Starting phenix.real_space_refine on Tue Aug 26 20:56:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bws_16299/08_2025/8bws_16299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bws_16299/08_2025/8bws_16299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bws_16299/08_2025/8bws_16299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bws_16299/08_2025/8bws_16299.map" model { file = "/net/cci-nas-00/data/ceres_data/8bws_16299/08_2025/8bws_16299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bws_16299/08_2025/8bws_16299.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 51 5.49 5 Mg 1 5.21 5 S 209 5.16 5 C 25860 2.51 5 N 7061 2.21 5 O 7825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41013 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1424, 11145 Classifications: {'peptide': 1424} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1359} Chain breaks: 3 Chain: "B" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8715 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 41, 'TRANS': 1062} 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: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1169 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 1 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: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 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: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 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: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1134 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} 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: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain breaks: 1 Chain: "S" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 402 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "T" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 492 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 158 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '4QM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 39.509 73.456 88.870 1.00 71.64 S ATOM 510 SG CYS A 70 41.684 72.227 89.360 1.00 71.31 S ATOM 557 SG CYS A 77 42.116 75.442 90.906 1.00 62.68 S ATOM 795 SG CYS A 107 71.909 99.976 60.939 1.00 59.20 S ATOM 818 SG CYS A 110 70.524 98.303 58.520 1.00 58.97 S ATOM 1184 SG CYS A 154 71.744 101.851 59.643 1.00 73.06 S ATOM 1208 SG CYS A 157 70.631 100.989 57.240 1.00 69.09 S ATOM 19433 SG CYS B1095 56.972 69.047 80.531 1.00 54.99 S ATOM 19456 SG CYS B1098 56.816 72.692 78.998 1.00 55.28 S ATOM 19522 SG CYS B1107 54.112 70.589 80.419 1.00 66.13 S ATOM 19542 SG CYS B1110 55.944 70.094 76.975 1.00 74.74 S ATOM 28825 SG CYS I 5 77.563 156.760 89.477 1.00127.03 S ATOM 28844 SG CYS I 8 73.617 156.371 88.362 1.00122.82 S ATOM 28972 SG CYS I 26 78.845 155.595 87.993 1.00136.92 S ATOM 28995 SG CYS I 29 76.422 156.955 85.372 1.00139.84 S ATOM 29272 SG CYS J 7 50.153 92.917 157.725 1.00 42.55 S ATOM 29295 SG CYS J 10 53.136 91.111 160.599 1.00 47.26 S ATOM 29575 SG CYS J 45 53.080 93.511 159.460 1.00 48.24 S ATOM 29581 SG CYS J 46 49.744 93.885 161.372 1.00 47.08 S ATOM 30632 SG CYS L 31 16.020 104.659 133.358 1.00 87.43 S ATOM 30652 SG CYS L 34 13.772 104.517 135.395 1.00 90.94 S ATOM 30756 SG CYS L 48 12.821 103.697 132.838 1.00 97.59 S ATOM 30779 SG CYS L 51 14.158 107.847 133.158 1.00100.57 S Time building chain proxies: 7.99, per 1000 atoms: 0.19 Number of scatterers: 41013 At special positions: 0 Unit cell: (141.075, 194.94, 200.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 209 16.00 P 51 15.00 Mg 1 11.99 O 7825 8.00 N 7061 7.00 C 25860 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: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 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 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb=" ZN I2002 " pdb="ZN ZN I2002 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2002 " - pdb=" SG CYS I 29 " pdb="ZN ZN I2002 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2002 " - pdb=" SG CYS I 8 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L2001 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 31 " Number of angles added : 33 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9476 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 58 sheets defined 40.2% alpha, 15.3% beta 21 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 133 through 151 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 191 through 208 Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.583A pdb=" N GLU A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 233 through 234 No H-bonds generated for 'chain 'A' and resid 233 through 234' Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 283 through 306 removed outlier: 3.547A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.590A pdb=" N LEU A 452 " --> pdb=" O ASP A 448 " (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: 4.098A 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: 3.981A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 605 through 615 Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 676 through 709 Proline residue: A 687 - end of helix removed outlier: 3.789A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 748 removed outlier: 3.944A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 785 Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 857 through 893 removed outlier: 4.726A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.593A 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 Processing helix chain 'A' and resid 968 through 973 removed outlier: 3.691A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 Processing helix chain 'A' and resid 1049 through 1060 removed outlier: 3.587A pdb=" N LYS A1053 " --> pdb=" O PRO A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1081 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1100 through 1104 Processing helix chain 'A' and resid 1122 through 1132 Processing helix chain 'A' and resid 1150 through 1161 removed outlier: 3.527A pdb=" N VAL A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1170 removed outlier: 3.687A pdb=" N ALA A1170 " --> pdb=" O SER A1167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1167 through 1170' Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.556A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1213 Processing helix chain 'A' and resid 1254 through 1266 Processing helix chain 'A' and resid 1287 through 1289 No H-bonds generated for 'chain 'A' and resid 1287 through 1289' Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1318 through 1327 Processing helix chain 'A' and resid 1328 through 1346 Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 3.870A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1378 removed outlier: 3.746A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A1378 " --> pdb=" O PHE A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 Processing helix chain 'A' and resid 1391 through 1402 Processing helix chain 'A' and resid 1410 through 1418 Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.636A pdb=" N GLY A1426 " --> pdb=" O ILE A1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.780A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 80 removed outlier: 4.992A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.360A 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 169 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 284 removed outlier: 3.531A pdb=" N ASP B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 288 through 293 removed outlier: 4.269A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.762A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 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 removed outlier: 3.664A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 440 removed outlier: 4.257A pdb=" N ASN B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.569A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.852A pdb=" N LYS B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 581 Processing helix chain 'B' and resid 625 through 633 Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 652 through 657 Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.595A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 681' Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.529A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.507A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.927A pdb=" N PHE B 782 " --> pdb=" O ILE B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.675A pdb=" N GLY B 948 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 949 " --> pdb=" O PRO B 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 945 through 949' Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.611A 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 removed