Starting phenix.real_space_refine on Tue Sep 15 12:45:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fjj_31622/09_2026/7fjj_31622.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjj_31622/09_2026/7fjj_31622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7fjj_31622/09_2026/7fjj_31622.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fjj_31622/09_2026/7fjj_31622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fjj_31622/09_2026/7fjj_31622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjj_31622/09_2026/7fjj_31622.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjj_31622/09_2026/7fjj_31622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjj_31622/09_2026/7fjj_31622.cif" } resolution = 3.6 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= 0.002 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 7 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 266 5.16 5 C 24803 2.51 5 N 6854 2.21 5 O 7491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39474 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 10675 Classifications: {'peptide': 1360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 1295} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8644 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 48, 'TRANS': 1046} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 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: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 848 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} 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: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1612 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 13, 'TRANS': 188} 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: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3546 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "Q" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 724 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Classifications: {'RNAv2': 4} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Chain: "X" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "Y" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 534 SG CYS A 69 89.615 41.744 62.913 1.00 96.02 S ATOM 556 SG CYS A 72 86.543 42.825 61.207 1.00 94.46 S ATOM 604 SG CYS A 79 89.321 45.366 63.663 1.00 88.70 S ATOM 845 SG CYS A 109 55.550 59.165 95.552 1.00104.59 S ATOM 1262 SG CYS A 159 52.070 58.415 95.415 1.00121.42 S ATOM 18906 SG CYS B1080 72.533 50.897 60.201 1.00 81.64 S ATOM 18925 SG CYS B1083 72.336 51.182 63.110 1.00 81.49 S ATOM 18991 SG CYS B1092 74.919 48.487 62.993 1.00 86.49 S ATOM 19019 SG CYS B1095 71.374 48.378 61.889 1.00 88.09 S ATOM 27929 SG CYS I 5 84.894 85.359 142.707 1.00 78.98 S ATOM 27946 SG CYS I 8 85.806 81.730 140.798 1.00 77.78 S ATOM 28076 SG CYS I 25 82.617 82.907 139.506 1.00 86.19 S ATOM 28097 SG CYS I 28 82.817 82.491 143.157 1.00 87.33 S ATOM 28791 SG CYS J 7 146.322 86.188 63.969 1.00 54.01 S ATOM 28815 SG CYS J 10 147.036 87.799 62.436 1.00 57.92 S ATOM 29079 SG CYS J 44 146.725 90.332 63.755 1.00 57.10 S ATOM 29085 SG CYS J 45 149.818 88.459 63.972 1.00 54.89 S ATOM 30128 SG CYS L 19 145.332 46.267 81.772 1.00 81.26 S ATOM 30290 SG CYS L 39 144.718 45.164 85.832 1.00 97.98 S ATOM 37535 SG CYS P 287 59.122 35.207 81.002 1.00121.28 S Time building chain proxies: 8.72, per 1000 atoms: 0.22 Number of scatterers: 39474 At special positions: 0 Unit cell: (182.342, 154.938, 177.072, 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 7 29.99 Fe 4 26.01 S 266 16.00 P 48 15.00 Mg 1 11.99 O 7491 8.00 N 6854 7.00 C 24803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A1902 " pdb="ZN ZN A1902 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 72 " pdb=" ZN A1903 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 109 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " 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 I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 21 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9116 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 51 sheets defined 40.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.544A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 135 through 152 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 208 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 279 through 300 Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 341 through 346 removed outlier: 3.617A pdb=" N LEU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 436 through 444 removed outlier: 3.540A pdb=" N MET A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) 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 512 through 524 removed outlier: 3.638A pdb=" N GLY A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.529A pdb=" N SER A 570 " --> pdb=" O GLN A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.768A pdb=" N VAL A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.967A 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 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 746 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 877 removed outlier: 3.504A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 920 through 932 removed outlier: 3.550A pdb=" N VAL A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 954 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 1047 Proline residue: A1044 - end of helix removed outlier: 3.505A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) 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 1114 Processing helix chain 'A' and resid 1135 through 1140 Processing helix