains 651 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 519 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 297 MET Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 399 ILE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 618 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 351 optimal weight: 10.0000 chunk 442 optimal weight: 20.0000 chunk 258 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 315 optimal weight: 5.9990 chunk 392 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 485 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 630 ASN A 746 ASN A 828 GLN A 950 GLN A 964 ASN A1317 ASN ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 88 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 32 ASN H 137 GLN ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN ** O 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 549 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.197802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137009 restraints weight = 47905.151| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.74 r_work: 0.3222 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 40897 Z= 0.240 Angle : 0.693 20.181 55209 Z= 0.348 Chirality : 0.047 0.317 6221 Planarity : 0.005 0.093 7106 Dihedral : 7.213 59.536 5610 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 5.93 % Allowed : 21.30 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.91 (0.12), residues: 4976 helix: 0.39 (0.12), residues: 1817 sheet: -0.74 (0.20), residues: 605 loop : -1.29 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 797 TYR 0.023 0.002 TYR O 132 PHE 0.029 0.002 PHE O 576 TRP 0.017 0.002 TRP C 31 HIS 0.012 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00563 (40873) covalent geometry : angle 0.67482 (55176) hydrogen bonds : bond 0.04445 ( 1636) hydrogen bonds : angle 5.15655 ( 4665) metal coordination : bond 0.01083 ( 24) metal coordination : angle 6.52494 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 525 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.6039 (p-80) cc_final: 0.5774 (p-80) REVERT: A 101 GLN cc_start: 0.7442 (mt0) cc_final: 0.7172 (mt0) REVERT: A 351 ARG cc_start: 0.4734 (OUTLIER) cc_final: 0.3621 (ttm-80) REVERT: A 446 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7322 (p90) REVERT: A 457 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7220 (mm-40) REVERT: A 728 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 736 HIS cc_start: 0.6860 (t70) cc_final: 0.6035 (m90) REVERT: A 884 TYR cc_start: 0.6959 (t80) cc_final: 0.6712 (t80) REVERT: A 909 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8231 (m-40) REVERT: A 1099 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6537 (tp30) REVERT: A 1121 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6946 (tm) REVERT: A 1230 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 1262 GLN cc_start: 0.6903 (pp30) cc_final: 0.6547 (pp30) REVERT: A 1301 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6327 (ttp80) REVERT: B 43 ASP cc_start: 0.7903 (m-30) cc_final: 0.7565 (m-30) REVERT: B 90 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5110 (pm20) REVERT: B 263 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6357 (pp) REVERT: B 338 GLU cc_start: 0.5978 (pm20) cc_final: 0.5440 (pm20) REVERT: B 369 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7401 (mmm160) REVERT: B 378 GLU cc_start: 0.7693 (pt0) cc_final: 0.7399 (tt0) REVERT: B 527 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: B 539 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: B 584 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8318 (m) REVERT: B 639 ASP cc_start: 0.7888 (m-30) cc_final: 0.7628 (m-30) REVERT: B 656 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6722 (m-30) REVERT: B 1101 MET cc_start: 0.8163 (mtm) cc_final: 0.7667 (ptt) REVERT: B 1114 GLU cc_start: 0.6868 (tp30) cc_final: 0.6578 (tt0) REVERT: C 1 MET cc_start: 0.4797 (mmm) cc_final: 0.4033 (tmm) REVERT: C 35 LYS cc_start: 0.7672 (tmtt) cc_final: 0.7453 (tptm) REVERT: C 71 MET cc_start: 0.9346 (mtm) cc_final: 0.9114 (mtm) REVERT: C 172 GLN cc_start: 0.7602 (mm110) cc_final: 0.7241 (mm110) REVERT: C 326 GLU cc_start: 0.8301 (tt0) cc_final: 0.8027 (tt0) REVERT: D 2 LYS cc_start: 0.6359 (pttp) cc_final: 0.5805 (pptt) REVERT: D 8 ASN cc_start: 0.5435 (t0) cc_final: 0.4981 (m110) REVERT: E 67 GLU cc_start: 0.7133 (mp0) cc_final: 0.6482 (tp30) REVERT: E 101 GLN cc_start: 0.7336 (tt0) cc_final: 0.6610 (tm130) REVERT: E 106 GLN cc_start: 0.5929 (OUTLIER) cc_final: 0.5634 (tt0) REVERT: E 148 GLU cc_start: 0.7866 (pt0) cc_final: 0.7538 (pp20) REVERT: E 191 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7264 (mmmm) REVERT: E 200 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7556 (ptp-170) REVERT: F 76 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7437 (ttpt) REVERT: F 116 ASP cc_start: 