outlier: 3.562A pdb=" N LEU B1079 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1135 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.516A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 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 251 removed outlier: 4.212A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.880A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.551A 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 30 through 37 Processing helix chain 'D' and resid 52 through 67 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.661A pdb=" N GLN D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.622A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 148 through 159 removed outlier: 4.144A pdb=" N GLU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.530A pdb=" N ARG E 26 " --> pdb=" O MET E 22 " (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 103 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.901A pdb=" N LEU E 188 " --> pdb=" O VAL E 184 " (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 18 Processing helix chain 'G' and resid 21 through 35 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 16 through 27 removed outlier: 4.528A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 55 through 61 removed outlier: 4.155A 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: 4.036A 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 removed outlier: 3.893A pdb=" N GLU M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 195 removed outlier: 3.511A pdb=" N GLN M 195 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 238 removed outlier: 3.672A pdb=" N ALA M 233 " --> pdb=" O GLY M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 260 Processing helix chain 'M' and resid 273 through 280 Processing helix chain 'N' and resid 275 through 297 Processing helix chain 'O' and resid 27 through 35 removed outlier: 4.342A pdb=" N THR O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 42 removed outlier: 3.885A 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 72 Processing helix chain 'O' and resid 75 through 82 Processing helix chain 'O' and resid 87 through 101 Processing helix chain 'O' and resid 123 through 132 removed outlier: 3.560A pdb=" N ILE O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.588A pdb=" N MET O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 167 Processing helix chain 'O' and resid 171 through 178 removed outlier: 3.567A pdb=" N VAL O 178 " --> pdb=" O TYR O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 198 Processing helix chain 'O' and resid 204 through 209 Processing helix chain 'O' and resid 210 through 220 removed outlier: 3.621A pdb=" N GLU O 220 " --> pdb=" O GLN O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 255 removed outlier: 3.708A pdb=" N THR O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP O 248 " --> pdb=" O ASN O 244 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 258 No H-bonds generated for 'chain 'O' and resid 256 through 258' Processing helix chain 'O' and resid 283 through 301 Processing helix chain 'O' and resid 305 through 320 Processing helix chain 'O' and resid 341 through 356 removed outlier: 4.020A pdb=" N PHE O 345 " --> pdb=" O GLU O 341 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN O 346 " --> pdb=" O ALA O 342 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 370 removed outlier: 3.768A pdb=" N LEU O 366 " --> pdb=" O ASN O 362 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 463 removed outlier: 3.791A pdb=" N SER O 463 " --> pdb=" O ILE O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 500 Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.588A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 527 Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.798A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 Processing helix chain 'O' and resid 599 through 607 removed outlier: 3.746A pdb=" N LEU O 603 " --> pdb=" O ASN O 599 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN O 607 " --> pdb=" O LEU O 603 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 653 removed outlier: 4.960A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 190 Processing helix chain 'P' and resid 194 through 198 Processing helix chain 'P' and resid 218 through 229 Processing helix chain 'P' and resid 236 through 249 removed outlier: 3.785A pdb=" N TYR P 249 " --> pdb=" O GLU P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 270 removed outlier: 3.677A pdb=" N ILE P 268 " --> pdb=" O THR P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 299 removed outlier: 5.354A pdb=" N PHE P 297 " --> pdb=" O PHE P 294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 Processing helix chain 'Q' and resid 41 through 45 removed outlier: 3.827A pdb=" N ASN Q 44 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY Q 45 " --> pdb=" O PRO Q 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 45' Processing helix chain 'Q' and resid 48 through 68 removed outlier: 3.951A pdb=" N PHE Q 61 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY Q 62 " --> pdb=" O TYR Q 58 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 139 removed outlier: 4.027A pdb=" N ASN Q 138 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 removed outlier: 6.704A pdb=" N ARG B1142 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 16 " --> pdb=" O ARG B1140 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B1140 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.782A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N LEU A 88 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N ILE A 257 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.429A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.562A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 6.209A pdb=" N VAL A 392 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG A 493 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL A 394 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 407 removed outlier: 4.049A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 626 through 629 removed outlier: 6.457A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 813 through 815 removed outlier: 4.055A pdb=" N GLY A 814 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 896 through 898 Processing sheet with id=AB2, first strand: chain 'A' and resid 1110 through 1111 removed outlier: 6.830A pdb=" N MET A1117 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1278 through 1285 removed outlier: 6.834A pdb=" N GLU A1296 " --> pdb=" O SER A1279 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A1281 " --> pdb=" O LEU A1294 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A1294 " --> pdb=" O ALA A1281 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE A1283 " --> pdb=" O GLU A1292 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU A1292 " --> pdb=" O ILE A1283 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 7.255A pdb=" N THR A1164 " --> pdb=" O VAL A1272 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1173 through 1177 removed outlier: 4.467A pdb=" N SER A1182 " --> pdb=" O VAL A1234 " (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: 3.735A pdb=" N ILE B 83 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.723A pdb=" N ALA B 127 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG B 151 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 129 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 135 " --> pdb=" O MET B 143 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 143 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.978A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 235 through 236 removed outlier: 3.814A pdb=" N ILE B 251 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.557A 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 519 through 520 Processing sheet with id=AC6, first strand: chain 'B' and resid 560 through 564 removed outlier: 7.061A pdb=" N VAL B 555 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.896A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.896A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 5.099A 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 753 through 759 removed outlier: 4.141A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 753 through 759 removed outlier: 4.141A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 839 through 843 removed outlier: 6.762A pdb=" N ILE B 841 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B 873 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 3.795A 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 1101 through 1102 removed outlier: 3.757A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.745A pdb=" N ILE C 7 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.745A pdb=" N ILE C 7 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 