chain 'A' and resid 1145 through 1154 Processing helix chain 'A' and resid 1186 through 1196 Processing helix chain 'A' and resid 1231 through 1236 Processing helix chain 'A' and resid 1242 through 1246 Processing helix chain 'A' and resid 1250 through 1259 removed outlier: 3.535A pdb=" N GLY A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1278 removed outlier: 3.501A pdb=" N ILE A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1274 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.842A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A1292 " --> pdb=" O MET A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1310 removed outlier: 3.606A pdb=" N LEU A1308 " --> pdb=" O THR A1304 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A1310 " --> pdb=" O PHE A1306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1304 through 1310' Processing helix chain 'A' and resid 1314 through 1320 removed outlier: 3.699A pdb=" N LEU A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1334 removed outlier: 3.524A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A1331 " --> pdb=" O HIS A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.767A pdb=" N PHE A1360 " --> pdb=" O THR A1357 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.088A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.983A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.675A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 47 " --> pdb=" O HIS B 43 " (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 159 removed outlier: 3.737A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 265 Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.544A pdb=" N GLU B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 removed outlier: 3.710A pdb=" N TYR B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 313 Processing helix chain 'B' and resid 328 through 349 Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.510A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.778A pdb=" N HIS B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.555A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 518 Processing helix chain 'B' and resid 527 through 533 Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.574A pdb=" N LEU B 555 " --> pdb=" O ASP B 551 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 620 through 627 removed outlier: 3.588A pdb=" N PHE B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.842A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.552A pdb=" N THR B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.709A pdb=" N LEU B 671 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.728A pdb=" N ASN B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 729 Processing helix chain 'B' and resid 759 through 765 Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.502A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.983A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.514A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1042 Processing helix chain 'B' and resid 1048 through 1059 Processing helix chain 'B' and resid 1060 through 1069 removed outlier: 3.606A pdb=" N LEU B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1099 No H-bonds generated for 'chain 'B' and resid 1097 through 1099' 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 Processing helix 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: 3.960A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 290 through 295 removed outlier: 4.320A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 344 Processing helix chain 'D' and resid 12 through 28 removed outlier: 3.526A pdb=" N LYS D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.863A pdb=" N SER D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.608A pdb=" N THR D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 77 removed outlier: 4.137A pdb=" N VAL D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.761A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.682A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 51 through 56 removed outlier: 4.242A pdb=" N THR E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.911A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.896A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 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 99 Processing helix chain 'G' and resid 14 through 18 removed outlier: 4.001A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.751A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.508A pdb=" N LEU I 53 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY I 54 " --> pdb=" O ASP I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 54' Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.620A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.789A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 48 through 60 removed outlier: 3.577A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 126 Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.591A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 154 removed outlier: 3.772A pdb=" N ASP M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 222 removed outlier: 3.621A 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 'N' and resid 147 through 151 removed outlier: 3.860A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 257 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: 3.639A pdb=" N LYS N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 removed outlier: 3.526A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 32 Processing helix chain 'O' and resid 35 through 43 Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 78 through 83 removed outlier: 4.119A pdb=" N VAL O 82 " --> pdb=" O GLN O 78 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 78 through 83' Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 87 through 99 removed outlier: 3.543A pdb=" N THR O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR O 95 " --> pdb=" O TYR O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 113 Processing helix chain 'O' and resid 118 through 133 removed outlier: 4.284A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP O 127 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 154 removed outlier: 3.572A pdb=" N VAL O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 152 " --> pdb=" O PHE O 148 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR O 154 " --> pdb=" O ARG O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 257 removed outlier: 3.710A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 273 removed outlier: 3.600A pdb=" N SER O 264 " --> pdb=" O ASP O 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 296 removed outlier: 3.602A pdb=" N ILE O 293 " --> pdb=" O SER O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 317 removed outlier: 3.539A pdb=" N ASP O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 358 removed outlier: 3.678A pdb=" N LEU O 342 " --> pdb=" O LEU O 338 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 367 removed outlier: 3.734A pdb=" N CYS O 362 " --> pdb=" O PHE O 358 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 387 through 401 removed outlier: 3.653A pdb=" N ASP O 393 " --> pdb=" O LYS O 389 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 429 through 453 removed outlier: 3.621A pdb=" N LEU O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA O 444 " --> pdb=" O TYR O 440 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG O 449 " --> pdb=" O ASN O 445 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 456 No H-bonds generated for 'chain 'O' and resid 454 through 456' Processing helix chain 'O' and resid 457 through 465 removed outlier: 3.752A pdb=" N LEU O 461 " --> pdb=" O ASN O 457 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU O 462 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS O 463 " --> pdb=" O ARG O 459 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER O 464 " --> pdb=" O LEU O 460 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN O 465 " --> pdb=" O LEU O 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 457 through 465' Processing helix chain 'O' and resid 492 through 516 removed outlier: 3.653A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL O 516 " --> pdb=" O SER O 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 516 through 530 removed outlier: 3.984A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 206 removed outlier: 3.936A pdb=" N GLN P 205 " --> pdb=" O ASN P 201 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG P 206 " --> pdb=" O PRO P 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 201 through 206' Processing helix chain 'P' and resid 219 through 228 removed outlier: 3.569A pdb=" N VAL P 228 " --> pdb=" O GLY P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 246 Processing helix chain 'P' and resid 246 through 254 removed outlier: 3.531A pdb=" N MET P 250 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA P 254 " --> pdb=" O MET P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.701A pdb=" N LEU P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS P 290 " --> pdb=" O PRO P 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 285 through 290' Processing helix chain 'P' and resid 291 through 295 Processing helix chain 'P' and resid 303 through 306 Processing helix chain 'P' and resid 307 through 314 removed outlier: 3.760A pdb=" N THR P 311 " --> pdb=" O CYS P 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 62 removed outlier: 4.101A pdb=" N THR Q 50 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 77 removed outlier: 3.865A pdb=" N PHE Q 74 " --> pdb=" O ARG Q 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.793A pdb=" N GLN A 5 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL G 8 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL D 3 " --> pdb=" O VAL G 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.793A pdb=" N GLN A 5 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AA4, first strand: chain 'A' and resid 1337 through 1339 Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 35 removed outlier: 7.508A pdb=" N TYR A 85 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN A 35 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP A 87 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.676A pdb=" N ILE A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 176 removed outlier: 4.075A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 361 Processing sheet with id=AA8, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 3.508A pdb=" N THR A 367 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 458 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 487 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 368 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER A 370 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.186A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB2, first strand: chain 'A' and resid 617 through 620 removed outlier: 5.949A pdb=" N THR A 639 " --> pdb=" O MET A 646 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1085 through 1086 Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 3.925A pdb=" N GLN A1202 " --> pdb=" O