0.8647 (t70) cc_final: 0.8310 (t0) REVERT: G 73 ARG cc_start: 0.6735 (mtm180) cc_final: 0.6471 (mtm180) REVERT: G 106 ASP cc_start: 0.2351 (OUTLIER) cc_final: 0.1559 (p0) REVERT: G 205 MET cc_start: 0.3783 (OUTLIER) cc_final: 0.3462 (mtp) REVERT: H 126 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: I 27 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6111 (mtp-110) REVERT: K 45 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7290 (mt-10) REVERT: L 33 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: L 38 LEU cc_start: 0.8138 (mt) cc_final: 0.7879 (mp) REVERT: L 68 GLU cc_start: 0.8010 (tt0) cc_final: 0.7648 (tp30) REVERT: M 81 GLU cc_start: 0.4131 (tt0) cc_final: 0.3579 (mp0) REVERT: M 195 GLN cc_start: 0.3011 (OUTLIER) cc_final: 0.2691 (pp30) REVERT: N 298 ASN cc_start: 0.5536 (OUTLIER) cc_final: 0.4955 (m110) REVERT: N 399 ILE cc_start: 0.5741 (OUTLIER) cc_final: 0.5472 (tp) REVERT: O 31 VAL cc_start: 0.2621 (t) cc_final: 0.2344 (p) REVERT: O 109 GLU cc_start: 0.3017 (mm-30) cc_final: 0.2661 (mt-10) REVERT: O 125 GLU cc_start: 0.5698 (tp30) cc_final: 0.4996 (tp30) REVERT: O 275 LYS cc_start: 0.3433 (OUTLIER) cc_final: 0.2717 (tttt) REVERT: O 288 MET cc_start: 0.4304 (tmm) cc_final: 0.3987 (mtp) REVERT: O 312 TYR cc_start: 0.1786 (m-80) cc_final: 0.1311 (m-10) REVERT: O 487 LEU cc_start: 0.2251 (OUTLIER) cc_final: 0.2007 (pp) REVERT: O 511 ILE cc_start: 0.3592 (OUTLIER) cc_final: 0.3253 (tp) REVERT: O 585 MET cc_start: 0.5254 (mtm) cc_final: 0.4704 (mtp) REVERT: O 589 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5545 (mt) REVERT: O 635 LEU cc_start: 0.5039 (mt) cc_final: 0.4816 (tp) REVERT: P 207 PHE cc_start: 0.2159 (OUTLIER) cc_final: 0.1694 (m-80) REVERT: P 269 LEU cc_start: 0.1802 (OUTLIER) cc_final: 0.1189 (tt) REVERT: P 299 MET cc_start: 0.1848 (OUTLIER) cc_final: 0.1181 (mmt) REVERT: Q 116 ARG cc_start: 0.3342 (OUTLIER) cc_final: 0.2287 (mmp-170) REVERT: W 617 LYS cc_start: 0.4280 (OUTLIER) cc_final: 0.3978 (ttpp) outliers start: 264 outliers final: 157 residues processed: 733 average time/residue: 0.7043 time to fit residues: 628.7055 Evaluate side-chains 694 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 502 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 890 MET Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1301 ARG Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 235 LYS Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 399 ILE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 323 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 377 ARG Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 618 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 299 MET Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 116 ARG Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 617 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 49 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 482 optimal weight: 8.9990 chunk 402 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 746 ASN A 753 GLN A 950 GLN A 964 ASN A1317 ASN B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN H 137 GLN M 156 ASN ** N 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 254 ASN ** 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 = 0.4282 r_free = 0.4282 target = 0.199597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142406 restraints weight = 47889.200| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.64 r_work: 0.3261 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40897 Z= 0.145 Angle : 0.614 18.280 55209 Z= 0.307 Chirality : 0.044 0.314 6221 Planarity : 0.004 0.093 7106 Dihedral : 6.930 59.760 5607 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 4.90 % Allowed : 22.58 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.77 (0.12), residues: 4976 helix: 0.58 (0.12), residues: 1817 sheet: -0.70 (0.21), residues: 597 loop : -1.26 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 364 TYR 0.021 0.001 TYR O 132 PHE 0.035 0.001 PHE O 576 TRP 0.018 0.001 TRP C 31 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00331 (40873) covalent geometry : angle 0.59735 (55176) hydrogen bonds : bond 0.03802 ( 1636) hydrogen bonds : angle 4.99826 ( 4665) metal coordination : bond 0.00867 ( 24) metal coordination : angle 5.84441 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 527 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.5993 (p-80) cc_final: 0.5712 (p-80) REVERT: A 101 GLN cc_start: 0.7379 (mt0) cc_final: 0.7135 (mt0) REVERT: A 351 ARG cc_start: 0.4734 (OUTLIER) cc_final: 0.3620 (ttm-80) REVERT: A 446 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7357 (p90) REVERT: A 728 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 736 HIS cc_start: 0.6795 (t70) cc_final: 0.6033 (m90) REVERT: A 884 TYR cc_start: 0.6871 (t80) cc_final: 0.6648 (t80) REVERT: A 1099 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: A 1121 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7007 (tm) REVERT: A 1230 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7551 (mt) REVERT: A 1262 GLN cc_start: 0.6905 (pp30) cc_final: 0.6568 (pp30) REVERT: A 1290 LYS cc_start: 0.5197 (tptt) cc_final: 0.4621 (mtmm) REVERT: A 1348 MET cc_start: 0.6035 (mmp) cc_final: 0.5736 (mmp) REVERT: B 43 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: B 230 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7576 (mtpp) REVERT: B 263 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6270 (pp) REVERT: B 309 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7021 (m) REVERT: B 332 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6871 (mm) REVERT: B 338 GLU cc_start: 0.5886 (pm20) cc_final: 0.5431 (pm20) REVERT: B 369 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7412 (mmm160) REVERT: B 378 GLU cc_start: 0.7656 (pt0) cc_final: 0.7392 (tt0) REVERT: B 527 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: B 539 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: B 639 ASP cc_start: 0.7823 (m-30) cc_final: 0.7561 (m-30) REVERT: B 653 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: B 904 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7773 (mmm-85) REVERT: B 1101 MET cc_start: 0.8284 (mtm) cc_final: 0.8041 (mpp) REVERT: B 1114 GLU cc_start: 0.6816 (tp30) cc_final: 0.6557 (tt0) REVERT: C 1 MET cc_start: 0.4691 (mmm) cc_final: 0.4008 (tmm) REVERT: C 35 LYS cc_start: 0.7622 (tmtt) cc_final: 0.6638 (ttpt) REVERT: C 172 GLN cc_start: 0.7570 (mm110) cc_final: 0.7227 (mm110) REVERT: C 326 GLU cc_start: 0.8286 (tt0) cc_final: 0.7981 (tt0) REVERT: D 2 LYS cc_start: 0.6377 (pttp) cc_final: 0.5763 (pptt) REVERT: D 8 ASN cc_start: 0.5466 (t0) cc_final: 0.4999 (m110) REVERT: D 95 ILE cc_start: 0.3705 (OUTLIER) cc_final: 0.3375 (mp) REVERT: E 67 GLU cc_start: 0.7132 (mp0) cc_final: 0.6477 (tp30) REVERT: E 101 GLN cc_start: 0.7395 (tt0) cc_final: 0.6675 (tm130) REVERT: E 106 GLN cc_start: 0.5931 (OUTLIER) cc_final: 0.5610 (tt0) REVERT: E 148 GLU cc_start: 0.7826 (pt0) cc_final: 0.7538 (pp20) REVERT: E 191 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7146 (mmmm) REVERT: E 200 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7417 (ptp-170) REVERT: F 76 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7363 (ttpt) REVERT: F 116 ASP cc_start: 0.8598 (t70) cc_final: 0.8236 (t0) REVERT: G 73 ARG cc_start: 0.6755 (mtm180) cc_final: 0.6508 (mtm180) REVERT: G 106 ASP cc_start: 0.2478 (OUTLIER) cc_final: 0.1670 (p0) REVERT: H 105 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: H 126 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: H 129 TYR cc_start: 0.4307 (m-10) cc_final: 0.4090 (m-10) REVERT: I 10 ASN cc_start: 0.7574 (t0) cc_final: 0.7345 (t0) REVERT: I 12 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6718 (mp) REVERT: I 16 SER cc_start: 0.3607 (OUTLIER) cc_final: 0.3119 (p) REVERT: I 27 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6113 (mtp-110) REVERT: L 33 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: L 38 LEU cc_start: 0.8136 (mt) cc_final: 0.7829 (mp) REVERT: L 68 GLU cc_start: 0.7956 (tt0) cc_final: 0.7607 (tp30) REVERT: M 81 GLU cc_start: 0.4182 (tt0) cc_final: 0.3606 (mp0) REVERT: N 294 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6037 (mt) REVERT: N 298 ASN cc_start: 0.5383 (OUTLIER) cc_final: 0.4740 (m110) REVERT: N 303 ARG cc_start: 0.5450 (mmm160) cc_final: 0.5139 (mmm160) REVERT: N 399 ILE cc_start: 0.5584 (OUTLIER) cc_final: 0.5305 (tp) REVERT: O 31 VAL cc_start: 0.2434 (t) cc_final: 0.2142 (p) REVERT: O 86 MET cc_start: 0.3480 (tmm) cc_final: 0.3037 (tmm) REVERT: O 125 GLU cc_start: 0.5699 (tp30) cc_final: 0.4998 (tp30) REVERT: O 140 ILE cc_start: 0.3203 (OUTLIER) cc_final: 0.2786 (mt) REVERT: O 275 LYS cc_start: 0.3360 (OUTLIER) cc_final: 0.2647 (tttt) REVERT: O 288 MET cc_start: 0.4440 (tmm) cc_final: 0.4119 (mtp) REVERT: O 312 TYR cc_start: 0.1927 (m-80) cc_final: 0.1522 (m-10) REVERT: O 574 TYR cc_start: 0.5307 (m-80) cc_final: 0.4988 (m-80) REVERT: O 585 MET cc_start: 0.5133 (mtm) cc_final: 0.4605 (mtp) REVERT: O 589 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5731 (mt) REVERT: P 207 PHE cc_start: 0.2154 (OUTLIER) cc_final: 0.1723 (m-80) REVERT: P 269 LEU cc_start: 0.1752 (OUTLIER) cc_final: 0.1147 (tt) REVERT: P 299 MET cc_start: 0.1681 (OUTLIER) cc_final: 0.1021 (mmt) REVERT: Q 116 ARG cc_start: 0.3365 (OUTLIER) cc_final: 0.2281 (mmp-170) outliers start: 218 outliers final: 133 residues processed: 700 average time/residue: 0.7288 time to fit residues: 620.1218 Evaluate side-chains 672 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 504 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 399 ILE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 270 SER Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 323 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 