132 through 139 removed outlier: 6.539A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL C 78 " --> 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 222 through 226 removed outlier: 7.547A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE4, first strand: chain 'D' and resid 3 through 5 removed outlier: 5.605A pdb=" N VAL D 3 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA G 8 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS G 6 " --> pdb=" O GLU D 5 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.425A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.793A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 3 through 4 removed outlier: 6.695A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 108 through 110 removed outlier: 4.023A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER G 90 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE G 150 " --> pdb=" O SER G 199 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER G 199 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG G 152 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.644A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.754A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 76 through 78 removed outlier: 7.590A pdb=" N PHE N 304 " --> pdb=" O GLY N 414 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ILE N 416 " --> pdb=" O PHE N 304 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL N 306 " --> pdb=" O ILE N 416 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL N 394 " --> pdb=" O VAL N 412 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL M 87 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU M 179 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN M 89 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN M 178 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL M 151 " --> pdb=" O GLN M 178 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR M 147 " --> pdb=" O PHE M 182 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN M 146 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE M 123 " --> pdb=" O GLN M 146 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP M 122 " --> pdb=" O ALA M 109 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA M 109 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA M 110 " --> pdb=" O LEU M 245 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 248 through 249 removed outlier: 6.664A pdb=" N ALA M 248 " --> pdb=" O LEU N 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'N' and resid 363 through 366 removed outlier: 3.788A pdb=" N LYS N 370 " --> pdb=" O HIS N 366 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 104 through 109 removed outlier: 3.507A pdb=" N LYS O 105 " --> pdb=" O TYR O 121 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 169 through 170 Processing sheet with id=AF9, first strand: chain 'O' and resid 380 through 381 Processing sheet with id=AG1, first strand: chain 'O' and resid 469 through 472 removed outlier: 5.158A pdb=" N GLU O 470 " --> pdb=" O TYR O 477 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR O 477 " --> pdb=" O GLU O 470 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS O 472 " --> pdb=" O VAL O 475 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 547 through 551 Processing sheet with id=AG3, first strand: chain 'P' and resid 165 through 166 Processing sheet with id=AG4, first strand: chain 'P' and resid 216 through 217 1669 hydrogen bonds defined for protein. 4644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 10.31 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6816 1.31 - 1.44: 10611 1.44 - 1.56: 23995 1.56 - 1.69: 99 1.69 - 1.81: 340 Bond restraints: 41861 Sorted by residual: bond pdb=" CA SER J 9 " pdb=" CB SER J 9 " ideal model delta sigma weight residual 1.529 1.465 0.064 1.58e-02 4.01e+03 1.64e+01 bond pdb=" C PRO B 503 " pdb=" O PRO B 503 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.43e+01 bond pdb=" C LYS J 12 " pdb=" N VAL J 13 " ideal model delta sigma weight residual 1.332 1.300 0.032 9.20e-03 1.18e+04 1.19e+01 bond pdb=" N VAL B 216 " pdb=" CA VAL B 216 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" N TYR G 121 " pdb=" CA TYR G 121 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.15e-02 7.56e+03 1.04e+01 ... (remaining 41856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 56108 2.39 - 4.78: 583 4.78 - 7.17: 64 7.17 - 9.56: 4 9.56 - 11.95: 1 Bond angle restraints: 56760 Sorted by residual: angle pdb=" N PHE Q 61 " pdb=" CA PHE Q 61 " pdb=" C PHE Q 61 " ideal model delta sigma weight residual 110.35 101.27 9.08 1.36e+00 5.41e-01 4.45e+01 angle pdb=" N LYS Q 57 " pdb=" CA LYS Q 57 " pdb=" C LYS Q 57 " ideal model delta sigma weight residual 113.20 106.22 6.98 1.21e+00 6.83e-01 3.33e+01 angle pdb=" N TYR Q 58 " pdb=" CA TYR Q 58 " pdb=" C TYR Q 58 " ideal model delta sigma weight residual 113.88 106.93 6.95 1.23e+00 6.61e-01 3.19e+01 angle pdb=" CA PHE J 8 " pdb=" CB PHE J 8 " pdb=" CG PHE J 8 " ideal model delta sigma weight residual 113.80 118.89 -5.09 1.00e+00 1.00e+00 2.59e+01 angle pdb=" N ALA B 507 " pdb=" CA ALA B 507 " pdb=" C ALA B 507 " ideal model delta sigma weight residual 111.87 105.03 6.84 1.41e+00 5.03e-01 2.36e+01 ... (remaining 56755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.35: 25022 31.35 - 62.70: 650 62.70 - 94.05: 37 94.05 - 125.40: 0 125.40 - 156.75: 2 Dihedral angle restraints: 25711 sinusoidal: 11066 harmonic: 14645 Sorted by residual: dihedral pdb=" CA GLU B 249 " pdb=" C GLU B 249 " pdb=" N GLU B 250 " pdb=" CA GLU B 250 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA HIS B 595 " pdb=" C HIS B 595 " pdb=" N GLN B 596 " pdb=" CA GLN B 596 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLY A 968 " pdb=" C GLY A 968 " pdb=" N PRO A 969 " pdb=" CA PRO A 969 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 25708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 6320 0.116 - 0.231: 102 0.231 - 0.347: 1 0.347 - 0.463: 2 0.463 - 0.579: 5 Chirality restraints: 6430 Sorted by residual: chirality pdb=" P DG S 37 " pdb=" OP1 DG S 37 " pdb=" OP2 DG S 37 " pdb=" O5' DG S 37 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" P DT T 15 " pdb=" OP1 DT T 15 " pdb=" OP2 DT T 15 " pdb=" O5' DT T 15 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" P DT T 13 " pdb=" OP1 DT T 13 " pdb=" OP2 DT T 13 " pdb=" O5' DT T 13 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.73e+00 ... (remaining 6427 not shown) Planarity restraints: 7105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 227 " 0.444 9.50e-02 1.11e+02 1.99e-01 2.42e+01 pdb=" NE ARG B 227 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG B 227 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 227 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 227 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 120 " -0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C TYR G 120 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR G 120 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR G 121 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 556 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.55e+00 pdb=" C ASP A 556 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP A 556 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE A 557 " 0.018 2.00e-02 2.50e+03 ... (remaining 7102 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 276 2.50 - 3.10: 30490 3.10 - 3.70: 63075 3.70 - 4.30: 90892 4.30 - 4.90: 152502 Nonbonded interactions: 337235 Sorted by model distance: nonbonded pdb=" CB ASP A 511 " pdb="MG MG A1503 " model vdw 1.905 2.570 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A1503 " model vdw 2.065 2.170 nonbonded pdb=" O3' A R 10 " pdb="MG MG A1503 " model vdw 2.067 2.170 nonbonded pdb=" OD2 ASP A 511 " pdb="MG MG A1503 " model vdw 2.107 2.170 nonbonded pdb=" OD2 ASP A 513 " pdb="MG MG A1503 " model vdw 2.120 2.170 ... (remaining 337230 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: 10.