THR A1108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1116 through 1121 removed outlier: 3.672A pdb=" N VAL A1173 " --> pdb=" O HIS A1168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.624A pdb=" N ALA G 57 " --> pdb=" O HIS A1364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 82 removed outlier: 6.475A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL B 82 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE B 117 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 130 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'B' and resid 360 through 363 removed outlier: 6.522A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.181A pdb=" N VAL B 199 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 218 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 423 through 426 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 603 through 604 Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 549 removed outlier: 6.176A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 537 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.810A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.810A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 720 through 721 Processing sheet with id=AC9, first strand: chain 'B' and resid 986 through 987 removed outlier: 5.801A pdb=" N LEU B 755 " --> pdb=" O CYS B 907 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 909 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ILE B 927 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR B 740 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N MET B 929 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA B 742 " --> pdb=" O MET B 929 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'B' and resid 795 through 796 Processing sheet with id=AD3, first strand: chain 'B' and resid 826 through 828 Processing sheet with id=AD4, first strand: chain 'B' and resid 918 through 919 Processing sheet with id=AD5, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.144A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 21 through 22 removed outlier: 4.618A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 230 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 57 removed outlier: 5.943A pdb=" N VAL C 51 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL C 66 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL C 53 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP C 64 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.172A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AE1, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AE2, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE3, first strand: chain 'E' and resid 62 through 63 removed outlier: 5.713A pdb=" N ASP E 70 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.573A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.823A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 83 through 87 removed outlier: 4.796A pdb=" N GLU G 83 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE G 150 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.739A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AF2, first strand: chain 'I' and resid 77 through 82 removed outlier: 3.712A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AF4, first strand: chain 'N' and resid 370 through 387 removed outlier: 6.832A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU M 59 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU N 357 " --> pdb=" O TYR M 30 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE N 356 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LYS N 380 " --> pdb=" O PHE N 356 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU N 266 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY N 327 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.675A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 116 through 117 1564 hydrogen bonds defined for protein. 4338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.50 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 13163 1.36 - 1.56: 26613 1.56 - 1.75: 97 1.75 - 1.94: 408 1.94 - 2.14: 12 Bond restraints: 40293 Sorted by residual: bond pdb=" C GLN B1082 " pdb=" N CYS B1083 " ideal model delta sigma weight residual 1.334 1.234 0.100 1.27e-02 6.20e+03 6.21e+01 bond pdb=" C PRO A 258 " pdb=" O PRO A 258 " ideal model delta sigma weight residual 1.246 1.194 0.052 8.50e-03 1.38e+04 3.74e+01 bond pdb=" C ARG A 694 " pdb=" O ARG A 694 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.19e-02 7.06e+03 3.27e+01 bond pdb=" C PHE A 559 " pdb=" O PHE A 559 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.18e-02 7.18e+03 3.23e+01 bond pdb=" C1' DT X 35 " pdb=" N1 DT X 35 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.01e+01 ... (remaining 40288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.39: 54169 5.39 - 10.79: 394 10.79 - 16.18: 25 16.18 - 21.58: 10 21.58 - 26.97: 2 Bond angle restraints: 54600 Sorted by residual: angle pdb=" C CYS B1083 " pdb=" CA CYS B1083 " pdb=" CB CYS B1083 " ideal model delta sigma weight residual 110.95 137.92 -26.97 1.55e+00 4.16e-01 3.03e+02 angle pdb=" N CYS B1083 " pdb=" CA CYS B1083 " pdb=" CB CYS B1083 " ideal model delta sigma weight residual 109.98 93.05 16.93 1.45e+00 4.76e-01 1.36e+02 angle pdb="FE2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.56 -16.86 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.55 -16.85 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.54 -16.84 1.50e+00 4.44e-01 1.26e+02 ... (remaining 54595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 23099 28.13 - 