Starting phenix.real_space_refine on Tue Jul 7 05:31:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k38_62008/07_2026/9k38_62008.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k38_62008/07_2026/9k38_62008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k38_62008/07_2026/9k38_62008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k38_62008/07_2026/9k38_62008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k38_62008/07_2026/9k38_62008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k38_62008/07_2026/9k38_62008.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 285 5.16 5 C 27799 2.51 5 N 7743 2.21 5 O 8575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44526 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 10814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10814 Classifications: {'peptide': 1378} Link IDs: {'PTRANS': 64, 'TRANS': 1313} Chain: "B" Number of atoms: 8736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8736 Classifications: {'peptide': 1105} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1053} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "V" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 246 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "X" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1048 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Y" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1043 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Z" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, '3AT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 58.023 113.600 82.639 1.00103.58 S ATOM 565 SG CYS A 72 58.587 117.171 83.884 1.00106.71 S ATOM 613 SG CYS A 79 61.908 115.032 82.745 1.00104.11 S ATOM 854 SG CYS A 109 67.852 88.743 122.696 1.00114.77 S ATOM 876 SG CYS A 112 65.731 91.103 124.638 1.00118.64 S ATOM 1245 SG CYS A 156 68.379 90.079 126.926 1.00130.18 S ATOM 1271 SG CYS A 159 65.705 87.987 126.194 1.00130.36 S ATOM 19137 SG CYS B1080 59.826 120.490 100.360 1.00102.14 S ATOM 19156 SG CYS B1083 61.102 116.782 100.762 1.00101.99 S ATOM 19222 SG CYS B1092 58.757 117.801 98.158 1.00 97.16 S ATOM 19250 SG CYS B1095 57.404 117.149 102.264 1.00100.21 S ATOM 28160 SG CYS I 5 117.340 48.067 107.915 1.00130.73 S ATOM 28177 SG CYS I 8 113.791 49.157 106.268 1.00130.05 S ATOM 28307 SG CYS I 25 113.478 50.847 109.309 1.00130.27 S ATOM 28328 SG CYS I 28 113.891 47.385 109.405 1.00128.16 S ATOM 28600 SG CYS J 7 116.819 123.431 43.056 1.00 75.41 S ATOM 28624 SG CYS J 10 118.290 126.668 41.740 1.00 75.83 S ATOM 28888 SG CYS J 44 120.579 124.467 43.254 1.00 81.33 S ATOM 28894 SG CYS J 45 119.862 123.693 39.715 1.00 82.39 S ATOM 29937 SG CYS L 19 84.225 97.281 33.736 1.00103.46 S ATOM 29956 SG CYS L 22 85.313 95.228 29.892 1.00109.30 S ATOM 30073 SG CYS L 36 81.220 97.130 31.346 1.00117.09 S ATOM 30099 SG CYS L 39 82.963 93.874 32.087 1.00117.30 S ATOM 41169 SG CYS P 307 41.548 100.043 105.804 1.00108.29 S Time building chain proxies: 8.27, per 1000 atoms: 0.19 Number of scatterers: 44526 At special positions: 0 Unit cell: (174.562, 182.558, 171.897, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 285 16.00 P 113 15.00 Mg 1 11.99 O 8575 8.00 N 7743 7.00 C 27799 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " Number of angles added : 9 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 33 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10004 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 57 sheets defined 42.5% alpha, 17.0% beta 34 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 5.42 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.730A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 212 Proline residue: A 209 - end of helix removed outlier: 4.466A pdb=" N GLY A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.597A pdb=" N ARG A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 5.923A pdb=" N GLU A 233 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 277 through 300 removed outlier: 3.788A pdb=" N MET A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.787A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 572 No H-bonds generated for 'chain 'A' and resid 571 through 572' Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.646A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.769A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 662 through 672 Processing helix chain 'A' and resid 672 through 695 removed outlier: 3.919A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 733 Processing helix chain 'A' and resid 743 through 771 Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.709A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.518A pdb=" N ASP A 905 " --> pdb=" O TYR A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 954 removed outlier: 3.542A pdb=" N LYS A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 987 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1007 through 1025 Processing helix chain 'A' and resid 1032 through 1048 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1094 through 1106 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 3.949A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1238 removed outlier: 3.571A pdb=" N VAL A1235 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1278 removed outlier: 7.738A pdb=" N ILE A1260 " --> pdb=" O LYS A1256 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N GLU A1261 " --> pdb=" O THR A1257 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.958A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1314 through 1322 Processing helix chain 'A' and resid 1323 through 1335 Processing helix chain 'A' and resid 1342 through 1350 removed outlier: 3.553A pdb=" N CYS A1346 " --> pdb=" O GLY A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.669A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1359 " --> pdb=" O GLY A1356 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A1360 " --> pdb=" O THR A1357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1355 through 1360' Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.260A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.835A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.582A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 275 Proline residue: B 267 - end of helix removed outlier: 3.673A pdb=" N ALA B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 304 through 315 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.641A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 422 removed outlier: 4.187A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 518 Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.600A pdb=" N LEU B 526 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.591A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 566 removed outlier: 3.734A pdb=" N LEU B 555 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.589A pdb=" N THR B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 691 Processing helix chain 'B' and resid 722 through 729 Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.411A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.764A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.589A pdb=" N VAL B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1048 through 1059 Processing helix chain 'B' and resid 1060 through 1069 Processing helix chain 'B' and resid 1108 through 1120 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.538A pdb=" N ILE C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.520A pdb=" N LEU C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.738A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 317 through 344 Processing helix chain 'D' and resid 12 through 30 removed outlier: 3.830A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.583A pdb=" N GLN D 39 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.141A pdb=" N ALA D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.850A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.542A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 126 Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 140 through 159 Processing helix chain 'M' and resid 182 through 191 Processing helix chain 'M' and resid 192 through 203 removed outlier: 3.982A pdb=" N GLU M 203 " --> pdb=" O LYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 222 removed outlier: 3.906A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 226 Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'M' and resid 269 through 275 Processing helix chain 'M' and resid 277 through 289 Processing helix chain 'M' and resid 293 through 302 Processing helix chain 'M' and resid 306 through 315 Processing helix chain 'M' and resid 328 through 333 removed outlier: 3.809A pdb=" N LEU M 332 " --> pdb=" O LYS M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 363 removed outlier: 3.559A pdb=" N LEU M 349 " --> pdb=" O PRO M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 376 Processing helix chain 'M' and resid 378 through 388 Processing helix chain 'M' and resid 405 through 412 removed outlier: 4.011A pdb=" N ILE M 409 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 435 Processing helix chain 'N' and resid 147 through 151 removed outlier: 4.096A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 259 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 388 through 396 removed outlier: 3.943A pdb=" N LYS N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 21 through 32 Processing helix chain 'O' and resid 35 through 44 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.787A pdb=" N HIS O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 78 through 85 Processing helix chain 'O' and resid 87 through 99 Processing helix chain 'O' and resid 100 through 114 Processing helix chain 'O' and resid 117 through 133 removed outlier: 4.017A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 4.063A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 Processing helix chain 'O' and resid 260 through 278 removed outlier: 4.517A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 297 Processing helix chain 'O' and resid 304 through 317 Processing helix chain 'O' and resid 337 through 359 Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 376 through 385 Processing helix chain 'O' and resid 390 through 401 Processing helix chain 'O' and resid 416 through 418 No H-bonds generated for 'chain 'O' and resid 416 through 418' Processing helix chain 'O' and resid 427 through 457 Processing helix chain 'O' and resid 457 through 473 removed outlier: 4.189A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.569A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 530 removed outlier: 4.041A pdb=" N GLU O 495 " --> pdb=" O ILE O 491 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 29 Processing helix chain 'P' and resid 34 through 42 Processing helix chain 'P' and resid 46 through 60 Processing helix chain 'P' and resid 88 through 103 removed outlier: 3.670A pdb=" N GLU P 92 " --> pdb=" O SER P 88 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'P' and resid 108 through 117 Processing helix chain 'P' and resid 119 through 133 removed outlier: 3.539A pdb=" N LYS P 133 " --> pdb=" O ASN P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.575A pdb=" N LYS P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 Processing helix chain 'P' and resid 213 through 224 Processing helix chain 'P' and resid 231 through 245 Processing helix chain 'P' and resid 281 through 285 Processing helix chain 'P' and resid 292 through 296 Processing helix chain 'P' and resid 307 through 316 Processing helix chain 'Q' and resid 51 through 69 removed outlier: 3.878A pdb=" N LYS Q 69 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 93 Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.798A pdb=" N MET Q 110 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 7.350A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B1123 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 93 removed outlier: 6.851A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N ILE A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 268 removed outlier: 3.703A pdb=" N SER A 268 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.796A pdb=" N LYS A 359 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 3.548A pdb=" N ARG A 487 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 368 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER A 370 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.259A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA9, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.658A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 883 through 884 removed outlier: 6.916A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1210 through 1215 removed outlier: 7.184A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N THR A1086 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR A1244 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN A1088 " --> pdb=" O LYS A1242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 6.947A pdb=" N THR A1108 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1114 through 1121 removed outlier: 3.869A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1361 through 1364 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 65 removed outlier: 7.285A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 79 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 131 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE B 117 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN B 129 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE B 127 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 363 removed outlier: 6.692A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 189 through 193 Processing sheet with id=AC1, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AC2, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC3, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 550 removed outlier: 5.379A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL B 583 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.572A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.572A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 986 through 987 removed outlier: 7.343A pdb=" N LEU B 755 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 910 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 