377 ARG Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 618 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 299 MET Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 116 ARG Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 318 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 301 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 445 optimal weight: 20.0000 chunk 408 optimal weight: 0.0970 chunk 283 optimal weight: 7.9990 chunk 455 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 746 ASN A 753 GLN A 950 GLN A 964 ASN A1317 ASN ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN H 137 GLN ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 254 ASN ** 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 = 0.4266 r_free = 0.4266 target = 0.198045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139767 restraints weight = 47570.578| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.65 r_work: 0.3236 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 40897 Z= 0.214 Angle : 0.679 18.525 55209 Z= 0.339 Chirality : 0.046 0.318 6221 Planarity : 0.005 0.093 7106 Dihedral : 7.118 59.241 5606 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 5.35 % Allowed : 22.22 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.90 (0.12), residues: 4976 helix: 0.41 (0.12), residues: 1822 sheet: -0.72 (0.20), residues: 611 loop : -1.30 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 509 TYR 0.024 0.002 TYR E 112 PHE 0.034 0.002 PHE O 576 TRP 0.018 0.002 TRP C 31 HIS 0.012 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00498 (40873) covalent geometry : angle 0.65931 (55176) hydrogen bonds : bond 0.04286 ( 1636) hydrogen bonds : angle 5.13988 ( 4665) metal coordination : bond 0.01125 ( 24) metal coordination : angle 6.68402 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 526 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.6065 (p-80) cc_final: 0.5797 (p-80) REVERT: A 101 GLN cc_start: 0.7378 (mt0) cc_final: 0.7177 (mt0) REVERT: A 351 ARG cc_start: 0.4751 (OUTLIER) cc_final: 0.3641 (ttm-80) REVERT: A 446 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.7330 (p90) REVERT: A 457 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7252 (mm-40) REVERT: A 728 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A 736 HIS cc_start: 0.6836 (t70) cc_final: 0.6052 (m90) REVERT: A 746 ASN cc_start: 0.6457 (m-40) cc_final: 0.6251 (m-40) REVERT: A 884 TYR cc_start: 0.6912 (t80) cc_final: 0.6678 (t80) REVERT: A 909 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8237 (m-40) REVERT: A 1099 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6545 (tp30) REVERT: A 1121 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6887 (tm) REVERT: A 1230 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7553 (mt) REVERT: A 1260 MET cc_start: 0.7364 (mmm) cc_final: 0.7029 (mmt) REVERT: A 1262 GLN cc_start: 0.6971 (pp30) cc_final: 0.6649 (pp30) REVERT: A 1348 MET cc_start: 0.6007 (mmp) cc_final: 0.5677 (mmp) REVERT: A 1373 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4959 (pmm-80) REVERT: B 43 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: B 230 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7566 (mtpp) REVERT: B 263 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6301 (pp) REVERT: B 369 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7405 (mmm160) REVERT: B 469 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7556 (tpp) REVERT: B 527 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: B 639 ASP cc_start: 0.7893 (m-30) cc_final: 0.7619 (m-30) REVERT: B 656 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: B 705 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8001 (mpp) REVERT: B 1101 MET cc_start: 0.8283 (mtm) cc_final: 0.7817 (ptt) REVERT: B 1114 GLU cc_start: 0.6843 (tp30) cc_final: 0.6568 (tt0) REVERT: C 1 MET cc_start: 0.4684 (mmm) cc_final: 0.4000 (tmm) REVERT: C 35 LYS cc_start: 0.7657 (tmtt) cc_final: 0.7427 (tptm) REVERT: C 71 MET cc_start: 0.9356 (mtm) cc_final: 0.9079 (mtm) REVERT: C 172 GLN cc_start: 0.7575 (mm110) cc_final: 0.7242 (mm110) REVERT: C 326 GLU cc_start: 0.8301 (tt0) cc_final: 0.8015 (tt0) REVERT: D 2 LYS cc_start: 0.6352 (pttp) cc_final: 0.5897 (pptt) REVERT: D 8 ASN cc_start: 0.5567 (t0) cc_final: 0.4975 (m110) REVERT: D 25 LYS cc_start: 0.4985 (mmmt) cc_final: 0.4517 (tptt) REVERT: E 46 TYR cc_start: 0.4917 (m-80) cc_final: 0.4507 (m-80) REVERT: E 67 GLU cc_start: 0.7170 (mp0) cc_final: 0.6526 (tp30) REVERT: E 101 GLN cc_start: 0.7306 (tt0) cc_final: 0.6626 (tm130) REVERT: E 106 GLN cc_start: 0.5927 (OUTLIER) cc_final: 0.5630 (tt0) REVERT: E 148 GLU cc_start: 0.7855 (pt0) cc_final: 0.7532 (pp20) REVERT: E 191 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7255 (mmmm) REVERT: E 200 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7569 (ptp-170) REVERT: F 76 