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 41.300 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 0.526 41885 Z= 0.245 Angle : 0.836 54.254 56793 Z= 0.359 Chirality : 0.046 0.579 6430 Planarity : 0.005 0.199 7105 Dihedral : 13.186 156.745 16235 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.54 % Favored : 92.44 % Rotamer: Outliers : 3.98 % Allowed : 7.50 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.57 (0.12), residues: 4959 helix: 1.03 (0.13), residues: 1826 sheet: -0.78 (0.21), residues: 585 loop : -1.35 (0.13), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 73 TYR 0.022 0.001 TYR B 232 PHE 0.017 0.001 PHE F 143 TRP 0.016 0.001 TRP F 146 HIS 0.004 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00358 (41861) covalent geometry : angle 0.59356 (56760) hydrogen bonds : bond 0.14818 ( 1692) hydrogen bonds : angle 6.11659 ( 4752) metal coordination : bond 0.18105 ( 24) metal coordination : angle 24.45808 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 669 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7204 (mmp80) cc_final: 0.6988 (mmp80) REVERT: A 219 MET cc_start: 0.8347 (mmt) cc_final: 0.7985 (mmm) REVERT: A 269 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7918 (ptt-90) REVERT: A 889 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 1333 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7089 (m-10) REVERT: B 42 GLN cc_start: 0.7794 (mt0) cc_final: 0.7543 (mp10) REVERT: B 67 TYR cc_start: 0.7159 (t80) cc_final: 0.6930 (t80) REVERT: B 221 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8658 (t) REVERT: B 234 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8643 (pt) REVERT: B 236 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8165 (ttmt) REVERT: B 263 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5350 (pp) REVERT: C 55 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8379 (m-30) REVERT: C 130 ASN cc_start: 0.8831 (t0) cc_final: 0.8428 (t0) REVERT: C 172 GLN cc_start: 0.8321 (mp10) cc_final: 0.7520 (mp10) REVERT: D 1 MET cc_start: 0.6399 (tpt) cc_final: 0.5760 (tpt) REVERT: E 54 GLN cc_start: 0.6347 (pp30) cc_final: 0.5112 (pm20) REVERT: E 146 HIS cc_start: 0.8162 (m170) cc_final: 0.7814 (m170) REVERT: G 130 TRP cc_start: 0.5964 (t60) cc_final: 0.5699 (t60) REVERT: I 32 GLU cc_start: 0.6287 (tp30) cc_final: 0.5957 (pp20) REVERT: J 1 MET cc_start: 0.6888 (mtp) cc_final: 0.6605 (mtp) REVERT: K 123 ASP cc_start: 0.8307 (m-30) cc_final: 0.8078 (m-30) REVERT: M 251 THR cc_start: 0.7243 (t) cc_final: 0.7003 (m) REVERT: M 275 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6488 (tm-30) REVERT: O 577 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7446 (mtp) REVERT: O 585 MET cc_start: 0.7897 (mtp) cc_final: 0.7596 (mtp) REVERT: O 624 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.6981 (tt) REVERT: O 635 LEU cc_start: 0.8536 (tp) cc_final: 0.8298 (mm) REVERT: P 296 TYR cc_start: 0.8434 (p90) cc_final: 0.7774 (p90) REVERT: Q 57 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7370 (mtpt) REVERT: Q 70 PHE cc_start: 0.8336 (m-80) cc_final: 0.8068 (m-10) outliers start: 176 outliers final: 68 residues processed: 811 average time/residue: 0.2179 time to fit residues: 294.3656 Evaluate side-chains 588 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 509 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 503 PRO Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.0970 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 3.9990 chunk 494 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.0670 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 386 ASN A 625 ASN A 630 ASN A1058 GLN A1174 GLN A1346 HIS B 286 ASN B 362 ASN B 493 GLN B 552 ASN B 695 GLN B 733 GLN B 754 ASN B 840 GLN B 918 GLN B 936 GLN B1014 GLN D 56 GLN D 71 ASN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN K 118 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN N 289 HIS ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 631 ASN P 219 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.157244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.117538 restraints weight = 61290.633| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.58 r_work: 0.3484 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41885 Z= 0.126 Angle : 0.675 37.629 56793 Z= 0.304 Chirality : 0.042 0.164 6430 Planarity : 0.004 0.058 7105 Dihedral : 11.581 159.029 6362 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.37 % Allowed : 11.11 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.39 (0.12), residues: 4959 helix: 1.18 (0.12), residues: 1829 sheet: -0.54 (0.21), residues: 590 loop : -1.30 (0.13), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 293 TYR 0.018 0.001 TYR D 50 PHE 0.024 0.001 PHE B 678 TRP 0.014 0.001 TRP A 197 HIS 0.007 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00282 (41861) covalent geometry : angle 0.56821 (56760) hydrogen bonds : bond 0.03998 ( 1692) hydrogen bonds : angle 4.83313 ( 4752) metal coordination : bond 0.00964 ( 24) metal coordination : angle 15.15186 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 564 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7374 (mmp80) cc_final: 0.7095 (mmp80) REVERT: A 126 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8027 (mt-10) REVERT: A 219 MET cc_start: 0.8221 (mmt) cc_final: 0.7956 (mmm) REVERT: A 269 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8584 (ptt-90) REVERT: A 483 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 890 MET cc_start: 0.8479 (tpp) cc_final: 0.7446 (tpt) REVERT: A 1060 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7433 (t80) REVERT: A 1333 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7215 (m-10) REVERT: A 1348 MET cc_start: 0.7542 (mtt) cc_final: 0.7302 (mtt) REVERT: B 42 GLN cc_start: 0.8067 (mt0) cc_final: 0.7837 (mp10) REVERT: B 67 TYR cc_start: 0.7301 (t80) cc_final: 0.7085 (t80) REVERT: B 132 ASP cc_start: 0.7512 (m-30) cc_final: 0.7269 (m-30) REVERT: B 263 LEU cc_start: 0.5573 (OUTLIER) cc_final: 0.5215 (pp) REVERT: B 312 MET cc_start: 0.6982 (mmm) cc_final: 0.4922 (tmm) REVERT: B 656 ASP cc_start: 0.7548 (t0) cc_final: 0.7073 (t0) REVERT: B 802 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6266 (p) REVERT: C 55 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8543 (m-30) REVERT: C 130 ASN cc_start: 0.9237 (t0) cc_final: 0.8678 (t0) REVERT: D 1 MET cc_start: 0.6212 (tpt) cc_final: 0.5560 (tpt) REVERT: E 146 HIS cc_start: 0.8446 (m170) cc_final: 0.7915 (m170) REVERT: F 144 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: G 9 ASP cc_start: 0.8167 (t0) cc_final: 0.7926 (t0) REVERT: J 1 MET cc_start: 0.7424 (mtp) cc_final: 0.7008 (mtp) REVERT: J 27 GLU cc_start: 0.6945 (pm20) cc_final: 0.6186 (pm20) REVERT: K 67 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7379 (mm-30) REVERT: K 123 ASP cc_start: 0.8637 (m-30) cc_final: 0.8401 (m-30) REVERT: M 111 ARG cc_start: 0.6877 (mtm180) cc_final: 0.6563 (mtm-85) REVERT: M 275 GLU cc_start: 0.6718 (tm-30) cc_final: 0.6360 (tm-30) REVERT: N 421 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6451 (pp30) REVERT: O 212 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7418 (mp0) REVERT: O 476 TYR cc_start: 0.7614 (m-80) cc_final: 0.7242 (m-80) REVERT: O 577 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7654 (mtp) REVERT: O 585 MET cc_start: 0.8105 (mtp) cc_final: 0.7837 (mtp) REVERT: O 624 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.6849 (tt) REVERT: Q 57 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6948 (mtpt) REVERT: Q 108 TYR cc_start: 0.6481 (t80) cc_final: 0.6185 (t80) outliers start: 149 outliers final: 87 residues processed: 674 average time/residue: 0.2156 time to fit residues: 242.6623 Evaluate side-chains 595 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 496 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 421 GLN Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 486 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 373 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 368 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 291 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 315 HIS A 320 GLN A 477 GLN ** A1318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1346 HIS B 286 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN B 733 GLN B 754 ASN B 837 GLN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN G 143 ASN H 52 GLN H 134 ASN N 288 GLN ** N 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN O 544 ASN O 631 ASN P 219 GLN ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.151145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110983 restraints weight = 62070.615| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.61 r_work: 0.3377 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 41885 Z= 0.302 Angle : 0.776 47.050 56793 Z= 0.362 Chirality : 0.047 0.245 6430 Planarity : 0.005 0.060 7105 Dihedral : 11.631 156.340 6317 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.34 % Allowed : 12.92 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.82 (0.12), residues: 4959 helix: 0.77 (0.12), residues: 1839 sheet: -0.90 (0.21), residues: 600 loop : -1.47 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 780 TYR 0.022 0.002 TYR B 765 PHE 0.027 0.002 PHE B 678 TRP 0.019 0.002 TRP A 201 HIS 0.023 0.002 HIS A1346 Details of bonding type rmsd covalent geometry : bond 0.00715 (41861) covalent geometry : angle 0.68884 (56760) hydrogen bonds : bond 0.04539 ( 1692) hydrogen bonds : angle 5.03435 ( 4752) metal coordination : bond 0.01464 ( 24) metal coordination : angle 14.81458 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 526 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6829 (pm20) REVERT: A 219 MET cc_start: 0.8350 (mmt) cc_final: 0.8081 (mmm) REVERT: A 269 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8680 (ptt-90) REVERT: A 511 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7774 (t0) REVERT: A 1060 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7684 (t80) REVERT: A 1260 MET cc_start: 0.7514 (ttp) cc_final: 0.7272 (ttm) REVERT: A 1333 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: B 42 GLN cc_start: 0.8172 (mt0) cc_final: 0.7871 (mp10) REVERT: B 132 ASP cc_start: 0.7715 (m-30) cc_final: 0.7368 (m-30) REVERT: B 263 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5598 (pp) REVERT: B 565 ILE cc_start: 0.8052 (tt) cc_final: 0.7808 (tt) REVERT: B 802 THR cc_start: 0.6510 (OUTLIER) cc_final: 0.6214 (p) REVERT: C 55 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8763 (m-30) REVERT: C 130 ASN cc_start: 0.9370 (t0) cc_final: 0.8983 (t0) REVERT: D 1 MET cc_start: 0.6730 (tpt) cc_final: 0.6161 (tpt) REVERT: D 51 ASN cc_start: 0.8015 (t0) cc_final: 0.7786 (t0) REVERT: D 52 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.5887 (m170) REVERT: E 57 MET cc_start: 0.7031 (ptp) cc_final: 0.6824 (ptp) REVERT: E 146 HIS cc_start: 0.8506 (m170) cc_final: 0.8080 (m170) REVERT: I 33 PHE cc_start: 0.7285 (t80) cc_final: 0.7025 (t80) REVERT: J 26 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7719 (tm-30) REVERT: J 27 GLU cc_start: 0.6993 (pm20) cc_final: 0.6789 (pm20) REVERT: K 67 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7833 (mm-30) REVERT: K 123 ASP cc_start: 0.8824 (m-30) cc_final: 0.8531 (m-30) REVERT: M 83 GLU cc_start: 0.7468 (tp30) cc_final: 0.7048 (tp30) REVERT: M 247 TRP cc_start: 0.7807 (m100) cc_final: 0.7542 (m100) REVERT: M 275 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6422 (tm-30) REVERT: O 522 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8031 (mt) REVERT: O 577 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7995 (mtp) REVERT: O 585 MET cc_start: 0.8303 (mtp) cc_final: 0.8103 (mtp) REVERT: O 624 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.6917 (tt) REVERT: P 188 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7520 (tm-30) REVERT: P 206 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7899 (t) REVERT: Q 108 TYR cc_start: 0.6415 (t80) cc_final: 0.6105 (t80) outliers start: 192 outliers final: 130 residues processed: 670 average time/residue: 0.2130 time to fit residues: 240.2710 Evaluate side-chains 626 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 483 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 522 ILE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 31 optimal weight: 0.8980 chunk 477 optimal weight: 9.9990 chunk 467 optimal weight: 0.9990 chunk 428 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 398 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 493 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 477 GLN B 286 ASN B 362 ASN B 513 ASN B 552 ASN B 733 GLN B 844 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 114 ASN G 143 ASN H 11 GLN H 52 GLN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN O 456 HIS ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.154107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.114432 restraints weight = 61304.353| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.50 r_work: 0.3452 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41885 Z= 0.147 Angle : 0.662 38.309 56793 Z= 0.303 Chirality : 0.043 0.275 6430 Planarity : 0.004 0.064 7105 Dihedral : 11.397 157.086 6303 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.04 % Allowed : 14.73 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.61 (0.12), residues: 4959 helix: 1.00 (0.12), residues: 1830 sheet: -0.81 (0.21), residues: 606 loop : -1.38 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 149 TYR 0.025 0.001 TYR E 46 PHE 0.020 0.001 PHE B 678 TRP 0.013 0.001 TRP O 583 HIS 0.006 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00344 (41861) covalent geometry : angle 0.57473 (56760) hydrogen bonds : bond 0.03687 ( 1692) hydrogen bonds : angle 4.74274 ( 4752) metal coordination : bond 0.00829 ( 24) metal coordination : angle 13.61265 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 528 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8042 (pm20) cc_final: 0.7809 (pm20) REVERT: A 126 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8109 (mt-10) REVERT: A 219 MET cc_start: 0.8279 (mmt) cc_final: 0.7996 (mmm) REVERT: A 269 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8659 (ptt-90) REVERT: A 314 GLU cc_start: 0.7679 (tp30) cc_final: 0.7467 (tp30) REVERT: A 483 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8352 (mp) REVERT: A 890 MET cc_start: 0.8668 (tpp) cc_final: 0.8353 (tpt) REVERT: A 1060 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7523 (t80) REVERT: A 1260 MET cc_start: 0.7430 (ttp) cc_final: 0.6969 (ttm) REVERT: A 1333 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7482 (m-10) REVERT: A 1348 MET cc_start: 0.7641 (mtt) cc_final: 0.7429 (mtt) REVERT: B 42 GLN cc_start: 0.8142 (mt0) cc_final: 0.7810 (pt0) REVERT: B 132 ASP cc_start: 0.7627 (m-30) cc_final: 0.7330 (m-30) REVERT: B 263 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5423 (pp) REVERT: B 545 ASP cc_start: 0.8673 (p0) cc_final: 0.8418 (p0) REVERT: B 802 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6267 (p) REVERT: C 130 ASN cc_start: 0.9350 (t0) cc_final: 0.8882 (t0) REVERT: D 1 MET cc_start: 0.6473 (tpt) cc_final: 0.6140 (tpt) REVERT: D 51 ASN cc_start: 0.8048 (t0) cc_final: 0.7783 (t0) REVERT: D 52 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.5745 (m170) REVERT: E 146 HIS cc_start: 0.8494 (m170) cc_final: 0.7960 (m170) REVERT: F 144 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: G 71 THR cc_start: 0.8493 (p) cc_final: 0.8203 (p) REVERT: G 149 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7788 (mtp-110) REVERT: H 77 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.8015 (ttp-170) REVERT: I 33 PHE cc_start: 0.7231 (t80) cc_final: 0.6965 (t80) REVERT: K 67 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7713 (mm-30) REVERT: K 123 ASP cc_start: 0.8774 (m-30) cc_final: 0.8521 (m-30) REVERT: M 173 ILE cc_start: 0.8438 (mt) cc_final: 0.8164 (mp) REVERT: M 275 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6318 (tm-30) REVERT: O 577 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7902 (mtp) REVERT: O 624 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6862 (tt) REVERT: Q 70 PHE cc_start: 0.8337 (m-80) cc_final: 0.8090 (m-10) outliers start: 179 outliers final: 125 residues processed: 660 average time/residue: 0.2120 time to fit residues: 236.7087 Evaluate side-chains 639 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 504 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 120 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 435 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 471 optimal weight: 9.9990 chunk 439 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 477 GLN A 816 GLN B 286 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN G 143 ASN N 288 GLN N 421 GLN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.151498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111978 restraints weight = 61865.068| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.50 r_work: 0.3393 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 41885 Z= 0.261 Angle : 0.734 40.421 56793 Z= 0.342 Chirality : 0.046 0.284 6430 Planarity : 0.005 0.063 7105 Dihedral : 11.450 155.223 6297 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.68 % Allowed : 15.04 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.83 (0.12), residues: 4959 helix: 0.77 (0.12), residues: 1841 sheet: -0.86 (0.20), residues: 622 loop : -1.50 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1211 TYR 0.029 0.002 TYR E 46 PHE 0.024 0.002 PHE B 678 TRP 0.015 0.002 TRP A 201 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00623 (41861) covalent geometry : angle 0.65296 (56760) hydrogen bonds : bond 0.04121 ( 1692) hydrogen bonds : angle 4.89870 ( 4752) metal coordination : bond 0.01146 ( 24) metal coordination : angle 13.94344 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 521 time to evaluate : 1.753 Fit side-chains REVERT: A 3 GLU cc_start: 0.8114 (pm20) cc_final: 0.7717 (pm20) REVERT: A 193 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: A 219 MET cc_start: 0.8275 (mmt) cc_final: 0.8054 (mmm) REVERT: A 269 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8723 (ptt-90) REVERT: A 314 GLU cc_start: 0.7738 (tp30) cc_final: 0.7537 (tp30) REVERT: A 483 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 890 MET cc_start: 0.8371 (tpp) cc_final: 0.8093 (tpt) REVERT: A 1260 MET cc_start: 0.7410 (ttp) cc_final: 0.7163 (ttm) REVERT: A 1333 