757 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 927 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 929 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.519A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 918 through 919 Processing sheet with id=AD2, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.270A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 21 through 22 removed outlier: 7.114A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.752A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.318A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 88 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.779A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.716A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.721A pdb=" N THR C 240 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE1, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.768A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA D 6 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU G 4 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU G 55 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL G 75 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 72 through 75 Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.759A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.600A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 105 through 108 removed outlier: 3.951A pdb=" N ASP G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 101 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE G 107 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL G 99 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.925A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 12 through 16 Processing sheet with id=AE8, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 17 removed outlier: 3.545A pdb=" N ALA M 115 " --> pdb=" O LEU N 269 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY N 327 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 25 through 34 removed outlier: 6.964A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG M 33 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 11.698A pdb=" N GLU N 359 " --> pdb=" O PRO M 31 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N VAL N 361 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N GLN M 29 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N VAL N 363 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LEU M 27 " --> pdb=" O VAL N 363 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 291 through 292 removed outlier: 3.544A pdb=" N TRP M 325 " --> pdb=" O MET M 292 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AF4, first strand: chain 'O' and resid 63 through 67 Processing sheet with id=AF5, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AF6, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AF7, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AF8, first strand: chain 'O' and resid 409 through 410 Processing sheet with id=AF9, first strand: chain 'P' and resid 63 through 68 Processing sheet with id=AG1, first strand: chain 'P' and resid 136 through 140 Processing sheet with id=AG2, first strand: chain 'P' and resid 211 through 212 Processing sheet with id=AG3, first strand: chain 'V' and resid 15 through 17 removed outlier: 6.461A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1908 hydrogen bonds defined for protein. 5394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 14.08 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.38: 15101 1.38 - 1.60: 29896 1.60 - 1.83: 562 1.83 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 45571 Sorted by residual: bond pdb=" O3' C Z 4 " pdb=" P U Z 5 " ideal model delta sigma weight residual 1.607 1.466 0.141 1.50e-02 4.44e+03 8.89e+01 bond pdb=" C LEU I 46 " pdb=" O LEU I 46 " ideal model delta sigma weight residual 1.234 1.149 0.086 1.07e-02 8.73e+03 6.39e+01 bond pdb=" O3B 3AT B1202 " pdb=" PG 3AT B1202 " ideal model delta sigma weight residual 1.745 1.608 0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C1' DT Y -23 " pdb=" N1 DT Y -23 " ideal model delta sigma weight residual 1.468 1.563 -0.095 1.40e-02 5.10e+03 4.56e+01 bond pdb=" O3' U Z 2 " pdb=" P G Z 3 " ideal model delta sigma weight residual 1.607 1.508 0.099 1.50e-02 4.44e+03 4.40e+01 ... (remaining 45566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 61930 4.38 - 8.76: 61 8.76 - 13.14: 11 13.14 - 17.53: 2 17.53 - 21.91: 3 Bond angle restraints: 62007 Sorted by residual: angle pdb=" C3' U Z 2 " pdb=" O3' U Z 2 " pdb=" P G Z 3 " ideal model delta sigma weight residual 120.20 98.29 21.91 1.50e+00 4.44e-01 2.13e+02 angle pdb=" O3' U Z 2 " pdb=" P G Z 3 " pdb=" O5' G Z 3 " ideal model delta sigma weight residual 104.00 125.70 -21.70 1.50e+00 4.44e-01 2.09e+02 angle pdb=" C3' U Z 5 " pdb=" C2' U Z 5 " pdb=" O2' U Z 5 " ideal model delta sigma weight residual 110.70 130.60 -19.90 1.50e+00 4.44e-01 1.76e+02 angle pdb=" N ASP I 51 " pdb=" CA ASP I 51 " pdb=" C ASP I 51 " ideal model delta sigma weight residual 110.17 121.95 -11.78 1.51e+00 4.39e-01 6.09e+01 angle pdb=" O4' C Z 6 " pdb=" C4' C Z 6 " pdb=" C3' C Z 6 " ideal model delta sigma weight residual 104.00 96.94 7.06 1.00e+00 1.00e+00 4.99e+01 ... (remaining 62002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 27205 35.76 - 71.51: 520 71.51 - 107.27: 25 107.27 - 143.02: 2 143.02 - 178.78: 10 Dihedral angle restraints: 27762 sinusoidal: 12283 harmonic: 15479 Sorted by residual: dihedral pdb=" O3A GTP Z 101 " pdb=" O3B GTP Z 101 " pdb=" PB GTP Z 101 " pdb=" PG GTP Z 101 " ideal model delta sinusoidal sigma weight residual 303.79 154.91 148.88 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C8 GTP Z 101 " pdb=" C1' GTP Z 101 " pdb=" N9 GTP Z 101 " pdb=" O4' GTP Z 101 " ideal model delta sinusoidal sigma weight residual 104.59 -33.09 137.68 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' GTP Z 101 " pdb=" O5' GTP Z 101 " pdb=" PA GTP Z 101 " pdb=" O3A GTP Z 101 " ideal model delta sinusoidal sigma weight residual 69.27 168.76 -99.50 1 2.00e+01 2.50e-03 2.80e+01 ... (remaining 27759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 6849 0.120 - 0.240: 120 0.240 - 0.360: 5 0.360 - 0.480: 2 0.480 - 0.600: 1 Chirality restraints: 6977 Sorted by residual: chirality pdb=" C2' U Z 5 " pdb=" C3' U Z 5 " pdb=" O2' U Z 5 " pdb=" C1' U Z 5 " both_signs ideal model delta sigma weight residual False -2.75 -2.15 -0.60 2.00e-01 2.50e+01 8.99e+00 chirality pdb=" CA ASP I 51 " pdb=" N ASP I 51 " pdb=" C ASP I 51 " pdb=" CB ASP I 51 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C3' U Z 5 " pdb=" C4' U Z 5 " pdb=" O3' U Z 5 " pdb=" C2' U Z 5 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 6974 not shown) Planarity restraints: 7603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 46 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C LEU I 46 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU I 46 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS I 47 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C Z 6 " 0.030 2.00e-02 2.50e+03 2.03e-02 9.23e+00 pdb=" N1 C Z 6 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C Z 6 " -0.030 2.00e-02 2.50e+03 pdb=" O2 C Z 6 " 0.010 2.00e-02 2.50e+03 pdb=" N3 C Z 6 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C Z 6 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C Z 6 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C Z 6 " 0.021 2.00e-02 2.50e+03 pdb=" C6 C Z 6 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G Z 3 " -0.021 2.00e-02 2.50e+03 1.73e-02 8.93e+00 pdb=" N9 G Z 3 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G Z 3 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G Z 3 " 0.012 2.00e-02 2.50e+03 pdb=" C5 G Z 3 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G Z 3 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G Z 3 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G Z 3 " -0.015 2.00e-02 2.50e+03 pdb=" C2 G Z 3 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G Z 3 " 0.029 2.00e-02 2.50e+03 pdb=" N3 G Z 3 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G Z 3 " -0.029 2.00e-02 2.50e+03 ... (remaining 7600 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 80 2.32 - 2.97: 21207 2.97 - 3.61: 65889 3.61 - 4.26: 103520 4.26 - 4.90: 170885 Nonbonded interactions: 361581 Sorted by model distance: nonbonded pdb=" OG1 THR A 303 " pdb=" NE2 GLN O 377 " model vdw 1.679 3.120 nonbonded pdb=" O6 DG X 11 " pdb=" N4 DC Y -11 " model vdw 1.826 3.120 nonbonded pdb=" OG1 THR A 303 " pdb=" OH TYR O 424 " model vdw 1.835 3.040 nonbonded pdb=" O ILE A 230 " pdb=" N THR O 2 " model vdw 1.878 3.120 nonbonded pdb=" OE1 GLN E 95 " pdb=" OH TYR E 125 " model vdw 2.010 3.040 ... (remaining 361576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 58.940 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 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 : 0.011 1.021 45600 Z= 0.625 Angle : 0.806 59.486 62049 Z= 0.367 Chirality : 0.043 0.600 6977 Planarity : 0.003 0.046 7603 Dihedral : 12.434 178.775 17758 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.53 % Allowed : 2.45 % Favored : 97.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.11), residues: 5269 helix: 0.39 (0.11), residues: 2025 sheet: -1.35 (0.17), residues: 717 loop : -1.68 (0.11), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 900 TYR 0.008 0.001 TYR L 41 PHE 0.006 0.001 PHE B1004 TRP 0.005 0.001 TRP P 313 HIS 0.003 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.31 (45571) covalent geometry : angle 0.54633 / 0.36 (62007) hydrogen bonds : bond 0.14511 / 9.69 ( 1961) hydrogen bonds : angle 5.45956 / 3.89 ( 5550) metal coordination : bond 0.35618 / 17.89 ( 27) metal coordination : angle 22.80220 / 13.86 ( 42) Misc. bond : bond 0.71838 / 36.88 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1533 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 1508 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8633 (t) cc_final: 0.8091 (m) REVERT: A 42 TYR cc_start: 0.7396 (m-80) cc_final: 0.6914 (m-80) REVERT: A 65 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7981 (tttm) REVERT: A 76 LEU cc_start: 0.8327 (tt) cc_final: 0.8104 (tp) REVERT: A 93 PHE cc_start: 0.6536 (m-80) cc_final: 0.6310 (m-10) REVERT: A 241 ASN cc_start: 0.6778 (t0) cc_final: 0.6380 (t0) REVERT: A 246 LYS cc_start: 0.6386 (mtmt) cc_final: 0.6039 (ptpt) REVERT: A 249 ASP cc_start: 0.6847 (m-30) cc_final: 0.5986 (m-30) REVERT: A 406 LYS cc_start: 0.7305 (ttpt) cc_final: 0.7069 (ttpt) REVERT: A 445 LYS cc_start: 0.7626 (mmpt) cc_final: 0.7082 (tttm) REVERT: A 449 ILE cc_start: 0.8749 (mt) cc_final: 0.8447 (mm) REVERT: A 468 LEU cc_start: 0.7662 (mt) cc_final: 0.7238 (mm) REVERT: A 513 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7298 (mp0) REVERT: A 536 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7033 (pt0) REVERT: A 542 ILE cc_start: 0.7711 (tp) cc_final: 0.7454 (tt) REVERT: A 556 ASP cc_start: 0.8319 (m-30) cc_final: 0.7855 (m-30) REVERT: A 582 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7731 (ttt90) REVERT: A 647 SER cc_start: 0.7845 (t) cc_final: 0.7418 (p) REVERT: A 740 PRO cc_start: 0.7685 (Cg_endo) cc_final: 0.7245 (Cg_exo) REVERT: A 789 PHE cc_start: 0.8037 (m-10) cc_final: 0.7742 (m-80) REVERT: A 836 ASN cc_start: 0.7190 (m-40) cc_final: 0.6862 (m-40) REVERT: A 917 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6522 (tp30) REVERT: A 918 PRO cc_start: 0.6229 (Cg_endo) cc_final: 0.5989 (Cg_exo) REVERT: A 947 LEU cc_start: 0.8298 (tt) cc_final: 0.7893 (mt) REVERT: A 967 GLN cc_start: 0.6209 (mm-40) cc_final: 0.5811 (mm110) REVERT: A 1023 MET cc_start: 0.8558 (mmt) cc_final: 0.8338 (mmm) REVERT: A 1026 GLN cc_start: 0.7395 (mt0) cc_final: 0.7016 (pp30) REVERT: A 1078 LYS cc_start: 0.8140 (mttp) cc_final: 0.7611 (mppt) REVERT: A 1096 ASP cc_start: 0.7960 (t0) cc_final: 0.7753 (t70) REVERT: A 1185 MET cc_start: 0.5937 (pmm) cc_final: 0.5529 (pmm) REVERT: A 1190 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7957 (mm-40) REVERT: A 1191 PHE cc_start: 0.7815 (t80) cc_final: 0.7170 (t80) REVERT: A 1196 LEU cc_start: 0.8401 (tp) cc_final: 0.8178 (mt) REVERT: A 1250 ASN cc_start: 0.8553 (t0) cc_final: 0.8056 (t0) REVERT: A 1299 GLU cc_start: 0.7714 (tt0) cc_final: 0.7431 (pt0) REVERT: A 1301 LEU cc_start: 0.8380 (mt) cc_final: 0.8029 (mt) REVERT: A 1345 GLU cc_start: 0.7567 (pm20) cc_final: 0.7204 (mp0) REVERT: B 64 LYS cc_start: 0.6300 (ttmt) cc_final: 0.5898 (ttmm) REVERT: B 211 LYS cc_start: 0.6154 (mttt) cc_final: 0.5800 (pttt) REVERT: B 226 ARG cc_start: 0.6726 (ttm110) cc_final: 0.6417 (ttm110) REVERT: B 249 GLN cc_start: 0.6166 (tt0) cc_final: 0.5901 (tp40) REVERT: B 285 LYS cc_start: 0.7715 (ttmm) cc_final: 0.7230 (tppt) REVERT: B 338 MET cc_start: 0.7094 (ttp) cc_final: 0.6803 (ttm) REVERT: B 357 TYR cc_start: 0.7498 (m-10) cc_final: 0.6980 (m-80) REVERT: B 380 PHE cc_start: 0.5674 (t80) cc_final: 0.5395 (t80) REVERT: B 407 ARG cc_start: 0.7930 (ttm110) cc_final: 0.7139 (ttp80) REVERT: B 499 MET cc_start: 0.8968 (ttp) cc_final: 0.8623 (ttp) REVERT: B 556 VAL cc_start: 0.6186 (t) cc_final: 0.5664 (m) REVERT: B 561 LEU cc_start: 0.8288 (tp) cc_final: 0.7991 (mt) REVERT: B 567 TYR cc_start: 0.8785 (m-80) cc_final: 0.8533 (m-80) REVERT: B 573 SER cc_start: 0.9161 (t) cc_final: 0.8958 (p) REVERT: B 609 LYS cc_start: 0.8318 (tmmt) cc_final: 0.7215 (tmtt) REVERT: B 613 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 627 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7144 (mt-10) REVERT: B 664 LEU cc_start: 0.8125 (tp) cc_final: 0.7843 (mp) REVERT: B 726 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 746 TYR cc_start: 0.8606 (t80) cc_final: 0.8366 (t80) REVERT: B 787 PHE cc_start: 0.7760 (p90) cc_final: 0.7408 (p90) REVERT: B 789 LYS cc_start: 0.5540 (ptmt) cc_final: 0.5067 (pttt) REVERT: B 791 MET cc_start: 0.7146 (mmt) cc_final: 0.6884 (mmm) REVERT: B 888 THR cc_start: 0.8555 (m) cc_final: 0.8049 (m) REVERT: B 996 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8036 (mt-10) REVERT: B 1049 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6439 (mt-10) REVERT: B 1062 MET cc_start: 0.8156 (mmm) cc_final: 0.7875 (mmp) REVERT: B 1105 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7933 (mmm-85) REVERT: C 137 THR cc_start: 0.7475 (t) cc_final: 0.7045 (m) REVERT: C 139 GLN cc_start: 0.7558 (mt0) cc_final: 0.7292 (mm-40) REVERT: C 180 ASN cc_start: 0.7896 (m110) cc_final: 0.7598 (p0) REVERT: C 290 ASN cc_start: 0.7831 (t0) cc_final: 0.7435 (t0) REVERT: C 296 VAL cc_start: 0.9242 (m) cc_final: 0.8941 (p) REVERT: D 3 VAL cc_start: 0.8444 (m) cc_final: 0.8111 (t) REVERT: D 42 LEU cc_start: 0.7617 (tt) cc_final: 0.7092 (tp) REVERT: D 82 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7121 (mm-30) REVERT: E 52 ARG cc_start: 0.6446 (mtp85) cc_final: 0.5775 (ttm170) REVERT: E 73 PHE cc_start: 0.5748 (t80) cc_final: 0.5303 (t80) REVERT: E 85 LYS cc_start: 0.8422 (mttt) cc_final: 0.8024 (mmtm) REVERT: E 94 MET cc_start: 0.7475 (mmp) cc_final: 0.6894 (mmp) REVERT: E 189 GLN cc_start: 0.8177 (mt0) cc_final: 0.7938 (mt0) REVERT: E 192 LYS cc_start: 0.7254 (ttpt) cc_final: 0.6927 (tttt) REVERT: F 98 LYS cc_start: 0.8508 (ttpp) cc_final: 0.7881 (mtmt) REVERT: F 101 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8411 (mttm) REVERT: F 114 SER cc_start: 0.8055 (t) cc_final: 0.7712 (p) REVERT: F 115 TYR cc_start: 0.7836 (p90) cc_final: 0.7534 (p90) REVERT: F 116 GLU cc_start: 0.7321 (pt0) cc_final: 0.6724 (pt0) REVERT: G 6 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6718 (mm-30) REVERT: G 53 LYS cc_start: 0.7940 (tptt) cc_final: 0.7567 (ttpt) REVERT: G 69 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7967 (tttt) REVERT: G 77 PHE cc_start: 0.8465 (t80) cc_final: 0.7970 (t80) REVERT: G 90 LYS cc_start: 0.5457 (mptt) cc_final: 0.5156 (mmtt) REVERT: G 100 SER cc_start: 0.6800 (t) cc_final: 0.6505 (p) REVERT: G 110 PRO cc_start: 0.2228 (Cg_exo) cc_final: 0.1962 (Cg_endo) REVERT: G 159 ASP cc_start: 0.6965 (t70) cc_final: 0.5777 (t0) REVERT: H 7 GLU cc_start: 0.8275 (tt0) cc_final: 0.7619 (tt0) REVERT: H 57 ARG cc_start: 0.7400 (ttp80) cc_final: 0.6269 (ttt180) REVERT: H 65 TYR cc_start: 0.7594 (m-10) cc_final: 0.7138 (m-80) REVERT: H 75 TYR cc_start: 0.7132 (t80) cc_final: 0.6922 (t80) REVERT: H 100 GLU cc_start: 0.6867 (tt0) cc_final: 0.6591 (tt0) REVERT: H 118 TYR cc_start: 0.8797 (m-80) cc_final: 0.8439 (m-80) REVERT: I 22 ARG cc_start: 0.5908 (ptt180) cc_final: 0.5661 (ptt180) REVERT: I 42 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7720 (mttp) REVERT: J 49 LEU cc_start: 0.9029 (mt) cc_final: 0.8730 (mt) REVERT: K 31 GLN cc_start: 0.6045 (pp30) cc_final: 0.5093 (pt0) REVERT: L 52 LEU cc_start: 0.5971 (tt) cc_final: 0.5711 (tt) REVERT: M 25 LEU cc_start: 0.7783 (tp) cc_final: 0.7449 (tp) REVERT: M 49 ILE cc_start: 0.7514 (tt) cc_final: 0.7251 (tp) REVERT: M 80 ASN cc_start: 0.7582 (m-40) cc_final: 0.6935 (m-40) REVERT: M 137 PRO cc_start: 0.8664 (Cg_endo) cc_final: 0.8422 (Cg_exo) REVERT: M 141 TYR cc_start: 0.7547 (p90) cc_final: 0.7057 (p90) REVERT: M 197 GLN cc_start: 0.7527 (tt0) cc_final: 0.6609 (mm110) REVERT: M 270 MET cc_start: 0.1786 (tpp) cc_final: 0.0468 (ptp) REVERT: M 319 MET cc_start: 0.2033 (mmm) cc_final: 0.1513 (mtp) REVERT: M 357 MET cc_start: 0.3886 (mtm) cc_final: 0.3059 (ptp) REVERT: N 275 LEU cc_start: 0.8280 (mp) cc_final: 0.8045 (mp) REVERT: O 14 GLN cc_start: 0.8376 (tt0) cc_final: 0.8143 (tp40) REVERT: O 20 ILE cc_start: 0.9101 (pt) cc_final: 0.8767 (mt) REVERT: O 65 TYR cc_start: 0.8015 (p90) cc_final: 0.7814 (p90) REVERT: O 85 MET cc_start: 0.8124 (ttm) cc_final: 0.7781 (ttp) REVERT: O 108 GLU cc_start: 0.7420 (tt0) cc_final: 0.7124 (tm-30) REVERT: O 132 THR cc_start: 0.6198 (m) cc_final: 0.5914 (p) REVERT: O 187 MET cc_start: 0.7454 (tpt) cc_final: 0.7142 (tpt) REVERT: O 233 ILE cc_start: 0.6985 (mm) cc_final: 0.6377 (mp) REVERT: O 248 ASP cc_start: 0.9044 (m-30) cc_final: 0.8678 (m-30) REVERT: O 322 PHE cc_start: 0.7972 (m-80) cc_final: 0.6718 (m-80) REVERT: O 336 ILE cc_start: 0.7163 (mp) cc_final: 0.6571 (mp) REVERT: O 383 PHE cc_start: 0.7197 (m-10) cc_final: 0.6561 (m-10) REVERT: O 390 GLU cc_start: 0.7251 (tt0) cc_final: 0.7030 (tp30) REVERT: O 401 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8099 (mm-30) REVERT: O 441 LYS cc_start: 0.7589 (tttt) cc_final: 0.7358 (tptm) REVERT: O 503 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7399 (tptp) REVERT: O 507 ASN cc_start: 0.8297 (m-40) cc_final: 0.7411 (m110) REVERT: P 218 LYS cc_start: 0.7560 (mmmm) cc_final: 0.7014 (mtpt) REVERT: P 232 MET cc_start: 0.5357 (ttp) cc_final: 0.4765 (mmm) REVERT: Q 43 TYR cc_start: 0.7190 (m-80) cc_final: 0.6975 (m-80) REVERT: Q 54 GLU cc_start: 0.7264 (mp0) cc_final: 0.6954 (mp0) REVERT: Q 55 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7892 (tp30) REVERT: Q 66 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7332 (mm-30) REVERT: Q 92 MET cc_start: 0.1157 (ptt) cc_final: 0.0164 (mtp) REVERT: Q 102 ASP cc_start: 0.7998 (t0) cc_final: 0.7651 (t0) REVERT: Q 103 TRP cc_start: 0.7600 (m100) cc_final: 0.7149 (m100) outliers start: 25 outliers final: 8 residues processed: 1524 average time/residue: 0.2789 time to fit residues: 679.3485 Evaluate side-chains 882 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 874 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain O residue 55 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 0.4980 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN A 114 HIS ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN A 465 GLN A 469 HIS A 599 GLN A 739 GLN A 794 GLN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 320 HIS ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 268 GLN G 31 ASN G 98 HIS H 29 HIS H 87 GLN H 131 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN M 100 GLN M 197 GLN N 270 GLN N 378 HIS O 41 HIS O 68 HIS O 306 GLN O 402 ASN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 ASN P 182 GLN P 240 ASN P 274 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.193174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123417 restraints weight = 63160.709| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.67 r_work: 0.3159 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 45600 Z= 0.231 Angle : 0.705 20.047 62049 Z= 0.354 Chirality : 0.048 0.297 6977 Planarity : 0.005 0.063 7603 Dihedral : 16.301 179.210 7048 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.41 % Allowed : 10.18 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.11), residues: 5269 helix: 0.94 (0.11), residues: 2064 sheet: -0.82 (0.19), residues: 671 loop : -1.24 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 464 TYR 0.023 0.002 TYR B1003 PHE 0.028 0.002 PHE A 462 TRP 0.012 0.002 TRP P 217 HIS 0.016 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (45571) covalent geometry : angle 0.68227 / 0.35 (62007) hydrogen bonds : bond 0.04302 / 2.90 ( 1961) hydrogen bonds : angle 4.50895 / 3.20 ( 5550) metal coordination : bond 0.02725 / 1.43 ( 27) metal coordination : angle 6.92562 / 3.88 ( 42) Misc. bond : bond 0.00307 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 896 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8890 (t) cc_final: 0.8403 (m) REVERT: A 53 TYR cc_start: 0.8081 (m-80) cc_final: 0.7401 (m-10) REVERT: A 163 ASN cc_start: 0.5872 (m-40) cc_final: 0.5448 (m110) REVERT: A 203 HIS cc_start: 0.7409 (m170) cc_final: 0.7174 (m-70) REVERT: A 246 LYS cc_start: 0.6848 (mtmt) cc_final: 0.6418 (ptpt) REVERT: A 249 ASP cc_start: 0.7936 (m-30) cc_final: 0.7469 (m-30) REVERT: A 312 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: A 406 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8211 (ttpt) REVERT: A 445 LYS cc_start: 0.8159 (mmpt) cc_final: 0.7718 (mttm) REVERT: A 458 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8659 (t0) REVERT: A 536 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8168 (pt0) REVERT: A 647 SER cc_start: 0.9040 (t) cc_final: 0.8756 (p) REVERT: A 709 LEU cc_start: 0.7718 (tt) cc_final: 0.7469 (tp) REVERT: A 789 PHE cc_start: 0.8788 (m-10) cc_final: 0.8561 (m-80) REVERT: A 822 GLU cc_start: 0.7714 (tp30) cc_final: 0.7503 (tp30) REVERT: A 947 LEU cc_start: 0.8518 (tt) cc_final: 0.8122 (mt) REVERT: A 1026 GLN cc_start: 0.8545 (mt0) cc_final: 0.8318 (mt0) REVERT: A 1078 LYS cc_start: 0.8480 (mttp) cc_final: 0.8132 (mppt) REVERT: A 1091 LYS cc_start: 0.8098 (mttt) cc_final: 0.7827 (mtpt) REVERT: A 1096 ASP cc_start: 0.8167 (t0) cc_final: 0.7957 (t70) REVERT: A 1112 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8320 (mt-10) REVERT: A 1135 GLU cc_start: 0.8119 (pm20) cc_final: 0.7866 (pm20) REVERT: A 1185 MET cc_start: 0.6422 (pmm) cc_final: 0.5875 (pmm) REVERT: A 1191 PHE cc_start: 0.7799 (t80) cc_final: 0.7050 (t80) REVERT: A 1196 LEU cc_start: 0.8547 (tp) cc_final: 0.8308 (mt) REVERT: B 35 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8287 (mptt) REVERT: B 41 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7245 (mppt) REVERT: B 64 LYS cc_start: 0.6005 (ttmt) cc_final: 0.4705 (ttmm) REVERT: B 86 ASP cc_start: 0.8149 (m-30) cc_final: 0.7941 (m-30) REVERT: B 211 LYS cc_start: 0.5641 (mttt) cc_final: 0.5131 (pttt) REVERT: B 226 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6675 (ttm110) REVERT: B 249 GLN cc_start: 0.6651 (tt0) cc_final: 0.5933 (tp40) REVERT: B 285 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7264 (tppt) REVERT: B 353 ASP cc_start: 0.7111 (p0) cc_final: 0.6786 (m-30) REVERT: B 374 GLU cc_start: 0.8244 (pt0) cc_final: 0.7970 (pt0) REVERT: B 488 GLU cc_start: 0.8207 (pt0) cc_final: 0.7307 (tm-30) REVERT: B 521 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7378 (mt-10) REVERT: B 526 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5923 (pp) REVERT: B 535 ASN cc_start: 0.8496 (p0) cc_final: 0.8038 (p0) REVERT: B 561 LEU cc_start: 0.8872 (tp) cc_final: 0.8330 (mt) REVERT: B 573 SER cc_start: 0.9361 (t) cc_final: 0.9129 (p) REVERT: B 581 ARG cc_start: 0.7498 (mtm110) cc_final: 0.7268 (mtm110) REVERT: B 609 LYS cc_start: 0.8337 (tmmt) cc_final: 0.8053 (tppt) REVERT: B 618 TYR cc_start: 0.7731 (m-10) cc_final: 0.7375 (m-10) REVERT: B 627 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7192 (mt-10) REVERT: B 653 ASP cc_start: 0.7402 (t0) cc_final: 0.7054 (p0) REVERT: B 781 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.7261 (mpt-90) REVERT: B 787 PHE cc_start: 0.7465 (p90) cc_final: 0.6982 (p90) REVERT: B 791 MET cc_start: 0.8034 (mmt) cc_final: 0.7620 (mmm) REVERT: B 800 ARG cc_start: 0.6794 (mmm160) cc_final: 0.6388 (mmm160) REVERT: B 916 MET cc_start: 0.9218 (mmt) cc_final: 0.8884 (mmm) REVERT: B 929 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8167 (ttp) REVERT: B 1041 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7451 (mtt90) REVERT: B 1049 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7433 (mt-10) REVERT: B 1062 MET cc_start: 0.9028 (mmm) cc_final: 0.8724 (mmp) REVERT: C 137 THR cc_start: 0.8319 (t) cc_final: 0.7800 (m) REVERT: C 296 VAL cc_start: 0.9252 (m) cc_final: 0.8990 (p) REVERT: D 53 ILE cc_start: 0.7359 (mm) cc_final: 0.7068 (mm) REVERT: D 59 ARG cc_start: 0.7037 (mpp80) cc_final: 0.6775 (mpp80) REVERT: D 82 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7469 (mm-30) REVERT: D 100 MET cc_start: 0.5200 (mtt) cc_final: 0.4865 (mtt) REVERT: D 114 GLU cc_start: 0.7178 (mp0) cc_final: 0.6476 (tp30) REVERT: E 73 PHE cc_start: 0.5507 (t80) cc_final: 0.5203 (t80) REVERT: E 75 PHE cc_start: 0.7657 (m-80) cc_final: 0.7271 (m-80) REVERT: E 85 LYS cc_start: 0.8342 (mttt) cc_final: 0.8039 (mmtm) REVERT: E 90 TYR cc_start: 0.8235 (m-10) cc_final: 0.7854 (m-80) REVERT: E 206 TYR cc_start: 0.9331 (m-80) cc_final: 0.9036 (m-80) REVERT: F 116 GLU cc_start: 0.8152 (pt0) cc_final: 0.7906 (pt0) REVERT: G 100 SER cc_start: 0.7043 (t) cc_final: 0.6736 (p) REVERT: H 57 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7690 (ttm-80) REVERT: H 66 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7574 (mp0) REVERT: H 118 TYR cc_start: 0.9388 (m-80) cc_final: 0.9054 (m-80) REVERT: I 14 VAL cc_start: 0.7869 (t) cc_final: 0.7519 (p) REVERT: I 26 ASN cc_start: 0.8041 (t0) cc_final: 0.7812 (t0) REVERT: I 42 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7772 (mttp) REVERT: J 54 ASP cc_start: 0.7776 (t0) cc_final: 0.7552 (t0) REVERT: K 31 GLN cc_start: 0.6685 (pp30) cc_final: 0.6421 (pm20) REVERT: M 10 VAL cc_start: 0.5033 (OUTLIER) cc_final: 0.4751 (t) REVERT: M 195 PHE cc_start: 0.6079 (t80) cc_final: 0.5465 (t80) REVERT: M 197 GLN cc_start: 0.7506 (tt0) cc_final: 0.6566 (mm110) REVERT: M 211 TYR cc_start: 0.6746 (m-80) cc_final: 0.6184 (m-80) REVERT: M 270 MET cc_start: 0.1015 (tpp) cc_final: 0.0127 (ptp) REVERT: N 350 MET cc_start: 0.6973 (tpp) cc_final: 0.6752 (tpp) REVERT: N 373 MET cc_start: 0.5217 (mtm) cc_final: 0.4786 (mtm) REVERT: O 14 GLN cc_start: 0.8456 (tt0) cc_final: 0.8091 (tp-100) REVERT: O 22 GLU cc_start: 0.8283 (pp20) cc_final: 0.8001 (pp20) REVERT: O 85 MET cc_start: 0.8490 (ttm) cc_final: 0.8230 (ttp) REVERT: O 108 GLU cc_start: 0.7472 (tt0) cc_final: 0.7106 (tm-30) REVERT: O 133 MET cc_start: 0.4346 (ptt) cc_final: 0.3819 (ptt) REVERT: O 139 MET cc_start: 0.6492 (mmm) cc_final: 0.5949 (tpp) REVERT: O 187 MET cc_start: 0.7444 (tpt) cc_final: 0.7018 (tpt) REVERT: O 248 ASP cc_start: 0.8950 (m-30) cc_final: 0.8741 (m-30) REVERT: O 275 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7056 (pt0) REVERT: O 314 LEU cc_start: 0.6715 (pp) cc_final: 0.6417 (tp) REVERT: O 322 PHE cc_start: 0.8137 (m-80) cc_final: 0.7273 (m-80) REVERT: O 333 MET cc_start: 0.6004 (tpt) cc_final: 0.5691 (mmm) REVERT: O 383 PHE cc_start: 0.7573 (m-10) cc_final: 0.7129 (m-10) REVERT: O 385 MET cc_start: 0.6579 (tpp) cc_final: 0.6305 (tpp) REVERT: O 401 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8163 (mm-30) REVERT: O 462 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7661 (pp20) REVERT: O 463 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7497 (tttp) REVERT: O 474 MET cc_start: 0.1469 (OUTLIER) cc_final: -0.0425 (ttp) REVERT: O 517 ASP cc_start: 0.8726 (t0) cc_final: 0.8473 (t0) REVERT: P 232 MET cc_start: 0.4646 (ttp) cc_final: 0.3835 (mmm) REVERT: P 236 GLU cc_start: 0.6965 (tt0) cc_final: 0.6082 (tp30) REVERT: P 256 LYS cc_start: 0.3685 (tptp) cc_final: 0.3299 (mtmt) REVERT: P 267 MET cc_start: 0.2434 (mmm) cc_final: 0.2219 (mmm) REVERT: Q 54 GLU cc_start: 0.7242 (mp0) cc_final: 0.6966 (mt-10) REVERT: Q 55 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8178 (tp30) REVERT: Q 60 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8211 (tp) REVERT: Q 62 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7469 (mm-40) REVERT: Q 66 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7664 (mm-30) REVERT: Q 92 MET cc_start: 0.1394 (ptt) cc_final: 0.0287 (mtp) REVERT: Q 103 TRP cc_start: 0.7685 (m100) cc_final: 0.7277 (m100) outliers start: 113 outliers final: 51 residues processed: 956 average time/residue: 0.2657 time to fit residues: 414.4705 Evaluate side-chains 801 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 742 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 464 SER Chi-restraints excluded: chain O residue 474 MET Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain V residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 380 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 496 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 337 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 398 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 75 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A1250 ASN ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 320 HIS B 346 GLN B 501 HIS B 930 ASN ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN D 61 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN O 158 GLN O 236 GLN O 245 HIS O 249 GLN O 457 ASN O 507 ASN P 189 GLN P 240 ASN P 274 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.183346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110995 restraints weight = 62032.467| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.66 r_work: 0.3013 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 45600 Z= 0.229 Angle : 0.665 13.628 62049 Z= 0.337 Chirality : 0.047 0.281 6977 Planarity : 0.005 0.068 7603 Dihedral : 16.240 179.457 7040 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.53 % Allowed : 12.07 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.11), residues: 5269 helix: 1.09 (0.12), residues: 2067 sheet: -0.71 (0.19), residues: 659 loop : -1.10 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 229 TYR 0.055 0.002 TYR P 219 PHE 0.023 0.002 PHE A 462 TRP 0.020 0.002 TRP P 217 HIS 0.015 0.002 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (45571) covalent geometry : angle 0.64959 / 0.34 (62007) hydrogen bonds : bond 0.04364 / 2.95 ( 1961) hydrogen bonds : angle 4.51658 / 3.19 ( 5550) metal coordination : bond 0.00942 / 0.46 ( 27) metal coordination : angle 5.55007 / 3.41 ( 42) Misc. bond : bond 0.01628 / 0.85 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 782 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.9175 (t) cc_final: 0.8745 (m) REVERT: A 60 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8602 (mtm) REVERT: A 111 THR cc_start: 0.8782 (m) cc_final: 0.8165 (p) REVERT: A 131 ARG cc_start: 0.6727 (ptp-170) cc_final: 0.6388 (mtp180) REVERT: A 146 ILE cc_start: 0.8572 (mt) cc_final: 0.8262 (mt) REVERT: A 163 ASN cc_start: 0.6569 (m-40) cc_final: 0.6005 (m110) REVERT: A 203 HIS cc_start: 0.7503 (m170) cc_final: 0.7133 (m170) REVERT: A 225 ASN cc_start: 0.7866 (t0) cc_final: 0.7279 (t0) REVERT: A 257 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8962 (m) REVERT: A 304 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7753 (tt0) REVERT: A 312 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: A 406 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8449 (ttpt) REVERT: A 445 LYS cc_start: 0.8246 (mmpt) cc_final: 0.7762 (mttt) REVERT: A 458 ASP cc_start: 0.9371 (OUTLIER) cc_final: 0.9003 (t0) REVERT: A 468 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 693 ASN cc_start: 0.8516 (m-40) cc_final: 0.8183 (m110) REVERT: A 709 LEU cc_start: 0.8267 (tt) cc_final: 0.8062 (tp) REVERT: A 722 LYS cc_start: 0.7404 (mtmt) cc_final: 0.7161 (mttm) REVERT: A 805 SER cc_start: 0.9103 (m) cc_final: 0.8835 (p) REVERT: A 947 LEU cc_start: 0.8723 (tt) cc_final: 0.8273 (mp) REVERT: A 1048 MET cc_start: 0.6680 (mtm) cc_final: 0.6354 (mtt) REVERT: A 1078 LYS cc_start: 0.8895 (mttp) cc_final: 0.8477 (mppt) REVERT: A 1091 LYS cc_start: 0.8169 (mttt) cc_final: 0.7878 (mtpt) REVERT: A 1096 ASP cc_start: 0.8282 (t0) cc_final: 0.8036 (t70) REVERT: A 1185 MET cc_start: 0.6366 (pmm) cc_final: 0.5864 (pmm) REVERT: A 1191 PHE cc_start: 0.7757 (t80) cc_final: 0.7413 (t80) REVERT: A 1196 LEU cc_start: 0.8604 (tp) cc_final: 0.8287 (mt) REVERT: A 1294 MET cc_start: 0.9337 (mtp) cc_final: 0.9010 (mtp) REVERT: B 35 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8518 (mptt) REVERT: B 64 LYS cc_start: 0.5969 (ttmt) cc_final: 0.5427 (ttmt) REVERT: B 84 LEU cc_start: 0.8396 (mt) cc_final: 0.8173 (mt) REVERT: B 86 ASP cc_start: 0.8372 (m-30) cc_final: 0.8109 (m-30) REVERT: B 211 LYS cc_start: 0.6306 (mttt) cc_final: 0.5400 (tttt) REVERT: B 226 ARG cc_start: 0.7438 (ttm110) cc_final: 0.6871 (ttm110) REVERT: B 249 GLN cc_start: 0.6991 (tt0) cc_final: 0.6786 (tt0) REVERT: B 285 LYS cc_start: 0.7831 (ttmm) cc_final: 0.7323 (tppt) REVERT: B 325 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6717 (mm-30) REVERT: B 332 CYS cc_start: 0.8938 (m) cc_final: 0.8711 (m) REVERT: B 417 ASN cc_start: 0.9087 (m-40) cc_final: 0.8768 (m-40) REVERT: B 478 MET cc_start: 0.9530 (mmt) cc_final: 0.8895 (mmp) REVERT: B 488 GLU cc_start: 0.8603 (pt0) cc_final: 0.7689 (tm-30) REVERT: B 521 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 535 ASN cc_start: 0.8580 (p0) cc_final: 0.8096 (p0) REVERT: B 573 SER cc_start: 0.9524 (t) cc_final: 0.9284 (p) REVERT: B 653 ASP cc_start: 0.7823 (t0) cc_final: 0.7479 (p0) REVERT: B 781 ARG cc_start: 0.7421 (mmm-85) cc_final: 0.7066 (mmm-85) REVERT: B 791 MET cc_start: 0.8398 (mmt) cc_final: 0.8087 (mmm) REVERT: B 863 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8689 (m-30) REVERT: B 870 MET cc_start: 0.9235 (ttp) cc_final: 0.8824 (ttp) REVERT: B 1049 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 1050 MET cc_start: 0.8891 (mtp) cc_final: 0.8657 (mtt) REVERT: B 1062 MET cc_start: 0.9198 (mmm) cc_final: 0.8770 (mmp) REVERT: C 286 GLU cc_start: 0.8930 (tp30) cc_final: 0.8637 (tp30) REVERT: C 296 VAL cc_start: 0.9328 (m) cc_final: 0.9115 (p) REVERT: D 2 GLU cc_start: 0.7751 (pm20) cc_final: 0.7243 (mp0) REVERT: D 53 ILE cc_start: 0.7563 (mm) cc_final: 0.7324 (mm) REVERT: D 59 ARG cc_start: 0.7153 (mpp80) cc_final: 0.6856 (mpp80) REVERT: D 82 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7429 (mm-30) REVERT: D 85 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: D 114 GLU cc_start: 0.7364 (mp0) cc_final: 0.6520 (tp30) REVERT: E 75 PHE cc_start: 0.7847 (m-80) cc_final: 0.7455 (m-80) REVERT: E 85 LYS cc_start: 0.8427 (mttt) cc_final: 0.8146 (mmtm) REVERT: E 94 MET cc_start: 0.7517 (mmp) cc_final: 0.6916 (mtm) REVERT: E 208 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8556 (tt) REVERT: F 51 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.4710 (mmp-170) REVERT: F 80 MET cc_start: 0.8386 (mtp) cc_final: 0.8186 (mtp) REVERT: F 91 LEU cc_start: 0.9418 (mt) cc_final: 0.9212 (mm) REVERT: F 98 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8835 (ttmt) REVERT: G 41 ASN cc_start: 0.8834 (m-40) cc_final: 0.8628 (m-40) REVERT: G 77 PHE cc_start: 0.8499 (t80) cc_final: 0.8210 (t80) REVERT: G 84 ILE cc_start: 0.7137 (mt) cc_final: 0.6905 (mm) REVERT: G 198 LEU cc_start: 0.7009 (pt) cc_final: 0.6439 (tt) REVERT: H 18 GLU cc_start: 0.8856 (mp0) cc_final: 0.8646 (mp0) REVERT: H 57 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7837 (ttm-80) REVERT: H 66 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7619 (mp0) REVERT: H 138 ASP cc_start: 0.8470 (t0) cc_final: 0.8218 (t0) REVERT: H 145 MET cc_start: 0.9076 (mtp) cc_final: 0.8739 (mtp) REVERT: I 14 VAL cc_start: 0.8066 (t) cc_final: 0.7527 (p) REVERT: I 42 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8085 (mttp) REVERT: J 26 GLN cc_start: 0.8364 (mt0) cc_final: 0.8002 (tp40) REVERT: J 54 ASP cc_start: 0.8400 (t0) cc_final: 0.8162 (t0) REVERT: K 104 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8665 (mtp) REVERT: K 124 GLN cc_start: 0.8834 (tt0) cc_final: 0.8450 (tm-30) REVERT: L 35 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7852 (mtp85) REVERT: M 80 ASN cc_start: 0.7351 (m110) cc_final: 0.7023 (m110) REVERT: M 141 TYR cc_start: 0.7277 (p90) cc_final: 0.6985 (p90) REVERT: M 197 GLN cc_start: 0.7884 (tt0) cc_final: 0.6654 (mm110) REVERT: M 234 GLU cc_start: 0.6808 (tp30) cc_final: 0.6248 (tm-30) REVERT: N 347 ASP cc_start: 0.6824 (p0) cc_final: 0.6220 (m-30) REVERT: N 352 THR cc_start: 0.7419 (p) cc_final: 0.7009 (p) REVERT: O 14 GLN cc_start: 0.8680 (tt0) cc_final: 0.8264 (tp40) REVERT: O 22 GLU cc_start: 0.8495 (pp20) cc_final: 0.8081 (pp20) REVERT: O 85 MET cc_start: 0.8708 (ttm) cc_final: 0.8489 (ttp) REVERT: O 108 GLU cc_start: 0.7703 (tt0) cc_final: 0.7334 (tm-30) REVERT: O 123 LYS cc_start: 0.8411 (tttm) cc_final: 0.8025 (mtpp) REVERT: O 133 MET cc_start: 0.4256 (ptt) cc_final: 0.3856 (ptt) REVERT: O 139 MET cc_start: 0.6330 (mmm) cc_final: 0.6051 (tpp) REVERT: O 187 MET cc_start: 0.7438 (tpt) cc_final: 0.6758 (tpt) REVERT: O 233 ILE cc_start: 0.6845 (mm) cc_final: 0.6317 (mp) REVERT: O 249 GLN cc_start: 0.8393 (mt0) cc_final: 0.8101 (mt0) REVERT: O 275 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: O 322 PHE cc_start: 0.8136 (m-80) cc_final: 0.7243 (m-80) REVERT: O 383 PHE cc_start: 0.7784 (m-10) cc_final: 0.7123 (m-10) REVERT: O 517 ASP cc_start: 0.8868 (t0) cc_final: 0.8592 (t0) REVERT: P 219 TYR cc_start: 0.6260 (t80) cc_final: 0.6030 (t80) REVERT: P 232 MET cc_start: 0.4661 (ttp) cc_final: 0.2897 (mmm) REVERT: P 267 MET cc_start: 0.3083 (mmm) cc_final: 0.2860 (mmm) REVERT: Q 31 VAL cc_start: 0.6958 (OUTLIER) cc_final: 0.6726 (m) REVERT: Q 33 LYS cc_start: 0.8315 (ptmt) cc_final: 0.8017 (mtmm) REVERT: Q 54 GLU cc_start: 0.7638 (mp0) cc_final: 0.7240 (mt-10) REVERT: Q 55 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8171 (tp30) REVERT: Q 62 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7622 (mm-40) REVERT: Q 66 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7769 (mm-30) REVERT: Q 92 MET cc_start: 0.1091 (ptt) cc_final: 0.0288 (mtp) REVERT: Q 102 ASP cc_start: 0.7980 (t0) cc_final: 0.7570 (t0) outliers start: 119 outliers final: 61 residues processed: 859 average time/residue: 0.2882 time to fit residues: 404.6163 Evaluate side-chains 764 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 692 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 375 ILE Chi-restraints excluded: chain O residue 464 SER Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 325 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 524 optimal weight: 40.0000 chunk 179 optimal weight: 1.9990 chunk 364 optimal weight: 0.9990 chunk 362 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 387 optimal weight: 7.9990 chunk 434 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 836 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 703 ASN B 930 ASN ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS E 92 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN O 236 GLN O 497 GLN P 240 ASN P 274 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.182727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109774 restraints weight = 61871.121| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.52 r_work: 0.3034 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 45600 Z= 0.173 Angle : 0.595 13.426 62049 Z= 0.301 Chirality : 0.044 0.277 6977 Planarity : 0.004 0.048 7603 Dihedral : 16.105 179.119 7038 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.45 % Allowed : 13.60 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.11), residues: 5269 helix: 1.26 (0.12), residues: 2067 sheet: -0.67 (0.19), residues: 642 loop : -0.98 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 998 TYR 0.032 0.002 TYR M 92 PHE 0.019 0.001 PHE G 120 TRP 0.022 0.001 TRP P 217 HIS 0.009 0.001 HIS E 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (45571) covalent geometry : angle 0.58385 / 0.30 (62007) hydrogen bonds : bond 0.03812 / 2.59 ( 1961) hydrogen bonds : angle 4.37296 / 3.10 ( 5550) metal coordination : bond 0.00940 / 0.51 ( 27) metal coordination : angle 4.41980 / 2.64 ( 42) Misc. bond : bond 0.00141 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 714 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: A 38 SER cc_start: 0.9152 (t) cc_final: 0.8728 (m) REVERT: A 60 MET cc_start: 0.9109 (mtm) cc_final: 0.8850 (mtm) REVERT: A 107 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.6989 (mpt) REVERT: A 111 THR cc_start: 0.8947 (m) cc_final: 0.8355 (p) REVERT: A 131 ARG cc_start: 0.6756 (ptp-170) cc_final: 0.6291 (mtp180) REVERT: A 163 ASN cc_start: 0.6545 (m-40) cc_final: 0.6066 (m110) REVERT: A 203 HIS cc_start: 0.7434 (m170) cc_final: 0.6996 (m170) REVERT: A 225 ASN cc_start: 0.7985 (t0) cc_final: 0.7606 (t0) REVERT: A 304 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7699 (tt0) REVERT: A 312 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: A 406 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8381 (ttpt) REVERT: A 458 ASP cc_start: 0.9274 (OUTLIER) cc_final: 0.8844 (t0) REVERT: A 468 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8839 (mt) REVERT: A 805 SER cc_start: 0.9125 (m) cc_final: 0.8866 (p) REVERT: A 947 LEU cc_start: 0.8746 (tt) cc_final: 0.8317 (mp) REVERT: A 1048 MET cc_start: 0.6607 (mtm) cc_final: 0.6406 (mtt) REVERT: A 1078 LYS cc_start: 0.8962 (mttp) cc_final: 0.8558 (mppt) REVERT: A 1091 LYS cc_start: 0.8165 (mttt) cc_final: 0.7886 (mtpt) REVERT: A 1096 ASP cc_start: 0.8238 (t0) cc_final: 0.8000 (t70) REVERT: A 1112 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 1185 MET cc_start: 0.6288 (pmm) cc_final: 0.5784 (pmm) REVERT: A 1191 PHE cc_start: 0.7530 (t80) cc_final: 0.7304 (t80) REVERT: A 1196 LEU cc_start: 0.8376 (tp) cc_final: 0.8128 (mt) REVERT: B 35 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8452 (mptt) REVERT: B 64 LYS cc_start: 0.5931 (ttmt) cc_final: 0.5395 (ttmt) REVERT: B 84 LEU cc_start: 0.8432 (mt) cc_final: 0.8152 (mt) REVERT: B 86 ASP cc_start: 0.8361 (m-30) cc_final: 0.8105 (m-30) REVERT: B 211 LYS cc_start: 0.6287 (mttt) cc_final: 0.5318 (pttt) REVERT: B 226 ARG cc_start: 0.7483 (ttm110) cc_final: 0.7058 (ttm110) REVERT: B 285 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7350 (tppt) REVERT: B 325 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6776 (mm-30) REVERT: B 417 ASN cc_start: 0.9025 (m-40) cc_final: 0.8697 (m-40) REVERT: B 478 MET cc_start: 0.9515 (mmt) cc_final: 0.8788 (mmp) REVERT: B 488 GLU cc_start: 0.8631 (pt0) cc_final: 0.7591 (tm-30) REVERT: B 521 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7924 (mt-10) REVERT: B 533 