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7391 (ttpt) REVERT: F 116 ASP cc_start: 0.8620 (t70) cc_final: 0.8264 (t0) REVERT: G 73 ARG cc_start: 0.6779 (mtm180) cc_final: 0.6525 (mtm180) REVERT: G 106 ASP cc_start: 0.2054 (OUTLIER) cc_final: 0.1236 (p0) REVERT: G 205 MET cc_start: 0.3847 (OUTLIER) cc_final: 0.3518 (mtp) REVERT: H 105 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: H 126 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: I 16 SER cc_start: 0.3578 (OUTLIER) cc_final: 0.3096 (p) REVERT: I 27 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6267 (mtp-110) REVERT: K 87 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8502 (pp20) REVERT: L 33 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: L 38 LEU cc_start: 0.8134 (mt) cc_final: 0.7892 (mp) REVERT: L 68 GLU cc_start: 0.7988 (tt0) cc_final: 0.7644 (tp30) REVERT: M 81 GLU cc_start: 0.4252 (tt0) cc_final: 0.3742 (mp0) REVERT: M 195 GLN cc_start: 0.3171 (OUTLIER) cc_final: 0.2843 (pp30) REVERT: N 210 GLU cc_start: 0.3580 (pt0) cc_final: 0.2461 (tm-30) REVERT: N 294 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5921 (mt) REVERT: N 298 ASN cc_start: 0.5423 (OUTLIER) cc_final: 0.4866 (m110) REVERT: N 399 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5514 (tp) REVERT: O 31 VAL cc_start: 0.2422 (t) cc_final: 0.2171 (p) REVERT: O 86 MET cc_start: 0.3589 (tmm) cc_final: 0.3229 (tmm) REVERT: O 125 GLU cc_start: 0.5702 (tp30) cc_final: 0.5036 (tp30) REVERT: O 140 ILE cc_start: 0.3003 (OUTLIER) cc_final: 0.2360 (mt) REVERT: O 275 LYS cc_start: 0.3557 (OUTLIER) cc_final: 0.2734 (tttt) REVERT: O 288 MET cc_start: 0.4459 (tmm) cc_final: 0.4074 (mtp) REVERT: O 312 TYR cc_start: 0.1719 (m-80) cc_final: 0.1365 (m-10) REVERT: O 516 LEU cc_start: 0.2236 (OUTLIER) cc_final: 0.1878 (tp) REVERT: O 574 TYR cc_start: 0.5307 (m-80) cc_final: 0.4973 (m-80) REVERT: O 585 MET cc_start: 0.5124 (mtm) cc_final: 0.4623 (mtp) REVERT: O 589 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5680 (mt) REVERT: O 635 LEU cc_start: 0.5226 (mt) cc_final: 0.4918 (tp) REVERT: P 207 PHE cc_start: 0.2170 (OUTLIER) cc_final: 0.1742 (m-80) REVERT: P 269 LEU cc_start: 0.1762 (OUTLIER) cc_final: 0.1143 (tt) REVERT: P 299 MET cc_start: 0.1675 (OUTLIER) cc_final: 0.1012 (mmt) REVERT: Q 116 ARG cc_start: 0.3256 (OUTLIER) cc_final: 0.2246 (mmp-170) outliers start: 238 outliers final: 162 residues processed: 715 average time/residue: 0.7252 time to fit residues: 632.2036 Evaluate side-chains 714 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 514 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 245 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 399 ILE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 270 SER Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 323 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 377 ARG Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 618 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 299 MET Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 116 ARG Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 249 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 465 optimal weight: 8.9990 chunk 457 optimal weight: 7.9990 chunk 404 optimal weight: 0.5980 chunk 263 optimal weight: 1.9990 chunk 328 optimal weight: 0.8980 chunk 398 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 72 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 ASN A 753 GLN A 950 GLN A 964 ASN A1142 ASN A1218 GLN A1317 ASN A1395 HIS B 144 HIS B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN M 156 ASN ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 421 GLN ** O 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.201299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142374 restraints weight = 48042.074| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.66 r_work: 0.3292 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40897 Z= 0.116 Angle : 0.593 14.853 55209 Z= 0.296 Chirality : 0.043 0.245 6221 Planarity : 0.004 0.092 7106 Dihedral : 6.561 59.270 5606 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 3.66 % Allowed : 23.96 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.60 (0.12), residues: 4976 helix: 0.73 (0.12), residues: 1828 sheet: -0.65 (0.21), residues: 590 loop : -1.17 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 509 TYR 0.020 0.001 TYR O 132 PHE 0.039 0.001 PHE O 576 TRP 0.017 0.001 TRP C 31 HIS 0.011 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00251 (40873) covalent geometry : angle 0.57820 (55176) hydrogen bonds : bond 0.03436 ( 1636) hydrogen bonds : angle 4.87135 ( 4665) metal coordination : bond 0.00682 ( 24) metal coordination : angle 5.34480 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 552 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.6012 (p-80) cc_final: 0.5711 (p-80) REVERT: A 446 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7321 (p90) REVERT: A 728 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 736 HIS cc_start: 0.6885 (t70) cc_final: 0.6066 (m90) REVERT: A 884 TYR cc_start: 0.6795 (t80) cc_final: 0.6584 (t80) REVERT: A 1099 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6623 (tp30) REVERT: A 1142 ASN cc_start: 0.7728 (t0) cc_final: 0.7357 (m-40) REVERT: A 1230 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7470 (mt) REVERT: A 1260 MET cc_start: 0.7257 (mmm) cc_final: 0.6958 (mmt) REVERT: A 1290 LYS cc_start: 0.4959 (tptt) cc_final: 0.4671 (mmtp) REVERT: A 1292 GLU cc_start: 0.7189 (pm20) cc_final: 0.6974 (pm20) REVERT: B 43 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: B 132 ASP cc_start: 0.6522 (m-30) cc_final: 0.6260 (m-30) REVERT: B 232 TYR cc_start: 0.8023 (m-80) cc_final: 0.7737 (m-80) REVERT: B 263 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6090 (pp) REVERT: B 369 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7443 (mmm160) REVERT: B 435 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7442 (ttp-170) REVERT: B 527 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: B 639 ASP cc_start: 0.7814 (m-30) cc_final: 0.7561 (m-30) REVERT: B 886 MET cc_start: 0.8598 (mtp) cc_final: 0.8391 (mmm) REVERT: B 904 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7594 (mmm-85) REVERT: B 1097 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7733 (mmtt) REVERT: B 1114 GLU cc_start: 0.6884 (tp30) cc_final: 0.6629 (tt0) REVERT: C 1 MET cc_start: 0.4741 (mmm) cc_final: 0.4073 (tmm) REVERT: C 32 ASN cc_start: 0.7898 (p0) cc_final: 0.7683 (t0) REVERT: C 35 LYS cc_start: 0.7632 (tmtt) cc_final: 0.7136 (tppt) REVERT: C 82 TYR cc_start: 0.8533 (m-80) cc_final: 0.8118 (m-80) REVERT: C 172 GLN cc_start: 0.7647 (mm110) cc_final: 0.7319 (mm110) REVERT: C 242 GLU cc_start: 0.6452 (pm20) cc_final: 0.6172 (pt0) REVERT: C 326 GLU cc_start: 0.8217 (tt0) cc_final: 0.7907 (tt0) REVERT: C 335 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6088 (tp40) REVERT: D 2 LYS cc_start: 0.6314 (pttp) cc_final: 0.5847 (pptt) REVERT: D 8 ASN cc_start: 0.5463 (t0) cc_final: 0.4895 (m110) REVERT: D 95 ILE cc_start: 0.3560 (OUTLIER) cc_final: 0.3264 (mt) REVERT: D 151 GLU cc_start: 0.1875 (OUTLIER) cc_final: 0.1568 (pm20) REVERT: E 14 ARG cc_start: 0.6709 (mtm180) cc_final: 0.6274 (mtp85) REVERT: E 46 TYR cc_start: 0.4976 (m-80) cc_final: 0.4601 (m-80) REVERT: E 60 PHE cc_start: 0.5884 (p90) cc_final: 0.5638 (p90) REVERT: E 67 GLU cc_start: 0.7239 (mp0) cc_final: 0.6556 (tp30) REVERT: E 79 TRP cc_start: 0.6616 (t-100) cc_final: 0.6061 (t-100) REVERT: E 101 GLN cc_start: 0.7407 (tt0) cc_final: 0.6569 (tm130) REVERT: E 106 GLN cc_start: 0.6199 (mm-40) cc_final: 0.5660 (tp40) REVERT: E 148 GLU cc_start: 0.7801 (pt0) cc_final: 0.7530 (pp20) REVERT: E 191 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7135 (mmmm) REVERT: F 116 ASP cc_start: 0.8550 (t70) cc_final: 0.8150 (t0) REVERT: G 106 ASP cc_start: 0.2464 (OUTLIER) cc_final: 0.1672 (p0) REVERT: H 87 ARG cc_start: 0.6467 (mmm160) cc_final: 0.5883 (ttm170) REVERT: H 126 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: I 10 ASN cc_start: 0.7625 (t0) cc_final: 0.7422 (t0) REVERT: I 12 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6825 (mp) REVERT: I 16 SER cc_start: 0.3553 (OUTLIER) cc_final: 0.3080 (p) REVERT: J 23 ASN cc_start: 0.7745 (t0) cc_final: 0.7427 (m110) REVERT: K 45 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7318 (mt-10) REVERT: K 48 LYS cc_start: 0.8476 (mttm) cc_final: 0.7479 (tttt) REVERT: K 129 ASP cc_start: 0.8299 (m-30) cc_final: 0.7873 (m-30) REVERT: K 137 GLU cc_start: 0.7663 (tt0) cc_final: 0.7392 (pt0) REVERT: L 33 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7684 (tp30) REVERT: L 38 LEU cc_start: 0.8159 (mt) cc_final: 0.7825 (mp) REVERT: L 68 GLU cc_start: 0.7894 (tt0) cc_final: 0.7595 (tp30) REVERT: M 81 GLU cc_start: 0.4301 (tt0) cc_final: 0.3934 (mp0) REVERT: M 166 MET cc_start: 0.4090 (tpt) cc_final: 0.3871 (tpp) REVERT: M 167 GLN cc_start: 0.5570 (mt0) cc_final: 0.5036 (mp10) REVERT: N 210 GLU cc_start: 0.3636 (pt0) cc_final: 0.2542 (tm-30) REVERT: N 294 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6065 (mt) REVERT: N 296 LYS cc_start: 0.6618 (mmmm) cc_final: 0.5988 (tptt) REVERT: N 297 MET cc_start: 0.4363 (mmm) cc_final: 0.4100 (ttm) REVERT: N 298 ASN cc_start: 0.5513 (OUTLIER) cc_final: 0.4957 (m110) REVERT: N 399 ILE cc_start: 0.5534 (OUTLIER) cc_final: 0.5261 (tp) REVERT: O 31 VAL cc_start: 0.2575 (t) cc_final: 0.2245 (p) REVERT: O 48 LEU cc_start: 0.6681 (tp) cc_final: 0.6463 (tp) REVERT: O 86 MET cc_start: 0.3220 (tmm) cc_final: 0.2807 (tmm) REVERT: O 125 GLU cc_start: 0.5648 (tp30) cc_final: 0.4951 (tp30) REVERT: O 275 LYS cc_start: 0.3415 (OUTLIER) cc_final: 0.2632 (tttt) REVERT: O 288 MET cc_start: 0.4394 (tmm) cc_final: 0.3967 (mtp) REVERT: O 312 TYR