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7509 (m-10) REVERT: A 1348 MET cc_start: 0.7551 (mtt) cc_final: 0.7273 (mtt) REVERT: B 42 GLN cc_start: 0.8111 (mt0) cc_final: 0.7793 (mp10) REVERT: B 132 ASP cc_start: 0.7658 (m-30) cc_final: 0.7340 (m-30) REVERT: B 263 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5450 (pp) REVERT: B 289 GLU cc_start: 0.7895 (mp0) cc_final: 0.7608 (mp0) REVERT: B 545 ASP cc_start: 0.8708 (p0) cc_final: 0.8454 (p0) REVERT: B 802 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.6266 (p) REVERT: B 1047 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8934 (t) REVERT: C 130 ASN cc_start: 0.9346 (t0) cc_final: 0.8907 (t0) REVERT: D 1 MET cc_start: 0.6646 (tpt) cc_final: 0.6164 (tpt) REVERT: D 51 ASN cc_start: 0.8065 (t0) cc_final: 0.7802 (t0) REVERT: D 52 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.5978 (m170) REVERT: E 52 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7803 (ttm-80) REVERT: E 146 HIS cc_start: 0.8533 (m170) cc_final: 0.8053 (m170) REVERT: F 144 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: G 149 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7992 (mtp-110) REVERT: H 77 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.8078 (ttp-170) REVERT: I 33 PHE cc_start: 0.7361 (t80) cc_final: 0.7136 (t80) REVERT: J 1 MET cc_start: 0.7939 (mtp) cc_final: 0.7707 (mtp) REVERT: J 27 GLU cc_start: 0.6857 (pm20) cc_final: 0.6189 (pm20) REVERT: J 49 MET cc_start: 0.8876 (tpp) cc_final: 0.8421 (tpp) REVERT: K 67 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7825 (mm-30) REVERT: K 123 ASP cc_start: 0.8820 (m-30) cc_final: 0.8540 (m-30) REVERT: M 83 GLU cc_start: 0.7434 (tp30) cc_final: 0.6990 (tp30) REVERT: M 275 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6325 (tm-30) REVERT: N 380 MET cc_start: 0.7359 (tmm) cc_final: 0.6221 (tmm) REVERT: O 577 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: O 624 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.6899 (tt) REVERT: P 188 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7547 (tm-30) REVERT: P 220 GLU cc_start: 0.8491 (mp0) cc_final: 0.8275 (mp0) outliers start: 207 outliers final: 157 residues processed: 674 average time/residue: 0.2189 time to fit residues: 247.7549 Evaluate side-chains 665 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 496 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 318 optimal weight: 0.6980 chunk 376 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 418 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 334 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 320 GLN A 367 ASN A 477 GLN B 286 ASN B 733 GLN B 754 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.154945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115339 restraints weight = 61414.357| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.56 r_work: 0.3460 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41885 Z= 0.125 Angle : 0.653 33.937 56793 Z= 0.298 Chirality : 0.042 0.260 6430 Planarity : 0.004 0.066 7105 Dihedral : 11.285 155.274 6296 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.91 % Allowed : 16.31 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.54 (0.12), residues: 4959 helix: 1.07 (0.12), residues: 1822 sheet: -0.75 (0.21), residues: 627 loop : -1.36 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1211 TYR 0.015 0.001 TYR E 112 PHE 0.017 0.001 PHE O 361 TRP 0.013 0.001 TRP A 197 HIS 0.007 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00287 (41861) covalent geometry : angle 0.57160 (56760) hydrogen bonds : bond 0.03462 ( 1692) hydrogen bonds : angle 4.64196 ( 4752) metal coordination : bond 0.00673 ( 24) metal coordination : angle 13.07538 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 526 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8090 (pm20) cc_final: 0.7720 (pm20) REVERT: A 126 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8108 (mt-10) REVERT: A 193 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: A 219 MET cc_start: 0.8274 (mmt) cc_final: 0.8008 (mmm) REVERT: A 269 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8527 (ptt-90) REVERT: A 314 GLU cc_start: 0.7726 (tp30) cc_final: 0.7513 (tp30) REVERT: A 483 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8363 (mp) REVERT: A 1060 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7551 (t80) REVERT: A 1333 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: A 1348 MET cc_start: 0.7665 (mtt) cc_final: 0.7423 (mtt) REVERT: A 1435 ASN cc_start: 0.8538 (t0) cc_final: 0.8233 (p0) REVERT: B 42 GLN cc_start: 0.8133 (mt0) cc_final: 0.7820 (pt0) REVERT: B 132 ASP cc_start: 0.7610 (m-30) cc_final: 0.7333 (m-30) REVERT: B 263 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5282 (pp) REVERT: B 289 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: B 330 THR cc_start: 0.8737 (m) cc_final: 0.8277 (p) REVERT: B 545 ASP cc_start: 0.8636 (p0) cc_final: 0.8381 (p0) REVERT: B 802 THR cc_start: 0.6648 (OUTLIER) cc_final: 0.6351 (p) REVERT: B 1078 LEU cc_start: 0.8757 (tt) cc_final: 0.8212 (tt) REVERT: C 130 ASN cc_start: 0.9331 (t0) cc_final: 0.8870 (t0) REVERT: C 282 TYR cc_start: 0.7686 (m-10) cc_final: 0.7294 (m-10) REVERT: D 1 MET cc_start: 0.6325 (tpt) cc_final: 0.6017 (tpt) REVERT: D 51 ASN cc_start: 0.8088 (t0) cc_final: 0.7843 (t0) REVERT: D 52 HIS cc_start: 0.6973 (OUTLIER) cc_final: 0.5720 (m170) REVERT: E 52 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7776 (ttm-80) REVERT: E 146 HIS cc_start: 0.8503 (m170) cc_final: 0.7996 (m170) REVERT: F 144 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: G 71 THR cc_start: 0.8509 (p) cc_final: 0.8210 (p) REVERT: G 149 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7989 (mtp-110) REVERT: I 33 PHE cc_start: 0.7300 (t80) cc_final: 0.7034 (t80) REVERT: J 27 GLU cc_start: 0.6782 (pm20) cc_final: 0.6211 (pm20) REVERT: K 67 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7703 (mm-30) REVERT: K 123 ASP cc_start: 0.8787 (m-30) cc_final: 0.8560 (m-30) REVERT: M 275 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6305 (tm-30) REVERT: N 302 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6616 (tp30) REVERT: O 368 ARG cc_start: 0.8489 (tmt-80) cc_final: 0.7813 (tmt170) REVERT: O 577 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: O 624 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.6955 (tt) REVERT: Q 70 PHE cc_start: 0.8320 (m-80) cc_final: 0.8023 (m-10) REVERT: Q 108 TYR cc_start: 0.6281 (t80) cc_final: 0.5952 (t80) outliers start: 173 outliers final: 113 residues processed: 657 average time/residue: 0.2140 time to fit residues: 235.6581 Evaluate side-chains 620 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 494 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 348 optimal weight: 1.9990 chunk 254 optimal weight: 0.0060 chunk 102 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN B 286 ASN B 733 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.153614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113753 restraints weight = 61615.250| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.49 r_work: 0.3424 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41885 Z= 0.183 Angle : 0.680 36.625 56793 Z= 0.313 Chirality : 0.044 0.282 6430 Planarity : 0.004 0.062 7105 Dihedral : 11.271 153.084 6294 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.25 % Allowed : 16.29 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.62 (0.12), residues: 4959 helix: 1.00 (0.12), residues: 1836 sheet: -0.77 (0.21), residues: 627 loop : -1.41 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1259 TYR 0.018 0.001 TYR O 132 PHE 0.018 0.001 PHE B 678 TRP 0.013 0.001 TRP A 201 HIS 0.009 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00435 (41861) covalent geometry : angle 0.60097 (56760) hydrogen bonds : bond 0.03684 ( 1692) hydrogen bonds : angle 4.68936 ( 4752) metal coordination : bond 0.00817 ( 24) metal coordination : angle 13.25343 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 516 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8173 (pm20) cc_final: 0.7769 (pm20) REVERT: A 46 ARG cc_start: 0.7509 (mmp80) cc_final: 0.7290 (mmp80) REVERT: A 193 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6826 (pm20) REVERT: A 219 MET cc_start: 0.8308 (mmt) cc_final: 0.8071 (mmm) REVERT: A 269 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8541 (ptt-90) REVERT: A 483 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8403 (mp) REVERT: A 511 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7730 (t0) REVERT: A 1333 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7505 (m-10) REVERT: A 1348 MET cc_start: 0.7627 (mtt) cc_final: 0.7355 (mtt) REVERT: B 42 GLN cc_start: 0.8119 (mt0) cc_final: 0.7770 (pt0) REVERT: B 132 ASP cc_start: 0.7605 (m-30) cc_final: 0.7297 (m-30) REVERT: B 263 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5378 (pp) REVERT: B 280 GLN cc_start: 0.8374 (mt0) cc_final: 0.7891 (mp10) REVERT: B 289 GLU cc_start: 0.7844 (mp0) cc_final: 0.7541 (mp0) REVERT: B 330 THR cc_start: 0.8740 (m) cc_final: 0.8278 (p) REVERT: B 545 ASP cc_start: 0.8668 (p0) cc_final: 0.8408 (p0) REVERT: B 802 THR cc_start: 0.6702 (OUTLIER) cc_final: 0.6418 (p) REVERT: B 1047 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.9017 (t) REVERT: B 1078 LEU cc_start: 0.8826 (tt) cc_final: 0.8428 (tt) REVERT: C 130 ASN cc_start: 0.9358 (t0) cc_final: 0.8910 (t0) REVERT: D 1 MET cc_start: 0.6380 (tpt) cc_final: 0.6164 (tpt) REVERT: D 51 ASN cc_start: 0.8112 (t0) cc_final: 0.7862 (t0) REVERT: D 52 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.5834 (m170) REVERT: E 52 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7782 (ttm-80) REVERT: E 57 MET cc_start: 0.7223 (pmm) cc_final: 0.6348 (ptp) REVERT: E 146 HIS cc_start: 0.8525 (m170) cc_final: 0.7993 (m170) REVERT: F 144 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: G 71 THR cc_start: 0.8550 (p) cc_final: 0.8244 (p) REVERT: G 149 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.8009 (mtp-110) REVERT: I 33 PHE cc_start: 0.7331 (t80) cc_final: 0.7078 (t80) REVERT: J 27 GLU cc_start: 0.6818 (pm20) cc_final: 0.6212 (pm20) REVERT: J 49 MET cc_start: 0.8753 (tpp) cc_final: 0.8457 (tpp) REVERT: K 67 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7728 (mm-30) REVERT: K 123 ASP cc_start: 0.8803 (m-30) cc_final: 0.8556 (m-30) REVERT: M 275 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6340 (tm-30) REVERT: N 302 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6710 (tp30) REVERT: O 368 ARG cc_start: 0.8468 (tmt-80) cc_final: 0.7772 (tmt170) REVERT: O 577 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: O 624 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.6880 (tt) REVERT: P 188 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7582 (tm-30) REVERT: P 245 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7919 (mm-30) REVERT: Q 51 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8364 (mm-30) REVERT: Q 70 PHE cc_start: 0.8368 (m-80) cc_final: 0.7970 (m-10) outliers start: 188 outliers final: 142 residues processed: 657 average time/residue: 0.2096 time to fit residues: 231.7171 Evaluate side-chains 644 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 489 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 277 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 chunk 300 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 207 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 385 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN B 286 ASN ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN N 288 GLN O 616 ASN ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.155994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.116562 restraints weight = 61030.275| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.54 r_work: 0.3475 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41885 Z= 0.117 Angle : 0.656 32.827 56793 Z= 0.299 Chirality : 0.042 0.335 6430 Planarity : 0.004 0.066 7105 Dihedral : 11.172 152.001 6294 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.59 % Allowed : 17.14 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.46 (0.12), residues: 4959 helix: 1.17 (0.12), residues: 1825 sheet: -0.65 (0.21), residues: 628 loop : -1.35 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1211 TYR 0.019 0.001 TYR D 65 PHE 0.028 0.001 PHE E 16 TRP 0.014 0.001 TRP A 197 HIS 0.013 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00265 (41861) covalent geometry : angle 0.57983 (56760) hydrogen bonds : bond 0.03341 ( 1692) hydrogen bonds : angle 4.54906 ( 4752) metal coordination : bond 0.00573 ( 24) metal coordination : angle 12.75034 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 516 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7801 (pm20) REVERT: A 46 ARG cc_start: 0.7346 (mmp80) cc_final: 0.7115 (mmp80) REVERT: A 193 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: A 219 MET cc_start: 0.8258 (mmt) cc_final: 0.8008 (mmm) REVERT: A 483 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 649 ASP cc_start: 0.8176 (t70) cc_final: 0.7828 (t0) REVERT: A 1333 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: A 1348 MET cc_start: 0.7733 (mtt) cc_final: 0.7507 (mtt) REVERT: A 1435 ASN cc_start: 0.8469 (t0) cc_final: 0.8235 (p0) REVERT: B 42 GLN cc_start: 0.8093 (mt0) cc_final: 0.7806 (pt0) REVERT: B 263 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5338 (pp) REVERT: B 280 GLN cc_start: 0.8335 (mt0) cc_final: 0.7862 (mp10) REVERT: B 289 GLU cc_start: 0.7792 (mp0) cc_final: 0.7428 (mp0) REVERT: B 296 TYR cc_start: 0.6422 (m-80) cc_final: 0.6144 (m-80) REVERT: B 330 THR cc_start: 0.8707 (m) cc_final: 0.8247 (p) REVERT: B 545 ASP cc_start: 0.8619 (p0) cc_final: 0.8351 (p0) REVERT: B 802 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6519 (p) REVERT: B 1078 LEU cc_start: 0.8756 (tt) cc_final: 0.8202 (tt) REVERT: C 130 ASN cc_start: 0.9357 (t0) cc_final: 0.8932 (t0) REVERT: C 278 GLU cc_start: 0.8686 (tp30) cc_final: 0.8457 (tp30) REVERT: D 1 MET cc_start: 0.6117 (tpt) cc_final: 0.5896 (tpt) REVERT: D 51 ASN cc_start: 0.8061 (t0) cc_final: 0.7823 (t0) REVERT: D 52 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.5810 (m170) REVERT: E 52 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7739 (ttm-80) REVERT: E 57 MET cc_start: 0.7117 (pmm) cc_final: 0.6156 (ptp) REVERT: E 146 HIS cc_start: 0.8488 (m170) cc_final: 0.7977 (m170) REVERT: F 144 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: G 149 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7993 (mtp-110) REVERT: I 33 PHE cc_start: 0.7227 (t80) cc_final: 0.6960 (t80) REVERT: J 27 GLU cc_start: 0.6791 (pm20) cc_final: 0.6210 (pm20) REVERT: J 49 MET cc_start: 0.8655 (tpp) cc_final: 0.8391 (tpp) REVERT: K 67 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7579 (mm-30) REVERT: M 275 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6294 (tm-30) REVERT: N 302 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6737 (tp30) REVERT: O 368 ARG cc_start: 0.8462 (tmt-80) cc_final: 0.7779 (tmt170) REVERT: O 577 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7825 (mtp) REVERT: O 624 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7369 (mt) REVERT: P 215 TYR cc_start: 0.8414 (p90) cc_final: 0.8207 (p90) REVERT: Q 70 PHE cc_start: 0.8212 (m-80) cc_final: 0.7771 (m-10) REVERT: Q 108 TYR cc_start: 0.6179 (t80) cc_final: 0.5844 (t80) outliers start: 159 outliers final: 125 residues processed: 640 average time/residue: 0.2139 time to fit residues: 229.9212 Evaluate side-chains 629 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 493 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1172 TYR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 171 optimal weight: 6.9990 chunk 496 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 471 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 466 optimal weight: 0.1980 chunk 457 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS B 286 ASN ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN O 626 GLN ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.155124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115906 restraints weight = 61523.828| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.54 r_work: 0.3464 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41885 Z= 0.144 Angle : 0.668 34.137 56793 Z= 0.305 Chirality : 0.043 0.246 6430 Planarity : 0.004 0.062 7105 Dihedral : 11.121 148.991 6290 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.64 % Allowed : 17.24 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.44 (0.12), residues: 4959 helix: 1.17 (0.12), residues: 1819 sheet: -0.62 (0.21), residues: 628 loop : -1.33 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 48 TYR 0.023 0.001 TYR B 304 PHE 0.025 0.001 PHE D 113 TRP 0.013 0.001 TRP A 197 HIS 0.013 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00338 (41861) covalent geometry : angle 0.59244 (56760) hydrogen bonds : bond 0.03416 ( 1692) hydrogen bonds : angle 4.56247 ( 4752) metal coordination : bond 0.00643 ( 24) metal coordination : angle 12.83005 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 499 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: A 46 ARG cc_start: 0.7380 (mmp80) cc_final: 0.7153 (mmp80) REVERT: A 193 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: A 219 MET cc_start: 0.8283 (mmt) cc_final: 0.8030 (mmm) REVERT: A 483 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 649 ASP cc_start: 0.8184 (t70) cc_final: 0.7889 (t0) REVERT: A 1333 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7483 (m-10) REVERT: A 1348 MET cc_start: 0.7713 (mtt) cc_final: 0.7497 (mtt) REVERT: A 1435 ASN cc_start: 0.8463 (t0) cc_final: 0.8238 (p0) REVERT: B 