TYR cc_start: 0.8787 (m-10) cc_final: 0.8524 (m-10) REVERT: B 535 ASN cc_start: 0.8608 (p0) cc_final: 0.8130 (p0) REVERT: B 573 SER cc_start: 0.9510 (t) cc_final: 0.9299 (p) REVERT: B 581 ARG cc_start: 0.8357 (mtm110) cc_final: 0.8061 (ttm110) REVERT: B 791 MET cc_start: 0.8360 (mmt) cc_final: 0.8036 (mmt) REVERT: B 863 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8636 (m-30) REVERT: B 870 MET cc_start: 0.9170 (ttp) cc_final: 0.8784 (ttp) REVERT: B 1047 LEU cc_start: 0.9105 (tp) cc_final: 0.8862 (tp) REVERT: C 286 GLU cc_start: 0.8878 (tp30) cc_final: 0.8438 (tp30) REVERT: C 296 VAL cc_start: 0.9352 (m) cc_final: 0.9022 (p) REVERT: D 14 TYR cc_start: 0.7012 (t80) cc_final: 0.6802 (t80) REVERT: D 82 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7214 (mm-30) REVERT: D 85 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: E 73 PHE cc_start: 0.5647 (t80) cc_final: 0.5382 (t80) REVERT: E 85 LYS cc_start: 0.8444 (mttt) cc_final: 0.8128 (mmtm) REVERT: E 208 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8589 (tt) REVERT: F 51 ARG cc_start: 0.6744 (mtm-85) cc_final: 0.4621 (mmp-170) REVERT: G 41 ASN cc_start: 0.8835 (m-40) cc_final: 0.8591 (m-40) REVERT: G 73 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8191 (mtm180) REVERT: G 198 LEU cc_start: 0.7061 (pt) cc_final: 0.6536 (tt) REVERT: H 14 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8427 (t70) REVERT: H 18 GLU cc_start: 0.8926 (mp0) cc_final: 0.8639 (mp0) REVERT: H 57 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7569 (ttm-80) REVERT: H 66 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7598 (mp0) REVERT: H 138 ASP cc_start: 0.8412 (t0) cc_final: 0.8141 (t0) REVERT: I 42 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8059 (mttp) REVERT: J 26 GLN cc_start: 0.8463 (mt0) cc_final: 0.8141 (tp40) REVERT: J 54 ASP cc_start: 0.8356 (t0) cc_final: 0.8101 (t0) REVERT: K 31 GLN cc_start: 0.6468 (pm20) cc_final: 0.5882 (pm20) REVERT: K 104 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8585 (mtp) REVERT: K 124 GLN cc_start: 0.8897 (tt0) cc_final: 0.8452 (tm-30) REVERT: L 35 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7805 (mtp85) REVERT: M 49 ILE cc_start: 0.6707 (tt) cc_final: 0.6459 (tp) REVERT: M 141 TYR cc_start: 0.7335 (p90) cc_final: 0.7101 (p90) REVERT: M 197 GLN cc_start: 0.7858 (tt0) cc_final: 0.6560 (mm110) REVERT: M 234 GLU cc_start: 0.6731 (tp30) cc_final: 0.5882 (mp0) REVERT: M 357 MET cc_start: 0.3221 (mmm) cc_final: 0.2898 (mmm) REVERT: M 421 MET cc_start: 0.3047 (OUTLIER) cc_final: 0.2688 (mmm) REVERT: N 347 ASP cc_start: 0.7243 (p0) cc_final: 0.6472 (m-30) REVERT: N 352 THR cc_start: 0.7416 (p) cc_final: 0.7027 (p) REVERT: O 14 GLN cc_start: 0.8618 (tt0) cc_final: 0.8171 (tp40) REVERT: O 22 GLU cc_start: 0.8490 (pp20) cc_final: 0.8144 (pp20) REVERT: O 85 MET cc_start: 0.8678 (ttm) cc_final: 0.8412 (ttp) REVERT: O 108 GLU cc_start: 0.7817 (tt0) cc_final: 0.7388 (tm-30) REVERT: O 139 MET cc_start: 0.6105 (mmm) cc_final: 0.5887 (tpp) REVERT: O 187 MET cc_start: 0.7307 (tpt) cc_final: 0.6850 (tpt) REVERT: O 233 ILE cc_start: 0.6741 (mm) cc_final: 0.6321 (mp) REVERT: O 249 GLN cc_start: 0.8333 (mt0) cc_final: 0.8060 (mt0) REVERT: O 275 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7035 (pt0) REVERT: O 322 PHE cc_start: 0.8152 (m-80) cc_final: 0.7225 (m-80) REVERT: O 333 MET cc_start: 0.5915 (tpt) cc_final: 0.5451 (mmm) REVERT: O 383 PHE cc_start: 0.7782 (m-10) cc_final: 0.7119 (m-10) REVERT: O 385 MET cc_start: 0.7049 (tpp) cc_final: 0.6789 (tpp) REVERT: O 462 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7951 (tp30) REVERT: O 517 ASP cc_start: 0.8884 (t0) cc_final: 0.8464 (t70) REVERT: P 219 TYR cc_start: 0.6681 (t80) cc_final: 0.6427 (t80) REVERT: P 232 MET cc_start: 0.4226 (ttp) cc_final: 0.3914 (mmm) REVERT: Q 33 LYS cc_start: 0.8284 (ptmt) cc_final: 0.7988 (mtmm) REVERT: Q 54 GLU cc_start: 0.7627 (mp0) cc_final: 0.7230 (mt-10) REVERT: Q 55 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8183 (tp30) REVERT: Q 62 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7576 (mm-40) REVERT: Q 66 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7779 (mm-30) REVERT: Q 92 MET cc_start: 0.1074 (ptt) cc_final: 0.0288 (mtp) REVERT: V 29 SER cc_start: 0.7824 (t) cc_final: 0.7542 (p) outliers start: 115 outliers final: 73 residues processed: 786 average time/residue: 0.2776 time to fit residues: 358.1401 Evaluate side-chains 744 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 658 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 930 ASN Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 154 optimal weight: 9.9990 chunk 415 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 305 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 506 optimal weight: 20.0000 chunk 461 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN B 253 GLN B 410 GLN ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS K 85 GLN M 68 ASN M 341 HIS O 306 GLN P 274 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.179446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106425 restraints weight = 61599.571| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.54 r_work: 0.2966 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 45600 Z= 0.248 Angle : 0.641 13.637 62049 Z= 0.328 Chirality : 0.046 0.277 6977 Planarity : 0.005 0.052 7603 Dihedral : 16.147 179.481 7038 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.21 % Allowed : 13.67 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.11), residues: 5269 helix: 1.18 (0.11), residues: 2072 sheet: -0.80 (0.19), residues: 637 loop : -0.98 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 140 TYR 0.020 0.002 TYR B 357 PHE 0.024 0.002 PHE C 225 TRP 0.024 0.002 TRP P 217 HIS 0.017 0.001 HIS E 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (45571) covalent geometry : angle 0.63077 / 0.33 (62007) hydrogen bonds : bond 0.04176 / 2.85 ( 1961) hydrogen bonds : angle 4.47764 / 3.18 ( 5550) metal coordination : bond 0.01221 / 0.69 ( 27) metal coordination : angle 4.49005 / 2.68 ( 42) Misc. bond : bond 0.00245 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 682 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.6782 (mpt) REVERT: A 111 THR cc_start: 0.9214 (m) cc_final: 0.8647 (p) REVERT: A 131 ARG cc_start: 0.6793 (ptp-170) cc_final: 0.6342 (mtp180) REVERT: A 144 LYS cc_start: 0.8789 (tttm) cc_final: 0.8331 (ttmt) REVERT: A 203 HIS cc_start: 0.7441 (m170) cc_final: 0.6977 (m170) REVERT: A 225 ASN cc_start: 0.8260 (t0) cc_final: 0.7978 (t0) REVERT: A 228 LYS cc_start: 0.8860 (mttt) cc_final: 0.8559 (mtpt) REVERT: A 239 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8657 (mm) REVERT: A 304 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 312 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: A 406 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8406 (ttpt) REVERT: A 737 GLN cc_start: 0.6920 (tp40) cc_final: 0.6673 (tm-30) REVERT: A 755 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7187 (tp30) REVERT: A 805 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8926 (p) REVERT: A 1091 LYS cc_start: 0.8226 (mttt) cc_final: 0.7923 (mtpt) REVERT: A 1105 ILE cc_start: 0.8403 (pt) cc_final: 0.8140 (pt) REVERT: A 1185 MET cc_start: 0.6360 (pmm) cc_final: 0.5851 (pmm) REVERT: A 1196 LEU cc_start: 0.8412 (tp) cc_final: 0.8109 (mt) REVERT: A 1206 GLU cc_start: 0.8218 (mp0) cc_final: 0.7961 (mp0) REVERT: A 1245 ARG cc_start: 0.9054 (mtp85) cc_final: 0.8568 (mpt90) REVERT: B 35 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8522 (mptt) REVERT: B 64 LYS cc_start: 0.5878 (ttmt) cc_final: 0.5396 (ttmt) REVERT: B 70 ASP cc_start: 0.8113 (t0) cc_final: 0.7912 (t0) REVERT: B 84 LEU cc_start: 0.8652 (mt) cc_final: 0.8313 (mt) REVERT: B 86 ASP cc_start: 0.8479 (m-30) cc_final: 0.8210 (m-30) REVERT: B 158 LEU cc_start: 0.9421 (mt) cc_final: 0.9220 (mp) REVERT: B 211 LYS cc_start: 0.6612 (mttt) cc_final: 0.5469 (tttt) REVERT: B 226 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7123 (ttm110) REVERT: B 240 PHE cc_start: 0.8178 (m-80) cc_final: 0.7950 (m-80) REVERT: B 254 MET cc_start: 0.8383 (mtm) cc_final: 0.8097 (mtm) REVERT: B 285 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7401 (ttpt) REVERT: B 296 MET cc_start: 0.1624 (mmt) cc_final: 0.1378 (mmm) REVERT: B 378 LYS cc_start: 0.7392 (mttm) cc_final: 0.6850 (mmtp) REVERT: B 417 ASN cc_start: 0.9061 (m-40) cc_final: 0.8731 (m-40) REVERT: B 478 MET cc_start: 0.9589 (mmt) cc_final: 0.8850 (mmp) REVERT: B 521 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7976 (mt-10) REVERT: B 573 SER cc_start: 0.9562 (t) cc_final: 0.9281 (p) REVERT: B 581 ARG cc_start: 0.8607 (mtm110) cc_final: 0.8323 (ttm110) REVERT: B 789 LYS cc_start: 0.7425 (ptmt) cc_final: 0.6271 (pttt) REVERT: B 791 MET cc_start: 0.8563 (mmt) cc_final: 0.8194 (mmt) REVERT: B 863 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: B 1015 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8567 (mtt) REVERT: B 1037 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8008 (tt0) REVERT: C 286 GLU cc_start: 0.8995 (tp30) cc_final: 0.8702 (tp30) REVERT: C 296 VAL cc_start: 0.9382 (m) cc_final: 0.9025 (p) REVERT: D 14 TYR cc_start: 0.7113 (t80) cc_final: 0.6870 (t80) REVERT: D 82 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7268 (mm-30) REVERT: D 85 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7222 (mt0) REVERT: E 73 PHE cc_start: 0.5932 (t80) cc_final: 0.5421 (t80) REVERT: E 85 LYS cc_start: 0.8521 (mttt) cc_final: 0.8215 (mmtm) REVERT: E 208 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8589 (tt) REVERT: F 51 ARG cc_start: 0.6823 (mtm-85) cc_final: 0.4620 (mmp-170) REVERT: F 64 ARG cc_start: 0.9251 (ttt180) cc_final: 0.9008 (ttt180) REVERT: F 91 LEU cc_start: 0.9398 (mt) cc_final: 0.9166 (mm) REVERT: G 41 ASN cc_start: 0.8851 (m-40) cc_final: 0.8602 (m-40) REVERT: G 198 LEU cc_start: 0.7389 (pt) cc_final: 0.6806 (tt) REVERT: H 14 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8545 (t70) REVERT: H 18 GLU cc_start: 0.9018 (mp0) cc_final: 0.8692 (mp0) REVERT: H 57 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7598 (ttm-80) REVERT: H 66 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7712 (mp0) REVERT: H 122 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9178 (mt) REVERT: H 138 ASP cc_start: 0.8513 (t0) cc_final: 0.8309 (t0) REVERT: I 42 LYS cc_start: 0.8425 (mtpp) cc_final: 0.7876 (mttp) REVERT: K 31 GLN cc_start: 0.6572 (pm20) cc_final: 0.5831 (pm20) REVERT: K 104 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8612 (mtp) REVERT: K 124 GLN cc_start: 0.8981 (tt0) cc_final: 0.8454 (tm-30) REVERT: L 35 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8130 (mtp85) REVERT: M 16 TYR cc_start: 0.7567 (m-80) cc_final: 0.7275 (m-80) REVERT: M 197 GLN cc_start: 0.7932 (tt0) cc_final: 0.6501 (mm110) REVERT: M 234 GLU cc_start: 0.6731 (tp30) cc_final: 0.5883 (mp0) REVERT: M 421 MET cc_start: 0.3182 (OUTLIER) cc_final: 0.2734 (mmm) REVERT: N 347 ASP cc_start: 0.7273 (p0) cc_final: 0.6578 (m-30) REVERT: N 352 THR cc_start: 0.7808 (p) cc_final: 0.7438 (p) REVERT: O 14 GLN cc_start: 0.8645 (tt0) cc_final: 0.8202 (tp40) REVERT: O 22 GLU cc_start: 0.8483 (pp20) cc_final: 0.8119 (pp20) REVERT: O 85 MET cc_start: 0.8753 (ttm) cc_final: 0.8537 (ttp) REVERT: O 108 GLU cc_start: 0.7630 (tt0) cc_final: 0.7273 (tm-30) REVERT: O 133 MET cc_start: 0.4349 (ptt) cc_final: 0.3949 (ptt) REVERT: O 139 MET cc_start: 0.6111 (mmm) cc_final: 0.5775 (tpp) REVERT: O 233 ILE cc_start: 0.6650 (mm) cc_final: 0.6242 (mp) REVERT: O 275 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6944 (pt0) REVERT: O 322 PHE cc_start: 0.8234 (m-80) cc_final: 0.7253 (m-80) REVERT: O 383 PHE cc_start: 0.7856 (m-10) cc_final: 0.7179 (m-10) REVERT: O 385 MET cc_start: 0.7060 (tpp) cc_final: 0.6691 (tpt) REVERT: O 459 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7774 (mmm160) REVERT: O 517 ASP cc_start: 0.9060 (t0) cc_final: 0.8543 (t70) REVERT: P 219 TYR cc_start: 0.6808 (t80) cc_final: 0.6600 (t80) REVERT: P 232 MET cc_start: 0.4785 (ttp) cc_final: 0.4249 (mmm) REVERT: Q 33 LYS cc_start: 0.8321 (ptmt) cc_final: 0.8069 (mtmm) REVERT: Q 54 GLU cc_start: 0.7464 (mp0) cc_final: 0.7073 (mt-10) REVERT: Q 55 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8147 (tp30) REVERT: Q 62 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7546 (mm-40) REVERT: Q 66 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7875 (mm-30) REVERT: Q 92 MET cc_start: 0.1108 (ptt) cc_final: 0.0311 (mtp) REVERT: Q 103 TRP cc_start: 0.7768 (m100) cc_final: 0.6863 (m100) REVERT: V 29 SER cc_start: 0.7843 (t) cc_final: 0.7573 (p) outliers start: 151 outliers final: 98 residues processed: 779 average time/residue: 0.2888 time to fit residues: 369.0517 Evaluate side-chains 743 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 632 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 375 ILE Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 50 optimal weight: 1.9990 chunk 355 optimal weight: 0.0770 chunk 271 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 492 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 455 optimal weight: 9.9990 chunk 226 optimal weight: 0.7980 chunk 279 optimal weight: 0.0980 chunk 289 optimal weight: 9.9990 chunk 480 optimal weight: 7.