56.27: 1409 56.27 - 84.40: 113 84.40 - 112.53: 4 112.53 - 140.67: 3 Dihedral angle restraints: 24628 sinusoidal: 10525 harmonic: 14103 Sorted by residual: dihedral pdb=" C4' G R 8 " pdb=" C3' G R 8 " pdb=" C2' G R 8 " pdb=" C1' G R 8 " ideal model delta sinusoidal sigma weight residual 36.34 0.98 35.36 1 3.10e+00 1.04e-01 1.84e+02 dihedral pdb=" N CYS B1095 " pdb=" C CYS B1095 " pdb=" CA CYS B1095 " pdb=" CB CYS B1095 " ideal model delta harmonic sigma weight residual 122.80 92.21 30.59 0 2.50e+00 1.60e-01 1.50e+02 dihedral pdb=" O4' G R 8 " pdb=" C2' G R 8 " pdb=" C1' G R 8 " pdb=" C3' G R 8 " ideal model delta sinusoidal sigma weight residual 25.59 -9.56 35.15 3 3.80e+00 6.93e-02 9.35e+01 ... (remaining 24625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 5086 0.164 - 0.328: 975 0.328 - 0.493: 73 0.493 - 0.657: 11 0.657 - 0.821: 5 Chirality restraints: 6150 Sorted by residual: chirality pdb="FE4 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.73 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb="FE1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False -10.55 -9.74 -0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.75 0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 6147 not shown) Planarity restraints: 6872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1072 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C SER B1072 " 0.079 2.00e-02 2.50e+03 pdb=" O SER B1072 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP B1073 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 693 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ASN A 693 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN A 693 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG A 694 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 39 " -0.020 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C GLN D 39 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN D 39 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN D 40 " -0.022 2.00e-02 2.50e+03 ... (remaining 6869 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 117 2.41 - 3.03: 23595 3.03 - 3.66: 58365 3.66 - 4.28: 90390 4.28 - 4.90: 149223 Nonbonded interactions: 321690 Sorted by model distance: nonbonded pdb=" OG1 THR H 78 " pdb=" NH2 ARG K 87 " model vdw 1.789 3.120 nonbonded pdb=" OE1 GLU A1112 " pdb=" CD LYS I 47 " model vdw 1.835 3.440 nonbonded pdb=" CE LYS B 721 " pdb=" OE2 GLU B 731 " model vdw 1.837 3.440 nonbonded pdb=" OE1 GLU A1143 " pdb=" OD1 ASP E 2 " model vdw 1.911 3.040 nonbonded pdb=" NZ LYS A 180 " pdb=" OD1 ASN A 182 " model vdw 1.964 3.120 ... (remaining 321685 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 48.710 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 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 : 0.014 0.935 40315 Z= 0.868 Angle : 1.726 56.156 54627 Z= 1.186 Chirality : 0.126 0.821 6150 Planarity : 0.007 0.073 6872 Dihedral : 16.446 140.668 15512 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.13 % Favored : 94.32 % Rotamer: Outliers : 9.73 % Allowed : 12.28 % Favored : 77.99 % Cbeta Deviations : 1.76 % 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: -0.42 (0.12), residues: 4791 helix: 0.48 (0.13), residues: 1674 sheet: 0.52 (0.21), residues: 619 loop : -1.01 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG B 222 TYR 0.034 0.003 TYR A 320 PHE 0.035 0.003 PHE B 380 TRP 0.030 0.003 TRP I 59 HIS 0.010 0.002 HIS B 552 Details of bonding type rmsd/Z covalent geometry : bond 0.01168 / 0.82 (40293) covalent geometry : angle 1.64723 / 1.18 (54600) hydrogen bonds : bond 0.24020 / 15.80 ( 1542) hydrogen bonds : angle 8.18314 / 5.90 ( 4338) metal coordination : bond 0.35762 / 19.49 ( 22) metal coordination : angle 23.17103 / 14.15 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 415 poor density : 1331 time to evaluate : 1.774 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: 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: 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 10 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6913 (p0) REVERT: A 55 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7399 (t) REVERT: A 167 LYS cc_start: 0.7131 (pttm) cc_final: 0.6556 (tttt) REVERT: A 226 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 262 ILE cc_start: 0.9039 (pt) cc_final: 0.8719 (mp) REVERT: A 281 MET cc_start: 0.7826 (mmm) cc_final: 0.7590 (mmt) REVERT: A 351 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8144 (tpp80) REVERT: A 514 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6779 (mt-10) REVERT: A 520 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8840 (tt) REVERT: A 751 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8477 (pp) REVERT: A 966 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8871 (mt) REVERT: A 1048 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5170 (mtt) REVERT: A 1080 ILE cc_start: 0.7978 (pt) cc_final: 0.7431 (pt) REVERT: A 1093 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8492 (p0) REVERT: A 1157 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8335 (tptp) REVERT: A 1191 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7502 (t80) REVERT: A 1278 HIS cc_start: 0.5559 (m90) cc_final: 0.4908 (m90) REVERT: B 552 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7222 (p-80) REVERT: B 697 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 708 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 750 ASP cc_start: 0.7070 (p0) cc_final: 0.6828 (p0) REVERT: C 100 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (mm) REVERT: C 151 HIS cc_start: 0.7087 (p90) cc_final: 0.6839 (p90) REVERT: C 169 TYR cc_start: 0.7297 (m-80) cc_final: 0.7011 (m-80) REVERT: D 3 VAL cc_start: 0.7327 (OUTLIER) cc_final: 0.6509 (p) REVERT: D 14 TYR cc_start: 0.2705 (OUTLIER) cc_final: 0.2389 (p90) REVERT: E 76 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: E 160 LEU cc_start: 0.8063 (mt) cc_final: 0.7148 (mm) REVERT: E 177 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6433 (t0) REVERT: F 125 ILE cc_start: 0.8347 (pt) cc_final: 0.8019 (pt) REVERT: I 20 CYS cc_start: 0.4729 (m) cc_final: 0.2172 (m) REVERT: J 54 ASP cc_start: 0.7547 (t0) cc_final: 0.7124 (p0) REVERT: J 59 LEU cc_start: 0.9063 (mt) cc_final: 0.8834 (mt) REVERT: L 17 TYR cc_start: 0.8004 (m-80) cc_final: 0.7672 (m-80) REVERT: M 30 TYR cc_start: 0.8143 (m-80) cc_final: 0.7532 (m-80) REVERT: M 107 THR cc_start: 0.8186 (p) cc_final: 0.7832 (p) REVERT: O 9 CYS cc_start: 0.8131 (m) cc_final: 0.7757 (m) REVERT: O 83 LEU cc_start: 0.8190 (mt) cc_final: 0.7987 (mp) REVERT: O 121 VAL cc_start: 0.8320 (p) cc_final: 0.6671 (p) REVERT: O 293 ILE cc_start: 0.8110 (mt) cc_final: 0.7866 (mt) REVERT: P 205 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.4164 (pp30) REVERT: Q 80 GLU cc_start: 0.3300 (OUTLIER) cc_final: 0.2691 (mm-30) outliers start: 415 outliers final: 87 residues processed: 1592 average time/residue: 0.2778 time to fit residues: 701.3588 Evaluate side-chains 807 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 699 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 616 GLN Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 76 PHE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 284 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS A 163 ASN A 203 HIS A 296 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 385 HIS A 422 GLN A 453 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 543 GLN A 611 ASN A 673 GLN A 791 ASN A 836 ASN A 885 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS A1371 ASN B 92 ASN B 187 ASN B 215 ASN B 228 ASN B 249 GLN B 260 HIS B 276 GLN B 294 GLN B 320 HIS B 395 GLN B 517 ASN B 577 ASN B 602 GLN B 610 HIS B 620 ASN B 648 HIS B 677 HIS B 686 GLN B 692 GLN B 738 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN C 48 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 13 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 98 GLN D 112 GLN E 98 ASN E 133 GLN H 76 ASN I 21 HIS J 52 HIS K 85 GLN M 106 GLN M 125 HIS M 149 HIS M 220 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN O 337 ASN O 379 GLN O 402 ASN O 415 HIS O 445 ASN O 457 ASN O 507 ASN P 200 GLN P 274 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.099627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.076443 restraints weight = 125410.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.078923 restraints weight = 64371.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.080544 restraints weight = 41208.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.081594 restraints weight = 30607.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.082173 restraints weight = 25150.299| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 40315 Z= 0.228 Angle : 0.928 57.093 54627 Z= 0.459 Chirality : 0.051 0.384 6150 Planarity : 0.006 0.071 6872 Dihedral : 12.250 146.963 5992 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.62 % Rotamer: Outliers : 6.09 % Allowed : 19.64 % Favored : 74.26 % 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: -0.67 (0.12), residues: 4791 helix: 0.20 (0.12), residues: 1733 sheet: 0.40 (0.21), residues: 624 loop : -1.13 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 433 TYR 0.029 0.002 TYR G 131 PHE 0.034 0.002 PHE G 18 TRP 0.035 0.002 TRP G 201 HIS 0.020 0.002 HIS M 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (40293) covalent geometry : angle 0.86429 / 0.46 (54600) hydrogen bonds : bond 0.06553 / 4.42 ( 1542) hydrogen bonds : angle 5.84000 / 4.19 ( 4338) metal coordination : bond 0.01810 / 1.07 ( 22) metal coordination : angle 15.26885 / 8.51 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 694 time to evaluate : 1.669 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: 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 66 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6988 (p0) REVERT: A 107 MET cc_start: 0.8873 (tpp) cc_final: 0.8647 (tpp) REVERT: A 513 GLU cc_start: 0.8139 (mp0) cc_final: 0.7922 (mm-30) REVERT: A 896 ASP cc_start: 0.7277 (t0) cc_final: 0.6793 (p0) REVERT: A 1051 LYS cc_start: 0.5828 (OUTLIER) cc_final: 0.5014 (tptm) REVERT: A 1236 MET cc_start: 0.8523 (ptm) cc_final: 0.8046 (mtm) REVERT: A 1294 MET cc_start: 0.8060 (tpp) cc_final: 0.7854 (tpp) REVERT: B 194 ASP cc_start: 0.8474 (t0) cc_final: 0.8194 (p0) REVERT: B 329 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8473 (mmm160) REVERT: B 697 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8982 (mp) REVERT: B 750 ASP cc_start: 0.7678 (p0) cc_final: 0.7466 (p0) REVERT: B 863 ASP cc_start: 0.7472 (m-30) cc_final: 0.7016 (m-30) REVERT: B 1042 ASP cc_start: 0.8282 (t0) cc_final: 0.7784 (t0) REVERT: B 1062 MET cc_start: 0.8023 (mmp) cc_final: 0.7784 (mmm) REVERT: C 212 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8293 (mtm) REVERT: D 70 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8423 (tt) REVERT: D 100 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6137 (mpp) REVERT: F 58 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8023 (p) REVERT: F 60 TYR cc_start: 0.8447 (m-80) cc_final: 0.8153 (m-80) REVERT: G 24 ASP cc_start: 0.8830 (t0) cc_final: 0.8551 (p0) REVERT: G 32 LYS cc_start: 0.6555 (mmtt) cc_final: 0.6042 (mmtt) REVERT: G 37 