cc_start: 0.1872 (m-80) cc_final: 0.1536 (m-10) REVERT: O 516 LEU cc_start: 0.2318 (OUTLIER) cc_final: 0.1990 (tp) REVERT: O 574 TYR cc_start: 0.5140 (m-80) cc_final: 0.4940 (m-80) REVERT: O 585 MET cc_start: 0.5179 (mtm) cc_final: 0.4692 (mtp) REVERT: O 589 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5742 (mt) REVERT: P 207 PHE cc_start: 0.2133 (OUTLIER) cc_final: 0.1502 (m-10) REVERT: P 269 LEU cc_start: 0.1776 (OUTLIER) cc_final: 0.1168 (tt) REVERT: W 619 MET cc_start: 0.4320 (mtt) cc_final: 0.4116 (mpp) outliers start: 163 outliers final: 100 residues processed: 683 average time/residue: 0.7412 time to fit residues: 616.0436 Evaluate side-chains 636 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 511 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 399 ILE Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 323 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 377 ARG Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 404 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 328 optimal weight: 0.9990 chunk 324 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A 808 GLN A 950 GLN A 964 ASN A1317 ASN B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN H 137 GLN O 56 HIS ** O 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.200392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140887 restraints weight = 47711.727| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.59 r_work: 0.3280 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40897 Z= 0.137 Angle : 0.611 15.744 55209 Z= 0.305 Chirality : 0.044 0.261 6221 Planarity : 0.004 0.091 7106 Dihedral : 6.445 58.545 5585 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 3.35 % Allowed : 24.47 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.59 (0.12), residues: 4976 helix: 0.73 (0.12), residues: 1828 sheet: -0.62 (0.21), residues: 590 loop : -1.16 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 509 TYR 0.024 0.001 TYR O 132 PHE 0.048 0.002 PHE P 191 TRP 0.017 0.002 TRP C 31 HIS 0.009 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00315 (40873) covalent geometry : angle 0.59701 (55176) hydrogen bonds : bond 0.03629 ( 1636) hydrogen bonds : angle 4.88364 ( 4665) metal coordination : bond 0.00686 ( 24) metal coordination : angle 5.37808 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 518 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.6034 (p-80) cc_final: 0.5698 (p-80) REVERT: A 240 GLU cc_start: 0.5594 (tp30) cc_final: 0.5334 (tt0) REVERT: A 446 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7310 (p90) REVERT: A 728 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 736 HIS cc_start: 0.6854 (t70) cc_final: 0.6011 (m90) REVERT: A 884 TYR cc_start: 0.6811 (t80) cc_final: 0.6555 (t80) REVERT: A 1099 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6568 (tp30) REVERT: A 1121 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7208 (tm) REVERT: A 1142 ASN cc_start: 0.7728 (t0) cc_final: 0.7346 (m-40) REVERT: A 1230 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7404 (mt) REVERT: A 1260 MET cc_start: 0.7283 (mmm) cc_final: 0.6990 (mmt) REVERT: A 1290 LYS cc_start: 0.5091 (tptt) cc_final: 0.4518 (mtmm) REVERT: A 1292 GLU cc_start: 0.7096 (pm20) cc_final: 0.6887 (pm20) REVERT: B 43 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: B 132 ASP cc_start: 0.6531 (m-30) cc_final: 0.6255 (m-30) REVERT: B 263 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6089 (pp) REVERT: B 309 VAL cc_start: 0.7004 (OUTLIER) cc_final: 0.6574 (m) REVERT: B 369 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7405 (mmm160) REVERT: B 527 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: B 639 ASP cc_start: 0.7805 (m-30) cc_final: 0.7465 (m-30) REVERT: B 904 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7705 (mmm-85) REVERT: B 1114 GLU cc_start: 0.6885 (tp30) cc_final: 0.6613 (tt0) REVERT: C 1 MET cc_start: 0.4631 (mmm) cc_final: 0.3999 (tmm) REVERT: C 32 ASN cc_start: 0.7853 (p0) cc_final: 0.7627 (t0) REVERT: C 71 MET cc_start: 0.9294 (mtm) cc_final: 0.9059 (mtm) REVERT: C 172 GLN cc_start: 0.7625 (mm110) cc_final: 0.7291 (mm110) REVERT: C 242 GLU cc_start: 0.6495 (pm20) cc_final: 0.6247 (pt0) REVERT: C 326 GLU cc_start: 0.8218 (tt0) cc_final: 0.7907 (tt0) REVERT: C 335 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.6049 (tp40) REVERT: D 2 LYS cc_start: 0.6392 (pttp) cc_final: 0.5839 (pptt) REVERT: D 8 ASN cc_start: 0.5491 (t0) cc_final: 0.4913 (m110) REVERT: D 26 LYS cc_start: 0.5167 (mtpt) cc_final: 0.4594 (mmmm) REVERT: D 95 ILE cc_start: 0.3609 (OUTLIER) cc_final: 0.3313 (mt) REVERT: E 46 TYR cc_start: 0.4913 (m-80) cc_final: 0.4573 (m-80) REVERT: E 67 GLU cc_start: 0.7144 (mp0) cc_final: 0.6455 (tp30) REVERT: E 101 GLN cc_start: 0.7309 (tt0) cc_final: 0.6462 (tm130) REVERT: E 106 GLN cc_start: 0.6323 (mm-40) cc_final: 0.6123 (mm110) REVERT: E 148 GLU cc_start: 