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 651 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 201 GLN C 268 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS O 306 GLN P 274 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.182377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110191 restraints weight = 61803.386| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.46 r_work: 0.3045 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 45600 Z= 0.111 Angle : 0.556 15.008 62049 Z= 0.282 Chirality : 0.043 0.258 6977 Planarity : 0.004 0.043 7603 Dihedral : 15.994 179.692 7038 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.21 % Allowed : 15.20 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5269 helix: 1.46 (0.12), residues: 2071 sheet: -0.62 (0.19), residues: 653 loop : -0.86 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 998 TYR 0.037 0.001 TYR M 141 PHE 0.023 0.001 PHE G 120 TRP 0.028 0.001 TRP Q 103 HIS 0.013 0.001 HIS I 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (45571) covalent geometry : angle 0.54450 / 0.28 (62007) hydrogen bonds : bond 0.03450 / 2.34 ( 1961) hydrogen bonds : angle 4.27642 / 3.02 ( 5550) metal coordination : bond 0.00579 / 0.28 ( 27) metal coordination : angle 4.39054 / 2.57 ( 42) Misc. bond : bond 0.00122 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 705 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 THR cc_start: 0.9074 (m) cc_final: 0.8522 (p) REVERT: A 131 ARG cc_start: 0.6897 (ptp-170) cc_final: 0.6424 (mtp180) REVERT: A 140 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.8000 (mtp-110) REVERT: A 144 LYS cc_start: 0.8776 (tttm) cc_final: 0.8313 (ttmt) REVERT: A 203 HIS cc_start: 0.7412 (m170) cc_final: 0.6934 (m170) REVERT: A 217 ASN cc_start: 0.8131 (m-40) cc_final: 0.7930 (m110) REVERT: A 228 LYS cc_start: 0.8811 (mttt) cc_final: 0.8526 (mtpt) REVERT: A 304 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7531 (tt0) REVERT: A 312 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8452 (m-80) REVERT: A 406 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8370 (ttpt) REVERT: A 458 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8816 (t0) REVERT: A 737 GLN cc_start: 0.6924 (tp40) cc_final: 0.6687 (tm-30) REVERT: A 805 SER cc_start: 0.9124 (m) cc_final: 0.8866 (p) REVERT: A 1078 LYS cc_start: 0.9142 (mppt) cc_final: 0.8738 (mppt) REVERT: A 1091 LYS cc_start: 0.8207 (mttt) cc_final: 0.7911 (mtpt) REVERT: A 1112 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 1185 MET cc_start: 0.6324 (pmm) cc_final: 0.5950 (pmm) REVERT: A 1196 LEU cc_start: 0.8359 (tp) cc_final: 0.8062 (mt) REVERT: A 1206 GLU cc_start: 0.8095 (mp0) cc_final: 0.7843 (mp0) REVERT: B 35 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8402 (mptt) REVERT: B 64 LYS cc_start: 0.5922 (ttmt) cc_final: 0.5425 (ttmt) REVERT: B 84 LEU cc_start: 0.8590 (mt) cc_final: 0.8280 (mt) REVERT: B 86 ASP cc_start: 0.8357 (m-30) cc_final: 0.8097 (m-30) REVERT: B 211 LYS cc_start: 0.6590 (mttt) cc_final: 0.5312 (tttt) REVERT: B 226 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7065 (ttm110) REVERT: B 285 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7334 (tppt) REVERT: B 296 MET cc_start: 0.1580 (mmt) cc_final: 0.1236 (mmm) REVERT: B 363 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8721 (mm-30) REVERT: B 367 GLN cc_start: 0.8067 (mp10) cc_final: 0.7768 (mp10) REVERT: B 378 LYS cc_start: 0.7403 (mttm) cc_final: 0.6817 (mmtp) REVERT: B 417 ASN cc_start: 0.9041 (m-40) cc_final: 0.8767 (m-40) REVERT: B 478 MET cc_start: 0.9580 (mmt) cc_final: 0.8962 (mmp) REVERT: B 521 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7974 (mt-10) REVERT: B 581 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8186 (mtm110) REVERT: B 791 MET cc_start: 0.8558 (mmt) cc_final: 0.8291 (mmm) REVERT: B 1015 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8312 (mtt) REVERT: B 1037 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7927 (tt0) REVERT: B 1041 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7395 (ttm110) REVERT: C 286 GLU cc_start: 0.8837 (tp30) cc_final: 0.8538 (tp30) REVERT: C 296 VAL cc_start: 0.9351 (m) cc_final: 0.9013 (p) REVERT: C 328 VAL cc_start: 0.8352 (p) cc_final: 0.8058 (m) REVERT: D 82 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7375 (mm-30) REVERT: E 73 PHE cc_start: 0.5650 (t80) cc_final: 0.5417 (t80) REVERT: E 85 LYS cc_start: 0.8541 (mttt) cc_final: 0.8227 (mmtm) REVERT: E 208 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8631 (tt) REVERT: F 51 ARG cc_start: 0.6753 (mtm-85) cc_final: 0.4717 (mmp-170) REVERT: F 91 LEU cc_start: 0.9388 (mt) cc_final: 0.9152 (mm) REVERT: G 41 ASN cc_start: 0.8779 (m-40) cc_final: 0.8488 (m-40) REVERT: G 198 LEU cc_start: 0.7381 (pt) cc_final: 0.6809 (tt) REVERT: H 14 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8428 (t70) REVERT: H 18 GLU cc_start: 0.8957 (mp0) cc_final: 0.8633 (mp0) REVERT: H 57 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7483 (ttm-80) REVERT: H 66 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7721 (mp0) REVERT: H 122 LEU cc_start: 0.9342 (mm) cc_final: 0.9062 (mt) REVERT: I 26 ASN cc_start: 0.8329 (t0) cc_final: 0.8100 (t0) REVERT: I 42 LYS cc_start: 0.8396 (mtpp) cc_final: 0.7873 (mttp) REVERT: J 54 ASP cc_start: 0.8401 (t0) cc_final: 0.7991 (t0) REVERT: K 31 GLN cc_start: 0.6512 (pm20) cc_final: 0.5747 (pm20) REVERT: K 104 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8540 (mtp) REVERT: K 115 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8625 (mt-10) REVERT: K 124 GLN cc_start: 0.8911 (tt0) cc_final: 0.8368 (tm-30) REVERT: L 35 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7892 (mtp85) REVERT: M 16 TYR cc_start: 0.7513 (m-80) cc_final: 0.7263 (m-80) REVERT: M 37 MET cc_start: 0.7897 (ptp) cc_final: 0.7659 (ptp) REVERT: M 197 GLN cc_start: 0.7870 (tt0) cc_final: 0.6439 (mm110) REVERT: M 234 GLU cc_start: 0.6697 (tp30) cc_final: 0.5864 (mp0) REVERT: M 357 MET cc_start: 0.2949 (mmm) cc_final: 0.2641 (mmm) REVERT: M 421 MET cc_start: 0.3153 (OUTLIER) cc_final: 0.2783 (mmm) REVERT: N 347 ASP cc_start: 0.7248 (p0) cc_final: 0.6678 (m-30) REVERT: N 352 THR cc_start: 0.7652 (p) cc_final: 0.7428 (p) REVERT: O 14 GLN cc_start: 0.8607 (tt0) cc_final: 0.8168 (tp40) REVERT: O 22 GLU cc_start: 0.8414 (pp20) cc_final: 0.8046 (pp20) REVERT: O 48 ASP cc_start: 0.8609 (p0) cc_final: 0.8044 (p0) REVERT: O 85 MET cc_start: 0.8546 (ttm) cc_final: 0.8293 (ttp) REVERT: O 108 GLU cc_start: 0.7710 (tt0) cc_final: 0.7303 (tm-30) REVERT: O 133 MET cc_start: 0.4372 (ptt) cc_final: 0.3991 (ptt) REVERT: O 139 MET cc_start: 0.6118 (mmm) cc_final: 0.5821 (tpp) REVERT: O 233 ILE cc_start: 0.6613 (mm) cc_final: 0.6205 (mp) REVERT: O 275 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6977 (pt0) REVERT: O 308 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6038 (tp) REVERT: O 322 PHE cc_start: 0.8192 (m-80) cc_final: 0.7211 (m-80) REVERT: O 333 MET cc_start: 0.5951 (tpt) cc_final: 0.5506 (mmm) REVERT: O 383 PHE cc_start: 0.7785 (m-10) cc_final: 0.7101 (m-10) REVERT: O 385 MET cc_start: 0.7009 (tpp) cc_final: 0.6632 (tpt) REVERT: O 459 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7804 (mmm160) REVERT: O 462 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7910 (tp30) REVERT: O 517 ASP cc_start: 0.9036 (t0) cc_final: 0.8481 (t70) REVERT: P 232 MET cc_start: 0.4758 (ttp) cc_final: 0.4249 (mmm) REVERT: Q 33 LYS cc_start: 0.8294 (ptmt) cc_final: 0.8028 (mtmm) REVERT: Q 54 GLU cc_start: 0.7499 (mp0) cc_final: 0.7077 (mt-10) REVERT: Q 55 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8201 (tp30) REVERT: Q 62 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7649 (mm-40) REVERT: Q 66 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7812 (mm-30) REVERT: Q 92 MET cc_start: 0.1427 (ptt) cc_final: 0.0770 (mtp) REVERT: V 29 SER cc_start: 0.7769 (t) cc_final: 0.7537 (p) outliers start: 104 outliers final: 61 residues processed: 773 average time/residue: 0.2925 time to fit residues: 369.2464 Evaluate side-chains 726 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 655 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 807 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 489 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 412 optimal weight: 20.0000 chunk 519 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 260 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 307 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A1054 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS O 306 GLN P 182 GLN P 274 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.182755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110503 restraints weight = 61539.445| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.46 r_work: 0.3034 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 45600 Z= 0.119 Angle : 0.558 15.771 62049 Z= 0.282 Chirality : 0.043 0.282 6977 Planarity : 0.004 0.045 7603 Dihedral : 15.897 177.603 7038 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.21 % Allowed : 15.39 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 5269 helix: 1.53 (0.12), residues: 2081 sheet: -0.52 (0.20), residues: 647 loop : -0.79 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 998 TYR 0.035 0.001 TYR A1186 PHE 0.020 0.001 PHE G 157 TRP 0.028 0.001 TRP P 217 HIS 0.008 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (45571) covalent geometry : angle 0.54736 / 0.28 (62007) hydrogen bonds : bond 0.03398 / 2.31 ( 1961) hydrogen bonds : angle 4.21367 / 2.99 ( 5550) metal coordination : bond 0.00528 / 0.28 ( 27) metal coordination : angle 4.10989 / 2.39 ( 42) Misc. bond : bond 0.00115 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 678 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.6906 (ptp-170) cc_final: 0.6421 (mtp180) REVERT: A 144 LYS cc_start: 0.8795 (tttm) cc_final: 0.8320 (ttmt) REVERT: A 203 HIS cc_start: 0.7446 (m170) cc_final: 0.6972 (m170) REVERT: A 228 LYS cc_start: 0.8757 (mttt) cc_final: 0.8512 (mtpt) REVERT: A 304 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7573 (tt0) REVERT: A 312 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: A 406 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8396 (ttpt) REVERT: A 430 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7818 (mtt-85) REVERT: A 737 GLN cc_start: 0.6963 (tp40) cc_final: 0.6714 (tm-30) REVERT: A 805 SER cc_start: 0.9125 (m) cc_final: 0.8866 (p) REVERT: A 947 LEU cc_start: 0.8793 (tt) cc_final: 0.8446 (mp) REVERT: A 1091 LYS cc_start: 0.8219 (mttt) cc_final: 0.7918 (mtpt) REVERT: A 1112 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7737 (mt-10) REVERT: A 1196 LEU cc_start: 0.8393 (tp) cc_final: 0.8100 (mt) REVERT: A 1206 GLU cc_start: 0.8132 (mp0) cc_final: 0.7827 (mp0) REVERT: B 35 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8486 (mptt) REVERT: B 64 LYS cc_start: 0.5938 (ttmt) cc_final: 0.5439 (ttmt) REVERT: B 70 ASP cc_start: 0.8092 (t0) cc_final: 0.6990 (m-30) REVERT: B 84 LEU cc_start: 0.8604 (mt) cc_final: 0.8265 (mt) REVERT: B 86 ASP cc_start: 0.8353 (m-30) cc_final: 0.8102 (m-30) REVERT: B 192 GLU cc_start: 0.7691 (pm20) cc_final: 0.7001 (pm20) REVERT: B 211 LYS cc_start: 0.6651 (mttt) cc_final: 0.5345 (tttt) REVERT: B 226 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7100 (ttm110) REVERT: B 254 MET cc_start: 0.8600 (mtm) cc_final: 0.8323 (mtm) REVERT: B 285 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7360 (tppt) REVERT: B 296 MET cc_start: 0.1588 (mmt) cc_final: 0.1355 (mmm) REVERT: B 378 LYS cc_start: 0.7319 (mttm) cc_final: 0.6804 (mmtp) REVERT: B 417 ASN cc_start: 0.9070 (m-40) cc_final: 0.8797 (m110) REVERT: B 478 MET cc_start: 0.9593 (mmt) cc_final: 0.8982 (mmp) REVERT: B 521 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 522 ASP cc_start: 0.7585 (t0) cc_final: 0.7332 (t0) REVERT: B 581 ARG cc_start: 0.8600 (mtm110) cc_final: 0.8322 (mtm110) REVERT: B 791 MET cc_start: 0.8587 (mmt) cc_final: 0.8300 (mmm) REVERT: B 1015 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: B 1037 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7980 (tt0) REVERT: B 1041 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7522 (ttm110) REVERT: C 286 GLU cc_start: 0.8849 (tp30) cc_final: 0.8551 (tp30) REVERT: C 296 VAL cc_start: 0.9358 (m) cc_final: 0.9018 (p) REVERT: C 328 VAL cc_start: 0.8310 (p) cc_final: 0.7999 (m) REVERT: D 14 TYR cc_start: 0.6816 (t80) cc_final: 0.6552 (t80) REVERT: D 82 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7534 (mm-30) REVERT: E 73 PHE cc_start: 0.5749 (t80) cc_final: 0.5164 (t80) REVERT: E 85 LYS cc_start: 0.8521 (mttt) cc_final: 0.8210 (mmtm) REVERT: E 208 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8695 (tt) REVERT: F 51 ARG cc_start: 0.6815 (mtm-85) cc_final: 0.4776 (mmp-170) REVERT: F 82 GLU cc_start: 0.8338 (pt0) cc_final: 0.8129 (mm-30) REVERT: F 91 LEU cc_start: 0.9403 (mt) cc_final: 0.9174 (mm) REVERT: G 41 ASN cc_start: 0.8778 (m-40) cc_final: 0.8476 (m-40) REVERT: G 198 LEU cc_start: 0.7342 (pt) cc_final: 0.6793 (tt) REVERT: H 18 GLU cc_start: 0.8955 (mp0) cc_final: 0.8607 (mp0) REVERT: H 57 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7589 (ttm-80) REVERT: H 66 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7717 (mp0) REVERT: I 42 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7957 (mmtm) REVERT: J 54 ASP cc_start: 0.8374 (t0) cc_final: 0.8016 (t0) REVERT: K 104 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8557 (mtp) REVERT: K 115 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8684 (mt-10) REVERT: K 124 GLN cc_start: 0.8885 (tt0) cc_final: 0.8315 (tm-30) REVERT: L 35 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7926 (mtp85) REVERT: M 16 TYR cc_start: 0.7517 (m-80) cc_final: 0.7292 (m-80) REVERT: M 197 GLN cc_start: 0.7914 (tt0) cc_final: 0.6454 (mm110) REVERT: M 234 GLU cc_start: 0.6678 (tp30) cc_final: 0.5854 (mp0) REVERT: M 357 MET cc_start: 0.3237 (mmm) cc_final: 0.2952 (mmm) REVERT: M 421 MET cc_start: 0.3171 (OUTLIER) cc_final: 0.2779 (mmm) REVERT: N 347 ASP cc_start: 0.7159 (p0) cc_final: 0.6617 (m-30) REVERT: N 350 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7175 (tpp) REVERT: O 14 GLN cc_start: 0.8634 (tt0) cc_final: 0.8194 (tp40) REVERT: O 22 GLU cc_start: 0.8410 (pp20) cc_final: 0.8051 (pp20) REVERT: O 48 ASP cc_start: 0.8633 (p0) cc_final: 0.8057 (p0) REVERT: O 85 MET cc_start: 0.8572 (ttm) cc_final: 0.8364 (ttp) REVERT: O 108 GLU cc_start: 0.7749 (tt0) cc_final: 0.7278 (tm-30) REVERT: O 133 MET cc_start: 0.4495 (ptt) cc_final: 0.4234 (ptt) REVERT: O 233 ILE cc_start: 0.6532 (mm) cc_final: 0.6150 (mp) REVERT: O 275 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6981 (pt0) REVERT: O 288 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6911 (mt) REVERT: O 308 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6210 (tp) REVERT: O 322 PHE cc_start: 0.8206 (m-80) cc_final: 0.7190 (m-80) REVERT: O 333 MET cc_start: 0.5911 (tpt) cc_final: 0.5446 (mmm) REVERT: O 383 PHE cc_start: 0.7801 (m-10) cc_final: 0.7131 (m-10) REVERT: O 385 MET cc_start: 0.7020 (tpp) cc_final: 0.6659 (tpt) REVERT: O 459 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7681 (mmm160) REVERT: O 462 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7817 (tp30) REVERT: O 517 ASP cc_start: 0.8899 (t0) cc_final: 0.8435 (t70) REVERT: P 236 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6515 (tp30) REVERT: P 240 ASN cc_start: 0.7666 (m-40) cc_final: 0.7462 (m-40) REVERT: Q 33 LYS cc_start: 0.8302 (ptmt) cc_final: 0.8038 (mtmm) REVERT: Q 54 GLU cc_start: 0.7507 (mp0) cc_final: 0.7079 (mt-10) REVERT: Q 55 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8227 (tp30) REVERT: Q 62 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7654 (mm-40) REVERT: Q 66 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7846 (mm-30) REVERT: Q 92 MET cc_start: 0.1274 (ptt) cc_final: 0.0671 (mtp) REVERT: V 29 SER cc_start: 0.7799 (t) cc_final: 0.7568 (p) outliers start: 104 outliers final: 76 residues processed: 748 average time/residue: 0.2432 time to fit residues: 297.6716 Evaluate side-chains 726 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 641 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 350 MET Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 288 LEU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 43 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 247 optimal weight: 0.3980 chunk 451 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 400 optimal weight: 30.0000 chunk 236 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 510 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN O 306 GLN P 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106984 restraints weight = 61893.652| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.64 r_work: 0.2966 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 45600 Z= 0.200 Angle : 0.615 17.326 62049 Z= 0.311 Chirality : 0.045 0.258 6977 Planarity : 0.004 0.052 7603 Dihedral : 15.910 175.836 7038 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.45 % Allowed : 15.37 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.12), residues: 5269 helix: 1.39 (0.12), residues: 2087 sheet: -0.67 (0.19), residues: 661 loop : -0.80 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 433 TYR 0.020 0.002 TYR A1186 PHE 0.020 0.002 PHE G 157 TRP 0.031 0.002 TRP P 217 HIS 0.010 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (45571) covalent geometry : angle 0.60474 / 0.31 (62007) hydrogen bonds : bond 0.03807 / 2.60 ( 1961) hydrogen bonds : angle 4.33314 / 3.08 ( 5550) metal coordination : bond 0.00937 / 0.53 ( 27) metal coordination : angle 4.32006 / 2.52 ( 42) Misc. bond : bond 0.00162 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 667 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.6988 (ptp-170) cc_final: 0.6386 (mtp180) REVERT: A 144 LYS cc_start: 0.8976 (tttm) cc_final: 0.8492 (ttmt) REVERT: A 203 HIS cc_start: 0.7202 (m170) cc_final: 0.6833 (m-70) REVERT: A 219 ASN cc_start: 0.8476 (m-40) cc_final: 0.8238 (p0) REVERT: A 228 LYS cc_start: 0.8844 (mttt) cc_final: 0.8636 (mtpt) REVERT: A 304 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7608 (tt0) REVERT: A 312 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: A 406 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8437 (ttpt) REVERT: A 430 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7823 (mtt-85) REVERT: A 737 GLN cc_start: 0.6890 (tp40) cc_final: 0.6613 (tm-30) REVERT: A 755 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7682 (tp30) REVERT: A 805 SER cc_start: 0.9182 (m) cc_final: 0.8958 (p) REVERT: A 1091 LYS cc_start: 0.8254 (mttt) cc_final: 0.7948 (mtpt) REVERT: A 1105 ILE cc_start: 0.8408 (pt) cc_final: 0.8163 (pt) REVERT: A 1112 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 1194 GLU cc_start: 0.7613 (pp20) cc_final: 0.7396 (pp20) REVERT: A 1196 LEU cc_start: 0.8418 (tp) cc_final: 0.8085 (mt) REVERT: A 1206 GLU cc_start: 0.8284 (mp0) cc_final: 0.7991 (mp0) REVERT: A 1245 ARG cc_start: 0.9076 (mtp85) cc_final: 0.8580 (mpt90) REVERT: B 35 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8515 (mptt) REVERT: B 64 LYS cc_start: 0.5834 (ttmt) cc_final: 0.5289 (ttmt) REVERT: B 70 ASP cc_start: 0.8022 (t0) cc_final: 0.6994 (m-30) REVERT: B 84 LEU cc_start: 0.8665 (mt) cc_final: 0.8326 (mt) REVERT: B 86 ASP cc_start: 0.8478 (m-30) cc_final: 0.8201 (m-30) REVERT: B 192 GLU cc_start: 0.7694 (pm20) cc_final: 0.7075 (pm20) REVERT: B 211 LYS cc_start: 0.6863 (mttt) cc_final: 0.5447 (tttt) REVERT: B 226 ARG cc_start: 0.7651 (ttm110) cc_final: 0.7158 (ttm110) REVERT: B 240 PHE cc_start: 0.8230 (m-80) cc_final: 0.7893 (m-80) REVERT: B 254 MET cc_start: 0.8626 (mtm) cc_final: 0.8291 (mtm) REVERT: B 278 PHE cc_start: 0.7964 (m-80) cc_final: 0.7713 (m-80) REVERT: B 285 LYS cc_start: 0.7942 (ttmm) cc_final: 0.7488 (ttpt) REVERT: B 296 MET cc_start: 0.1619 (mmt) cc_final: 0.1273 (mmm) REVERT: B 378 LYS cc_start: 0.7395 (mttm) cc_final: 0.6925 (mmtp) REVERT: B 417 ASN cc_start: 0.9054 (m-40) cc_final: 0.8785 (m-40) REVERT: B 478 MET cc_start: 0.9578 (mmt) cc_final: 0.8971 (mmp) REVERT: B 521 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 526 LEU cc_start: 0.8168 (pp) cc_final: 0.7894 (pp) REVERT: B 791 MET cc_start: 0.8653 (mmt) cc_final: 0.8364 (mmm) REVERT: B 1015 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8646 (mtt) REVERT: B 1037 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8009 (tt0) REVERT: B 1062 MET cc_start: 0.9288 (tpp) cc_final: 0.9021 (mmp) REVERT: C 286 GLU cc_start: 0.8933 (tp30) cc_final: 0.8647 (tp30) REVERT: C 296 VAL cc_start: 0.9390 (m) cc_final: 0.9041 (p) REVERT: D 14 TYR cc_start: 0.6938 (t80) cc_final: 0.6582 (t80) REVERT: D 51 LYS cc_start: 0.5263 (tptp) cc_final: 0.4935 (mmtm) REVERT: D 82 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7506 (mm-30) REVERT: D 83 LYS cc_start: 0.8232 (ptpp) cc_final: 0.8010 (pttt) REVERT: E 5 GLU cc_start: 0.6809 (pm20) cc_final: 0.6432 (pm20) REVERT: E 85 LYS cc_start: 0.8548 (mttt) cc_final: 0.8270 (mmtm) REVERT: E 208 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8666 (tt) REVERT: F 51 ARG cc_start: 0.6921 (mtm-85) cc_final: 0.4643 (mmp-170) REVERT: F 82 GLU cc_start: 0.8379 (pt0) cc_final: 0.8141 (mm-30) REVERT: F 91 LEU cc_start: 0.9412 (mt) cc_final: 0.9189 (mm) REVERT: G 41 ASN cc_start: 0.8820 (m-40) cc_final: 0.8531 (m-40) REVERT: G 198 LEU cc_start: 0.7362 (pt) cc_final: 0.6820 (tt) REVERT: H 14 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8515 (t70) REVERT: H 57 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7655 (ttm-80) REVERT: H 66 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7734 (mp0) REVERT: H 122 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9158 (mt) REVERT: I 42 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8030 (mmmm) REVERT: K 104 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8639 (mtp) REVERT: K 115 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8801 (mt-10) REVERT: K 124 GLN cc_start: 0.8840 (tt0) cc_final: 0.8286 (tm-30) REVERT: L 35 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8104 (mtp85) REVERT: M 16 TYR cc_start: 0.7638 (m-80) cc_final: 0.7386 (m-80) REVERT: M 197 GLN cc_start: 0.7952 (tt0) cc_final: 0.6464 (mm110) REVERT: M 357 MET cc_start: 0.3041 (mmm) cc_final: 0.2801 (mmm) REVERT: M 421 MET cc_start: 0.2962 (OUTLIER) cc_final: 0.2615 (mmm) REVERT: N 347 ASP cc_start: 0.7362 (p0) cc_final: 0.6772 (m-30) REVERT: N 350 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7433 (tpp) REVERT: O 14 GLN cc_start: 0.8693 (tt0) cc_final: 0.8195 (tp40) REVERT: O 22 GLU cc_start: 0.8413 (pp20) cc_final: 0.8065 (pp20) REVERT: O 48 ASP cc_start: 0.8856 (p0) cc_final: 0.8253 (p0) REVERT: O 85 MET cc_start: 0.8712 (ttm) cc_final: 0.8505 (ttp) REVERT: O 108 GLU cc_start: 0.7644 (tt0) cc_final: 0.7293 (tm-30) REVERT: O 133 MET cc_start: 0.4589 (ptt) cc_final: 0.4358 (ptt) REVERT: O 233 ILE cc_start: 0.6510 (mm) cc_final: 0.6122 (mp) REVERT: O 275 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6888 (pt0) REVERT: O 308 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6365 (tp) REVERT: O 309 ASP cc_start: 0.6810 (t0) cc_final: 0.6509 (m-30) REVERT: O 322 PHE cc_start: 0.8169 (m-80) cc_final: 0.7159 (m-80) REVERT: O 333 MET cc_start: 0.5962 (tpt) cc_final: 0.5471 (mmm) REVERT: O 383 PHE cc_start: 0.7830 (m-10) cc_final: 0.7192 (m-10) REVERT: O 385 MET cc_start: 0.7164 (tpp) cc_final: 0.6845 (tpt) REVERT: O 459 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7843 (mmm160) REVERT: O 462 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7700 (tp30) REVERT: O 517 ASP cc_start: 0.9053 (t0) cc_final: 0.8523 (t70) REVERT: O 523 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8577 (mt) REVERT: Q 33 LYS cc_start: 0.8367 (ptmt) cc_final: 0.8034 (mtmm) REVERT: Q 55 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8237 (tp30) REVERT: Q 62 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7653 (mm-40) REVERT: Q 66 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7903 (mm-30) REVERT: Q 92 MET cc_start: 0.1302 (ptt) cc_final: 0.0697 (mtp) REVERT: V 29 SER cc_start: 0.8068 (t) cc_final: 0.7848 (p) outliers start: 115 outliers final: 84 residues processed: 743 average time/residue: 0.2355 time to fit residues: 286.6980 Evaluate side-chains 732 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 637 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 348 VAL Chi-restraints excluded: chain N residue 350 MET Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 375 ILE Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 329 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 494 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 495 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 446 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 215 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 410 GLN ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN G 115 GLN M 80 ASN O 306 GLN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.180568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107920 restraints weight = 61460.811| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.59 r_work: 0.2995 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45600 Z= 0.146 Angle : 0.593 17.653 62049 Z= 0.298 Chirality : 0.044 0.288 6977 Planarity : 0.004 0.050 7603 Dihedral : 15.837 175.039 7038 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.34 % Allowed : 15.63 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.12), residues: 5269 helix: 1.45 (0.12), residues: 2080 sheet: -0.56 (0.20), residues: 652 loop : -0.76 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 998 TYR 0.022 0.001 TYR E 90 PHE 0.033 0.001 PHE M 177 TRP 0.030 0.001 TRP P 217 HIS 0.007 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (45571) covalent geometry : angle 0.58333 / 0.30 (62007) hydrogen bonds : bond 0.03554 / 2.42 ( 1961) hydrogen bonds : angle 4.27630 / 3.03 ( 5550) metal coordination : bond 0.00716 / 0.39 ( 27) metal coordination : angle 4.23227 / 2.44 ( 42) Misc. bond : bond 0.00130 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 660 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.7142 (ptp-170) cc_final: 0.6682 (mtp180) REVERT: A 144 LYS cc_start: 0.8950 (tttm) cc_final: 0.8446 (ttmt) REVERT: A 155 ILE cc_start: 0.8072 (pt) cc_final: 0.7872 (pt) REVERT: A 203 HIS cc_start: 0.7209 (m170) cc_final: 0.6821 (m-70) REVERT: A 219 ASN cc_start: 0.8435 (m-40) cc_final: 0.8233 (p0) REVERT: A 228 LYS cc_start: 0.8822 (mttt) cc_final: 0.8578 (mtpt) REVERT: A 237 LEU cc_start: 0.9125 (mm) cc_final: 0.8868 (mm) REVERT: A 304 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7613 (tt0) REVERT: A 312 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: A 406 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8386 (ttpt) REVERT: A 430 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7990 (mtt-85) REVERT: A 458 ASP cc_start: 0.9288 (OUTLIER) cc_final: 0.8892 (t0) REVERT: A 737 GLN cc_start: 0.6884 (tp40) cc_final: 0.6602 (tm-30) REVERT: A 755 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7652 (tp30) REVERT: A 805 SER cc_start: 0.9167 (m) cc_final: 0.8911 (p) REVERT: A 1091 LYS cc_start: 0.8245 (mttt) cc_final: 0.7933 (mtpt) REVERT: A 1112 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 1196 LEU cc_start: 0.8429 (tp) cc_final: 0.8131 (mt) REVERT: A 1206 GLU cc_start: 0.8279 (mp0) cc_final: 0.7998 (mp0) REVERT: A 1245 ARG cc_start: 0.9016 (mtp85) cc_final: 0.8509 (mpt90) REVERT: B 35 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8474 (mptt) REVERT: B 64 LYS cc_start: 0.5772 (ttmt) cc_final: 0.5228 (ttmt) REVERT: B 70 ASP cc_start: 0.8065 (t0) cc_final: 0.7054 (m-30) REVERT: B 82 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7429 (m) REVERT: B 84 LEU cc_start: 0.8650 (mt) cc_final: 0.8305 (mt) REVERT: B 86 ASP cc_start: 0.8458 (m-30) cc_final: 0.8181 (m-30) REVERT: B 192 GLU cc_start: 0.7583 (pm20) cc_final: 0.6932 (pm20) REVERT: B 226 ARG cc_start: 0.7459 (ttm110) cc_final: 0.6957 (ttm110) REVERT: B 254 MET cc_start: 0.8603 (mtm) cc_final: 0.8271 (mtm) REVERT: B 278 PHE cc_start: 0.8003 (m-80) cc_final: 0.7666 (m-80) REVERT: B 285 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7423 (tppt) REVERT: B 296 MET cc_start: 0.1618 (mmt) cc_final: 0.1276 (mmm) REVERT: B 378 LYS cc_start: 0.7487 (mttm) cc_final: 0.6897 (mmtp) REVERT: B 417 ASN cc_start: 0.9031 (m-40) cc_final: 0.8713 (m110) REVERT: B 431 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.5411 (tmm) REVERT: B 478 MET cc_start: 0.9577 (mmt) cc_final: 0.8978 (mmp) REVERT: B 521 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7985 (mt-10) REVERT: B 526 LEU cc_start: 0.8173 (pp) cc_final: 0.7880 (pp) REVERT: B 791 MET cc_start: 0.8618 (mmt) cc_final: 0.8298 (mmm) REVERT: B 1015 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8425 (mtt) REVERT: B 1062 MET cc_start: 0.9269 (tpp) cc_final: 0.8994 (mmp) REVERT: C 286 GLU cc_start: 0.8884 (tp30) cc_final: 0.8599 (tp30) REVERT: C 296 VAL cc_start: 0.9383 (m) cc_final: 0.9031 (p) REVERT: D 14 TYR cc_start: 0.6804 (t80) cc_final: 0.6550 (t80) REVERT: D 51 LYS cc_start: 0.5252 (tptp) cc_final: 0.4869 (mmtm) REVERT: D 82 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7517 (mm-30) REVERT: D 83 LYS cc_start: 0.8242 (ptpp) cc_final: 0.8010 (pttt) REVERT: E 5 GLU cc_start: 0.6800 (pm20) cc_final: 0.6408 (pm20) REVERT: E 73 PHE cc_start: 0.5567 (t80) cc_final: 0.5088 (t80) REVERT: E 85 LYS cc_start: 0.8565 (mttt) cc_final: 0.8280 (mmtm) REVERT: E 208 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8684 (tt) REVERT: F 51 ARG cc_start: 0.6888 (mtm-85) cc_final: 0.4597 (mmp-170) REVERT: F 82 GLU cc_start: 0.8366 (pt0) cc_final: 0.8117 (mm-30) REVERT: F 91 LEU cc_start: 0.9386 (mt) cc_final: 0.9159 (mm) REVERT: G 19 GLU cc_start: 0.8153 (pm20) cc_final: 0.7941 (pm20) REVERT: G 41 