42 GLN cc_start: 0.8106 (mt0) cc_final: 0.7784 (pt0) REVERT: B 263 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5404 (pp) REVERT: B 280 GLN cc_start: 0.8348 (mt0) cc_final: 0.7888 (mp10) REVERT: B 325 GLU cc_start: 0.7562 (tp30) cc_final: 0.6966 (tm-30) REVERT: B 330 THR cc_start: 0.8745 (m) cc_final: 0.8079 (p) REVERT: B 545 ASP cc_start: 0.8614 (p0) cc_final: 0.8357 (p0) REVERT: B 802 THR cc_start: 0.6726 (OUTLIER) cc_final: 0.6466 (p) REVERT: B 1078 LEU cc_start: 0.8750 (tt) cc_final: 0.8207 (tt) REVERT: C 130 ASN cc_start: 0.9351 (t0) cc_final: 0.8901 (t0) REVERT: D 1 MET cc_start: 0.6159 (tpt) cc_final: 0.5938 (tpt) REVERT: D 51 ASN cc_start: 0.8055 (t0) cc_final: 0.7816 (t0) REVERT: D 52 HIS cc_start: 0.6961 (OUTLIER) cc_final: 0.5949 (m170) REVERT: E 52 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7749 (ttm-80) REVERT: E 57 MET cc_start: 0.7100 (pmm) cc_final: 0.6278 (ptp) REVERT: E 146 HIS cc_start: 0.8520 (m170) cc_final: 0.7982 (m170) REVERT: F 144 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: G 149 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7986 (mtp-110) REVERT: H 77 ARG cc_start: 0.8427 (ttp-170) cc_final: 0.8079 (ttp-170) REVERT: I 33 PHE cc_start: 0.7226 (t80) cc_final: 0.7001 (t80) REVERT: J 27 GLU cc_start: 0.6833 (pm20) cc_final: 0.6270 (pm20) REVERT: J 49 MET cc_start: 0.8720 (tpp) cc_final: 0.8386 (tpp) REVERT: K 67 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7564 (mm-30) REVERT: K 123 ASP cc_start: 0.8369 (m-30) cc_final: 0.7995 (m-30) REVERT: M 275 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6316 (tm-30) REVERT: O 368 ARG cc_start: 0.8460 (tmt-80) cc_final: 0.7768 (tmt170) REVERT: O 577 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7861 (mtp) REVERT: O 582 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: O 624 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7440 (mt) REVERT: P 188 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7570 (tm-30) REVERT: P 215 TYR cc_start: 0.8373 (p90) cc_final: 0.8112 (p90) REVERT: Q 70 PHE cc_start: 0.8231 (m-80) cc_final: 0.7936 (m-10) REVERT: Q 108 TYR cc_start: 0.6297 (t80) cc_final: 0.5950 (t80) outliers start: 161 outliers final: 127 residues processed: 623 average time/residue: 0.2228 time to fit residues: 233.0548 Evaluate side-chains 624 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 485 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1172 TYR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 582 GLU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 108 optimal weight: 9.9990 chunk 479 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 335 optimal weight: 0.5980 chunk 213 optimal weight: 0.8980 chunk 494 optimal weight: 7.9990 chunk 433 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 386 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS B 286 ASN ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN N 288 GLN ** N 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.155427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116186 restraints weight = 61381.839| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.52 r_work: 0.3455 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41885 Z= 0.161 Angle : 0.682 34.916 56793 Z= 0.312 Chirality : 0.043 0.323 6430 Planarity : 0.004 0.064 7105 Dihedral : 11.114 144.207 6288 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.37 % Allowed : 17.62 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.48 (0.12), residues: 4959 helix: 1.15 (0.12), residues: 1818 sheet: -0.65 (0.21), residues: 621 loop : -1.35 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1211 TYR 0.020 0.001 TYR B 304 PHE 0.023 0.001 PHE E 16 TRP 0.013 0.001 TRP O 583 HIS 0.013 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00383 (41861) covalent geometry : angle 0.60659 (56760) hydrogen bonds : bond 0.03496 ( 1692) hydrogen bonds : angle 4.58801 ( 4752) metal coordination : bond 0.00691 ( 24) metal coordination : angle 12.94271 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 488 time to evaluate : 1.862 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: A 46 ARG cc_start: 0.7401 (mmp80) cc_final: 0.7181 (mmp80) REVERT: A 193 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: A 219 MET cc_start: 0.8290 (mmt) cc_final: 0.8037 (mmm) REVERT: A 483 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 649 ASP cc_start: 0.8202 (t70) cc_final: 0.7911 (t0) REVERT: A 1333 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7506 (m-10) REVERT: A 1348 MET cc_start: 0.7712 (mtt) cc_final: 0.7448 (mtt) REVERT: A 1435 ASN cc_start: 0.8472 (t0) cc_final: 0.8242 (p0) REVERT: B 42 GLN cc_start: 0.8094 (mt0) cc_final: 0.7764 (pt0) REVERT: B 263 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5325 (pp) REVERT: B 280 GLN cc_start: 0.8372 (mt0) cc_final: 0.7900 (mp10) REVERT: B 312 MET cc_start: 0.7043 (mmm) cc_final: 0.5022 (tpp) REVERT: B 325 GLU cc_start: 0.7550 (tp30) cc_final: 0.6955 (tm-30) REVERT: B 330 THR cc_start: 0.8718 (m) cc_final: 0.8022 (p) REVERT: B 545 ASP cc_start: 0.8624 (p0) cc_final: 0.8373 (p0) REVERT: B 676 GLU cc_start: 0.7211 (pt0) cc_final: 0.6976 (pt0) REVERT: B 802 THR cc_start: 0.6702 (OUTLIER) cc_final: 0.6437 (p) REVERT: B 1078 LEU cc_start: 0.8764 (tt) cc_final: 0.8235 (tt) REVERT: C 84 TYR cc_start: 0.8955 (m-80) cc_final: 0.8344 (m-80) REVERT: C 130 ASN cc_start: 0.9345 (t0) cc_final: 0.8878 (t0) REVERT: D 1 MET cc_start: 0.6230 (tpt) cc_final: 0.6003 (tpt) REVERT: D 51 ASN cc_start: 0.8076 (t0) cc_final: 0.7836 (t0) REVERT: D 52 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6009 (m170) REVERT: E 52 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7736 (ttm-80) REVERT: E 57 MET cc_start: 0.7121 (pmm) cc_final: 0.6265 (ptp) REVERT: E 146 HIS cc_start: 0.8527 (m170) cc_final: 0.8018 (m170) REVERT: F 144 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: G 149 ARG cc_start: 0.8244 (mtp-110) cc_final: 0.7967 (mtp-110) REVERT: I 33 PHE cc_start: 0.7252 (t80) cc_final: 0.7024 (t80) REVERT: J 27 GLU cc_start: 0.6844 (pm20) cc_final: 0.6317 (pm20) REVERT: J 49 MET cc_start: 0.8717 (tpp) cc_final: 0.8344 (tpp) REVERT: K 67 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7556 (mm-30) REVERT: K 123 ASP cc_start: 0.8419 (m-30) cc_final: 0.8059 (m-30) REVERT: L 66 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8334 (tp40) REVERT: M 275 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6304 (tm-30) REVERT: O 577 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7880 (mtp) REVERT: O 582 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: O 624 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7432 (mt) REVERT: P 215 TYR cc_start: 0.8399 (p90) cc_final: 0.8173 (p90) REVERT: Q 70 PHE cc_start: 0.8205 (m-80) cc_final: 0.7896 (m-10) outliers start: 149 outliers final: 125 residues processed: 607 average time/residue: 0.2476 time to fit residues: 252.4389 Evaluate side-chains 622 residues out of total 4433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 484 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1172 TYR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 582 GLU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 79 optimal weight: 0.7980 chunk 445 optimal weight: 0.2980 chunk 407 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 chunk 366 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 306 optimal weight: 0.8980 chunk 180 optimal weight: 0.1980 chunk 313 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN ** N 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 GLN ** P 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.157071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.117661 restraints weight = 61313.085| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.52 r_work: 0.3489 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41885 Z= 0.115 Angle : 0.659 32.252 56793 Z= 0.300 Chirality : 0.042 0.349 6430 Planarity : 0.004 0.063 7105 Dihedral : 11.029 138.652 6285 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.00 % Allowed : 18.12 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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 aren not related in a simple way. whole: -0.37 (0.12), residues: 4959 helix: 1.24 (0.12), residues: 1812 sheet: -0.55 (0.21), residues: 621 loop : -1.31 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1211 TYR 0.021 0.001 TYR B 304 PHE 0.025 0.001 PHE E 16 TRP 0.016 0.001 TRP A 197 HIS 0.012 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00259 (41861) covalent geometry : angle 0.58518 (56760) hydrogen bonds : bond 0.03274 ( 1692) hydrogen bonds : angle 4.49426 ( 4752) metal coordination : bond 0.00529 ( 24) metal coordination : angle 12.62394 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12865.20 seconds wall clock time: 220 minutes 3.83 seconds (13203.83 seconds total)