0.7838 (pt0) cc_final: 0.7566 (pp20) REVERT: E 191 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7121 (mmmm) REVERT: E 200 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7440 (ptp-170) REVERT: F 116 ASP cc_start: 0.8588 (t70) cc_final: 0.8203 (t0) REVERT: G 106 ASP cc_start: 0.2522 (OUTLIER) cc_final: 0.1623 (p0) REVERT: G 114 MET cc_start: 0.4898 (mmt) cc_final: 0.4556 (tmt) REVERT: H 87 ARG cc_start: 0.6408 (mmm160) cc_final: 0.5855 (ttm170) REVERT: H 105 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: H 126 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: I 12 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6770 (mp) REVERT: I 16 SER cc_start: 0.3587 (OUTLIER) cc_final: 0.3105 (p) REVERT: I 27 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6232 (mtp-110) REVERT: J 23 ASN cc_start: 0.7728 (t0) cc_final: 0.7435 (m110) REVERT: K 45 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7305 (mt-10) REVERT: L 33 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: L 38 LEU cc_start: 0.8110 (mt) cc_final: 0.7842 (mp) REVERT: L 68 GLU cc_start: 0.7872 (tt0) cc_final: 0.7556 (tp30) REVERT: M 81 GLU cc_start: 0.4394 (tt0) cc_final: 0.3911 (mp0) REVERT: M 167 GLN cc_start: 0.5568 (mt0) cc_final: 0.4980 (mp10) REVERT: N 210 GLU cc_start: 0.3616 (pt0) cc_final: 0.2527 (tm-30) REVERT: N 288 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: N 294 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.6076 (mt) REVERT: N 297 MET cc_start: 0.4329 (mmm) cc_final: 0.4077 (ttm) REVERT: N 298 ASN cc_start: 0.5571 (OUTLIER) cc_final: 0.4984 (m110) REVERT: N 399 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5124 (tp) REVERT: O 31 VAL cc_start: 0.2522 (t) cc_final: 0.2237 (p) REVERT: O 48 LEU cc_start: 0.6652 (tp) cc_final: 0.6441 (tp) REVERT: O 86 MET cc_start: 0.3385 (tmm) cc_final: 0.3003 (tmm) REVERT: O 275 LYS cc_start: 0.3465 (OUTLIER) cc_final: 0.2710 (tttt) REVERT: O 288 MET cc_start: 0.4384 (tmm) cc_final: 0.4033 (mtp) REVERT: O 312 TYR cc_start: 0.1714 (m-80) cc_final: 0.1390 (m-10) REVERT: O 516 LEU cc_start: 0.2378 (OUTLIER) cc_final: 0.2027 (tp) REVERT: O 574 TYR cc_start: 0.5138 (m-80) cc_final: 0.4926 (m-80) REVERT: O 585 MET cc_start: 0.5215 (mtm) cc_final: 0.4694 (mtp) REVERT: O 589 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5730 (mt) REVERT: P 207 PHE cc_start: 0.1890 (OUTLIER) cc_final: 0.1467 (m-10) REVERT: P 269 LEU cc_start: 0.1677 (OUTLIER) cc_final: 0.1056 (tt) REVERT: Q 116 ARG cc_start: 0.3248 (OUTLIER) cc_final: 0.2240 (mmp-170) outliers start: 149 outliers final: 102 residues processed: 639 average time/residue: 0.7275 time to fit residues: 562.9373 Evaluate side-chains 635 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 503 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 288 GLN Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain N residue 298 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 399 ILE Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 275 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 322 LYS Chi-restraints excluded: chain O residue 323 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 116 ARG Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain W residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 158 optimal weight: 7.9990 chunk 267 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 378 optimal weight: 6.9990 chunk 337 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 ASN A 746 ASN A 808 GLN A 950 GLN A 964 ASN A1317 ASN B 217 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN H 137 GLN M 156 ASN ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 366 HIS O 56 HIS ** O 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.198158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140122 restraints weight = 47741.994| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.58 r_work: 0.3244 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 40897 Z= 0.212 Angle : 0.688 17.235 55209 Z= 0.344 Chirality : 0.046 0.278 6221 Planarity : 0.005 0.091 7106 Dihedral : 6.846 59.746 5580 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.87 % Rotamer: Outliers : 3.75 % Allowed : 24.27 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.83 (0.12), residues: 4976 helix: 0.50 (0.12), residues: 1823 sheet: -0.76 (0.20), residues: 607 loop : -1.26 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 509 TYR 0.021 0.002 TYR O 132 PHE 0.055 0.002 PHE P 191 TRP 0.018 0.002 TRP A 201 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00494 (40873) covalent geometry : angle 0.67153 (55176) hydrogen bonds : bond 0.04252 ( 1636) hydrogen bonds : angle 5.11724 ( 4665) metal coordination : bond 0.00926 ( 24) metal coordination : angle 6.13443 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20476.37 seconds wall clock time: 347 minutes 49.20 seconds (20869.20 seconds total)