ASN cc_start: 0.8814 (m-40) cc_final: 0.8549 (m-40) REVERT: G 198 LEU cc_start: 0.7378 (pt) cc_final: 0.6833 (tt) REVERT: H 14 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8481 (t70) REVERT: H 18 GLU cc_start: 0.8945 (mp0) cc_final: 0.8663 (mp0) REVERT: H 57 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7586 (ttm-80) REVERT: H 66 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7713 (mp0) REVERT: H 122 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9136 (mt) REVERT: I 42 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8081 (mmmm) REVERT: J 54 ASP cc_start: 0.8387 (t0) cc_final: 0.8009 (t0) REVERT: K 104 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8558 (mtp) REVERT: K 115 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8826 (mt-10) REVERT: K 124 GLN cc_start: 0.8836 (tt0) cc_final: 0.8268 (tm-30) REVERT: L 35 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.8041 (mtp85) REVERT: M 16 TYR cc_start: 0.7692 (m-80) cc_final: 0.7411 (m-80) REVERT: M 37 MET cc_start: 0.8067 (ptp) cc_final: 0.7786 (ptp) REVERT: M 102 PHE cc_start: 0.7169 (m-80) cc_final: 0.6725 (m-80) REVERT: M 197 GLN cc_start: 0.7946 (tt0) cc_final: 0.6458 (mm110) REVERT: M 421 MET cc_start: 0.3139 (OUTLIER) cc_final: 0.2781 (mmm) REVERT: N 347 ASP cc_start: 0.7249 (p0) cc_final: 0.6821 (m-30) REVERT: N 350 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7624 (tpp) REVERT: O 14 GLN cc_start: 0.8667 (tt0) cc_final: 0.8178 (tp40) REVERT: O 22 GLU cc_start: 0.8396 (pp20) cc_final: 0.8019 (pp20) REVERT: O 48 ASP cc_start: 0.8673 (p0) cc_final: 0.8073 (p0) REVERT: O 108 GLU cc_start: 0.7622 (tt0) cc_final: 0.7269 (tm-30) REVERT: O 133 MET cc_start: 0.4085 (ptt) cc_final: 0.3808 (ptt) REVERT: O 139 MET cc_start: 0.7154 (tpt) cc_final: 0.6816 (tpp) REVERT: O 233 ILE cc_start: 0.6622 (mm) cc_final: 0.6192 (mp) REVERT: O 275 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: O 288 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6978 (mt) REVERT: O 308 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6351 (tp) REVERT: O 309 ASP cc_start: 0.6973 (t0) cc_final: 0.6623 (m-30) REVERT: O 322 PHE cc_start: 0.8141 (m-80) cc_final: 0.7109 (m-80) REVERT: O 333 MET cc_start: 0.5900 (tpt) cc_final: 0.5400 (mmm) REVERT: O 383 PHE cc_start: 0.7863 (m-10) cc_final: 0.7182 (m-10) REVERT: O 385 MET cc_start: 0.7176 (tpp) cc_final: 0.6846 (tpt) REVERT: O 459 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7717 (mmm160) REVERT: O 462 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7653 (tp30) REVERT: O 517 ASP cc_start: 0.9039 (t0) cc_final: 0.8518 (t70) REVERT: P 232 MET cc_start: 0.4668 (tpp) cc_final: 0.3986 (tpt) REVERT: Q 33 LYS cc_start: 0.8288 (ptmt) cc_final: 0.8007 (mtmm) REVERT: Q 55 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8240 (tp30) REVERT: Q 62 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7614 (mm-40) REVERT: Q 66 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7900 (mm-30) REVERT: Q 92 MET cc_start: 0.1298 (ptt) cc_final: 0.0699 (mtp) REVERT: Q 110 MET cc_start: 0.6364 (ptm) cc_final: 0.6013 (ptp) outliers start: 110 outliers final: 74 residues processed: 731 average time/residue: 0.2423 time to fit residues: 291.3424 Evaluate side-chains 728 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 640 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 807 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 348 VAL Chi-restraints excluded: chain N residue 350 MET Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 288 LEU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 136 optimal weight: 0.0970 chunk 225 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 244 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 482 optimal weight: 7.9990 chunk 436 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 299 optimal weight: 5.9990 chunk 527 optimal weight: 40.0000 chunk 274 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 738 GLN B 183 GLN B 410 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN M 80 ASN O 306 GLN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.181593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109787 restraints weight = 61758.327| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.48 r_work: 0.3034 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 45600 Z= 0.113 Angle : 0.570 17.060 62049 Z= 0.287 Chirality : 0.043 0.241 6977 Planarity : 0.004 0.052 7603 Dihedral : 15.722 174.404 7038 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.98 % Allowed : 15.95 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.12), residues: 5269 helix: 1.57 (0.12), residues: 2071 sheet: -0.51 (0.20), residues: 640 loop : -0.68 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 998 TYR 0.024 0.001 TYR A1116 PHE 0.023 0.001 PHE G 120 TRP 0.031 0.001 TRP P 217 HIS 0.011 0.001 HIS O 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (45571) covalent geometry : angle 0.56014 / 0.29 (62007) hydrogen bonds : bond 0.03322 / 2.24 ( 1961) hydrogen bonds : angle 4.20683 / 2.97 ( 5550) metal coordination : bond 0.00516 / 0.27 ( 27) metal coordination : angle 4.09416 / 2.35 ( 42) Misc. bond : bond 0.00115 / 0.06 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 669 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.7164 (ptp-170) cc_final: 0.6695 (mtp180) REVERT: A 144 LYS cc_start: 0.8987 (tttm) cc_final: 0.8465 (ttmt) REVERT: A 203 HIS cc_start: 0.7135 (m170) cc_final: 0.6737 (m-70) REVERT: A 228 LYS cc_start: 0.8811 (mttt) cc_final: 0.8568 (mtpt) REVERT: A 237 LEU cc_start: 0.9195 (mm) cc_final: 0.8909 (mm) REVERT: A 304 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7615 (tt0) REVERT: A 312 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: A 406 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8394 (ttpt) REVERT: A 430 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7943 (mtt-85) REVERT: A 458 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.8855 (t0) REVERT: A 737 GLN cc_start: 0.6859 (tp40) cc_final: 0.6560 (tm-30) REVERT: A 755 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7627 (tp30) REVERT: A 805 SER cc_start: 0.9153 (m) cc_final: 0.8907 (p) REVERT: A 1091 LYS cc_start: 0.8169 (mttt) cc_final: 0.7923 (mtpt) REVERT: A 1112 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 1118 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: A 1196 LEU cc_start: 0.8420 (tp) cc_final: 0.8118 (mt) REVERT: A 1206 GLU cc_start: 0.8244 (mp0) cc_final: 0.7950 (mp0) REVERT: A 1245 ARG cc_start: 0.9008 (mtp85) cc_final: 0.8542 (mpt90) REVERT: B 35 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8491 (mptt) REVERT: B 64 LYS cc_start: 0.5731 (ttmt) cc_final: 0.5227 (ttmt) REVERT: B 70 ASP cc_start: 0.8053 (t0) cc_final: 0.7103 (m-30) REVERT: B 82 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7425 (m) REVERT: B 192 GLU cc_start: 0.7606 (pm20) cc_final: 0.6949 (pm20) REVERT: B 226 ARG cc_start: 0.7530 (ttm110) cc_final: 0.7018 (ttm110) REVERT: B 254 MET cc_start: 0.8593 (mtm) cc_final: 0.8280 (mtm) REVERT: B 278 PHE cc_start: 0.8069 (m-80) cc_final: 0.7736 (m-80) REVERT: B 285 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7424 (tppt) REVERT: B 296 MET cc_start: 0.1611 (mmt) cc_final: 0.1267 (mmm) REVERT: B 363 GLU cc_start: 0.8904 (tp30) cc_final: 0.8653 (tp30) REVERT: B 367 GLN cc_start: 0.7703 (mp10) cc_final: 0.7346 (mp10) REVERT: B 378 LYS cc_start: 0.7487 (mttm) cc_final: 0.6850 (mmtp) REVERT: B 417 ASN cc_start: 0.9029 (m-40) cc_final: 0.8737 (m110) REVERT: B 478 MET cc_start: 0.9561 (mmt) cc_final: 0.8960 (mmp) REVERT: B 521 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 526 LEU cc_start: 0.8186 (pp) cc_final: 0.7977 (pp) REVERT: B 647 GLU cc_start: 0.9017 (mp0) cc_final: 0.8741 (mp0) REVERT: B 791 MET cc_start: 0.8628 (mmt) cc_final: 0.8279 (mmm) REVERT: B 1015 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8343 (mtt) REVERT: B 1051 GLU cc_start: 0.8924 (mp0) cc_final: 0.8685 (mp0) REVERT: B 1062 MET cc_start: 0.9262 (tpp) cc_final: 0.8977 (mmp) REVERT: C 255 ARG cc_start: 0.8564 (mtp180) cc_final: 0.8339 (mtm180) REVERT: C 286 GLU cc_start: 0.8816 (tp30) cc_final: 0.8561 (tp30) REVERT: C 296 VAL cc_start: 0.9379 (m) cc_final: 0.9036 (p) REVERT: C 328 VAL cc_start: 0.8444 (p) cc_final: 0.8199 (m) REVERT: D 51 LYS cc_start: 0.5230 (tptp) cc_final: 0.4854 (mmtm) REVERT: D 82 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7441 (mm-30) REVERT: D 83 LYS cc_start: 0.8237 (ptpp) cc_final: 0.8000 (pttt) REVERT: E 5 GLU cc_start: 0.6772 (pm20) cc_final: 0.6254 (pm20) REVERT: E 73 PHE cc_start: 0.5015 (t80) cc_final: 0.4671 (t80) REVERT: E 85 LYS cc_start: 0.8609 (mttt) cc_final: 0.8339 (mmtm) REVERT: E 130 PHE cc_start: 0.8128 (m-80) cc_final: 0.7857 (m-80) REVERT: E 208 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8733 (tt) REVERT: F 51 ARG cc_start: 0.6885 (mtm-85) cc_final: 0.4576 (mmp-170) REVERT: F 82 GLU cc_start: 0.8304 (pt0) cc_final: 0.8090 (mm-30) REVERT: F 91 LEU cc_start: 0.9387 (mt) cc_final: 0.9173 (mm) REVERT: G 19 GLU cc_start: 0.8121 (pm20) cc_final: 0.7897 (pm20) REVERT: G 41 ASN cc_start: 0.8815 (m-40) cc_final: 0.8563 (m-40) REVERT: G 198 LEU cc_start: 0.7376 (pt) cc_final: 0.6840 (tt) REVERT: H 14 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8445 (t70) REVERT: H 18 GLU cc_start: 0.8987 (mp0) cc_final: 0.8684 (mp0) REVERT: H 57 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7584 (ttm-80) REVERT: H 66 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7703 (mp0) REVERT: H 122 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9087 (mt) REVERT: I 42 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8038 (mmmm) REVERT: J 54 ASP cc_start: 0.8273 (t0) cc_final: 0.7896 (t0) REVERT: K 104 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8534 (mtp) REVERT: K 115 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8838 (mt-10) REVERT: K 124 GLN cc_start: 0.8875 (tt0) cc_final: 0.8319 (tm-30) REVERT: L 35 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.8055 (mtp85) REVERT: M 16 TYR cc_start: 0.7675 (m-80) cc_final: 0.7387 (m-80) REVERT: M 37 MET cc_start: 0.8038 (ptp) cc_final: 0.7760 (ptp) REVERT: M 60 MET cc_start: 0.5478 (pmm) cc_final: 0.5149 (pmm) REVERT: M 102 PHE cc_start: 0.7284 (m-80) cc_final: 0.7079 (m-80) REVERT: M 197 GLN cc_start: 0.7939 (tt0) cc_final: 0.6420 (mm110) REVERT: M 421 MET cc_start: 0.3093 (OUTLIER) cc_final: 0.2722 (mmm) REVERT: N 347 ASP cc_start: 0.7187 (p0) cc_final: 0.6839 (m-30) REVERT: N 350 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7581 (tpp) REVERT: O 14 GLN cc_start: 0.8680 (tt0) cc_final: 0.8208 (tp40) REVERT: O 22 GLU cc_start: 0.8381 (pp20) cc_final: 0.8007 (pp20) REVERT: O 48 ASP cc_start: 0.8676 (p0) cc_final: 0.8068 (p0) REVERT: O 108 GLU cc_start: 0.7767 (tt0) cc_final: 0.7277 (tm-30) REVERT: O 133 MET cc_start: 0.4450 (ptt) cc_final: 0.4158 (ptt) REVERT: O 139 MET cc_start: 0.7386 (tpt) cc_final: 0.6933 (tpp) REVERT: O 233 ILE cc_start: 0.6567 (mm) cc_final: 0.6125 (mp) REVERT: O 275 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7120 (pt0) REVERT: O 288 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7011 (mt) REVERT: O 322 PHE cc_start: 0.8213 (m-80) cc_final: 0.7194 (m-80) REVERT: O 333 MET cc_start: 0.5939 (tpt) cc_final: 0.5451 (mmm) REVERT: O 383 PHE cc_start: 0.7845 (m-10) cc_final: 0.7198 (m-10) REVERT: O 385 MET cc_start: 0.7153 (tpp) cc_final: 0.6821 (tpt) REVERT: O 459 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7782 (mmm160) REVERT: O 462 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7722 (tp30) REVERT: O 517 ASP cc_start: 0.9011 (t0) cc_final: 0.8472 (t70) REVERT: P 151 MET cc_start: 0.1938 (mmm) cc_final: 0.1536 (mmt) REVERT: Q 33 LYS cc_start: 0.8282 (ptmt) cc_final: 0.8006 (mtmm) REVERT: Q 54 GLU cc_start: 0.7588 (mp0) cc_final: 0.7249 (mt-10) REVERT: Q 55 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8242 (tp30) REVERT: Q 62 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7559 (mm-40) REVERT: Q 66 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7852 (mm-30) REVERT: Q 92 MET cc_start: 0.1285 (ptt) cc_final: 0.0693 (mtp) REVERT: Q 103 TRP cc_start: 0.7354 (m100) cc_final: 0.7081 (m100) REVERT: Q 111 MET cc_start: 0.5253 (tpt) cc_final: 0.4966 (tpt) outliers start: 93 outliers final: 68 residues processed: 732 average time/residue: 0.1775 time to fit residues: 214.5385 Evaluate side-chains 729 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 648 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 738 GLN Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 807 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 348 VAL Chi-restraints excluded: chain N residue 350 MET Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 288 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 243 optimal weight: 0.5980 chunk 516 optimal weight: 0.0030 chunk 320 optimal weight: 0.9980 chunk 277 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 449 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 446 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 265 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 410 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.181608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109858 restraints weight = 61755.254| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.41 r_work: 0.3038 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.361 45600 Z= 0.202 Angle : 0.690 59.200 62049 Z= 0.383 Chirality : 0.046 1.275 6977 Planarity : 0.004 0.147 7603 Dihedral : 15.722 174.404 7038 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 1.92 % Allowed : 16.22 % Favored : 81.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.12), residues: 5269 helix: 1.57 (0.12), residues: 2071 sheet: -0.51 (0.20), residues: 640 loop : -0.67 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 22 TYR 0.021 0.001 TYR A1116 PHE 0.017 0.001 PHE C 336 TRP 0.029 0.001 TRP P 217 HIS 0.012 0.001 HIS O 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (45571) covalent geometry : angle 0.68217 / 0.38 (62007) hydrogen bonds : bond 0.03327 / 2.24 ( 1961) hydrogen bonds : angle 4.20965 / 2.98 ( 5550) metal coordination : bond 0.00510 / 0.27 ( 27) metal coordination : angle 4.08950 / 2.35 ( 42) Misc. bond : bond 0.00122 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16586.65 seconds wall clock time: 282 minutes 54.34 seconds (16974.34 seconds total)