LYS cc_start: 0.7018 (mmtp) cc_final: 0.6795 (mmmm) REVERT: G 41 ASN cc_start: 0.9209 (t0) cc_final: 0.8991 (m110) REVERT: G 51 ILE cc_start: 0.8750 (mm) cc_final: 0.8516 (mm) REVERT: G 190 ILE cc_start: 0.3838 (mp) cc_final: 0.3155 (mp) REVERT: I 36 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.6645 (tmm-80) REVERT: I 91 MET cc_start: 0.7411 (mtp) cc_final: 0.6812 (ttt) REVERT: J 25 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8808 (mm) REVERT: K 46 GLU cc_start: 0.7871 (tp30) cc_final: 0.7405 (tp30) REVERT: K 74 HIS cc_start: 0.7525 (t-90) cc_final: 0.7296 (t-90) REVERT: K 77 GLU cc_start: 0.8204 (mp0) cc_final: 0.7944 (mp0) REVERT: L 45 TYR cc_start: 0.8274 (m-80) cc_final: 0.8044 (m-80) REVERT: M 222 ARG cc_start: 0.8666 (mtp-110) cc_final: 0.8441 (ttm170) REVERT: N 278 GLN cc_start: 0.4703 (tm-30) cc_final: 0.4485 (tm-30) REVERT: O 63 VAL cc_start: 0.7487 (m) cc_final: 0.7229 (m) REVERT: O 139 MET cc_start: 0.2079 (ttp) cc_final: 0.1819 (ttp) REVERT: O 281 SER cc_start: 0.7915 (p) cc_final: 0.7603 (m) REVERT: O 394 MET cc_start: 0.8261 (mmm) cc_final: 0.7519 (mmm) REVERT: O 421 PHE cc_start: 0.7456 (t80) cc_final: 0.6953 (t80) REVERT: O 513 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7097 (pt0) REVERT: P 196 ARG cc_start: 0.8969 (ptm-80) cc_final: 0.8614 (ptm-80) REVERT: P 205 GLN cc_start: 0.4609 (OUTLIER) cc_final: 0.3724 (pp30) REVERT: P 214 HIS cc_start: 0.8328 (p90) cc_final: 0.8115 (p90) REVERT: P 232 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.5414 (mmp) outliers start: 260 outliers final: 125 residues processed: 877 average time/residue: 0.2545 time to fit residues: 363.3504 Evaluate side-chains 692 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 557 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1321 PHE Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1127 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 232 MET Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 343 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 508 HIS A 511 GLN A1039 GLN B 381 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS E 189 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS H 130 ASN M 149 HIS M 220 HIS O 310 GLN O 377 GLN O 407 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.092126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.069372 restraints weight = 126526.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.071780 restraints weight = 63589.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.073351 restraints weight = 40692.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.074361 restraints weight = 30338.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.075064 restraints weight = 25013.937| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 40315 Z= 0.346 Angle : 0.944 72.773 54627 Z= 0.460 Chirality : 0.050 0.306 6150 Planarity : 0.006 0.083 6872 Dihedral : 11.584 151.799 5871 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 6.19 % Allowed : 20.23 % Favored : 73.58 % 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: -0.91 (0.12), residues: 4791 helix: 0.11 (0.12), residues: 1734 sheet: -0.04 (0.19), residues: 649 loop : -1.28 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG F 69 TYR 0.027 0.003 TYR I 43 PHE 0.023 0.003 PHE A 403 TRP 0.047 0.003 TRP G 201 HIS 0.013 0.002 HIS A1364 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.35 (40293) covalent geometry : angle 0.86923 / 0.46 (54600) hydrogen bonds : bond 0.05654 / 3.83 ( 1542) hydrogen bonds : angle 5.63974 / 4.06 ( 4338) metal coordination : bond 0.01589 / 0.87 ( 22) metal coordination : angle 16.63770 / 9.04 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 547 time to evaluate : 1.658 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: symmetry clash REVERT: A 66 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7183 (p0) REVERT: A 99 ARG cc_start: 0.7721 (mmm160) cc_final: 0.7472 (mmm160) REVERT: A 107 MET cc_start: 0.8915 (tpp) cc_final: 0.8463 (tpp) REVERT: A 896 ASP cc_start: 0.7446 (t0) cc_final: 0.7123 (p0) REVERT: A 1051 LYS cc_start: 0.5610 (OUTLIER) cc_final: 0.4989 (tptm) REVERT: A 1128 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8930 (tp) REVERT: A 1157 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7807 (tptp) REVERT: A 1280 MET cc_start: 0.6926 (mtt) cc_final: 0.6646 (mtt) REVERT: B 59 MET cc_start: 0.7932 (ttp) cc_final: 0.7717 (tmm) REVERT: B 94 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7879 (p) REVERT: B 384 MET cc_start: 0.8196 (mmp) cc_final: 0.7814 (mmp) REVERT: B 460 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: B 529 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: B 530 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: B 747 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8948 (p) REVERT: B 750 ASP cc_start: 0.8055 (p0) cc_final: 0.7788 (p0) REVERT: B 900 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8475 (ttp-110) REVERT: C 98 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9102 (p) REVERT: C 212 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8422 (mtm) REVERT: D 70 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8501 (tt) REVERT: D 100 MET cc_start: 0.7176 (mmt) cc_final: 0.6541 (mpp) REVERT: E 2 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7552 (p0) REVERT: F 58 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8353 (p) REVERT: F 64 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8381 (tpp80) REVERT: G 37 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7636 (mmmm) REVERT: G 82 ASP cc_start: 0.4855 (t0) cc_final: 0.4255 (t0) REVERT: H 123 MET cc_start: 0.8410 (tmm) cc_final: 0.8180 (tmm) REVERT: I 36 ARG cc_start: 0.7347 (ttp-110) cc_final: 0.6763 (tmm-80) REVERT: I 91 MET cc_start: 0.7911 (mtp) cc_final: 0.7124 (ttt) REVERT: J 9 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9107 (t) REVERT: J 25 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8842 (mm) REVERT: K 47 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6509 (mm-30) REVERT: K 77 GLU cc_start: 0.8281 (mp0) cc_final: 0.8017 (pm20) REVERT: L 21 GLU cc_start: 0.8709 (pt0) cc_final: 0.8328 (pp20) REVERT: M 11 GLN cc_start: 0.8308 (mp10) cc_final: 0.8062 (mp10) REVERT: M 37 MET cc_start: 0.8457 (mpp) cc_final: 0.8208 (pmm) REVERT: M 220 HIS cc_start: 0.8765 (OUTLIER) cc_final: 0.8344 (p-80) REVERT: M 222 ARG cc_start: 0.8673 (mtp-110) cc_final: 0.8232 (ttt180) REVERT: N 278 GLN cc_start: 0.5017 (tm-30) cc_final: 0.4667 (tm-30) REVERT: N 350 MET cc_start: 0.8492 (tpp) cc_final: 0.8167 (mmm) REVERT: O 52 LYS cc_start: 0.9318 (tppt) cc_final: 0.9064 (tptt) REVERT: O 85 MET cc_start: 0.9124 (mmm) cc_final: 0.8891 (mmm) REVERT: O 133 MET cc_start: 0.5089 (ptp) cc_final: 0.4068 (ptm) REVERT: O 281 SER cc_start: 0.8032 (p) cc_final: 0.7727 (m) REVERT: O 394 MET cc_start: 0.7953 (mmm) cc_final: 0.7541 (mmm) REVERT: O 421 PHE cc_start: 0.7479 (t80) cc_final: 0.7114 (t80) REVERT: O 427 ASN cc_start: 0.8239 (t0) cc_final: 0.7967 (t0) REVERT: P 196 ARG cc_start: 0.9029 (ptm-80) cc_final: 0.8706 (ptm-80) REVERT: P 199 LYS cc_start: 0.7525 (mttt) cc_final: 0.6027 (ttpt) REVERT: P 205 GLN cc_start: 0.5123 (OUTLIER) cc_final: 0.4704 (pp30) REVERT: P 293 PHE cc_start: 0.4878 (m-80) cc_final: 0.4602 (m-80) outliers start: 264 outliers final: 157 residues processed: 747 average time/residue: 0.2537 time to fit residues: 312.8422 Evaluate side-chains 652 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 476 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 527 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 337 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 292 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 294 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 372 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 872 GLN A1039 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 85 GLN D 98 GLN E 148 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 146 ASN ** O 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.093740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.071000 restraints weight = 125413.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.073506 restraints weight = 61959.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.075148 restraints weight = 39310.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.076193 restraints weight = 29045.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.076844 restraints weight = 23911.887| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 40315 Z= 0.169 Angle : 0.800 66.886 54627 Z= 0.377 Chirality : 0.045 0.266 6150 Planarity : 0.005 0.062 6872 Dihedral : 11.297 151.628 5855 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.09 % Rotamer: Outliers : 4.81 % Allowed : 21.85 % Favored : 73.35 % 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: -0.59 (0.12), residues: 4791 helix: 0.53 (0.12), residues: 1724 sheet: -0.02 (0.19), residues: 651 loop : -1.17 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG M 214 TYR 0.020 0.002 TYR H 75 PHE 0.021 0.002 PHE P 210 TRP 0.033 0.002 TRP G 201 HIS 0.021 0.001 HIS M 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (40293) covalent geometry : angle 0.72525 / 0.38 (54600) hydrogen bonds : bond 0.04730 / 3.17 ( 1542) hydrogen bonds : angle 5.22085 / 3.77 ( 4338) metal coordination : bond 0.00840 / 0.46 ( 22) metal coordination : angle 15.21629 / 8.20 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 550 time to evaluate : 1.683 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7464 (p0) REVERT: A 99 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7305 (mmm160) REVERT: A 107 MET cc_start: 0.8845 (tpp) cc_final: 0.8440 (tpp) REVERT: A 307 MET cc_start: 0.8460 (mmm) cc_final: 0.8135 (mmm) REVERT: A 370 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9051 (m) REVERT: A 513 GLU cc_start: 0.7964 (mp0) cc_final: 0.7706 (mm-30) REVERT: A 578 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8740 (mmmt) REVERT: A 896 ASP cc_start: 0.7439 (t0) cc_final: 0.7139 (p0) REVERT: A 1051 LYS cc_start: 0.5653 (OUTLIER) cc_final: 0.5099 (tptm) REVERT: A 1236 MET cc_start: 0.8721 (ptm) cc_final: 0.8404 (ptp) REVERT: B 94 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7877 (p) REVERT: B 384 MET cc_start: 0.8236 (mmp) cc_final: 0.7950 (mmp) REVERT: B 460 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: B 689 MET cc_start: 0.7334 (mtt) cc_final: 0.6925 (mtt) REVERT: B 750 ASP cc_start: 0.7853 (p0) cc_final: 0.7573 (p0) REVERT: B 800 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7880 (tpp-160) REVERT: C 98 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9094 (p) REVERT: C 330 MET cc_start: 0.8155 (mmt) cc_final: 0.7874 (mmt) REVERT: E 159 LEU cc_start: 0.9580 (tp) cc_final: 0.9319 (tt) REVERT: F 59 LYS cc_start: 0.8808 (ptpt) cc_final: 0.8442 (ptpp) REVERT: F 64 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8227 (tpp80) REVERT: F 82 GLU cc_start: 0.8890 (pp20) cc_final: 0.8648 (pp20) REVERT: F 84 GLU cc_start: 0.8385 (pm20) cc_final: 0.8038 (pm20) REVERT: G 37 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7663 (mmmm) REVERT: G 82 ASP cc_start: 0.5148 (t0) cc_final: 0.4789 (t0) REVERT: G 199 SER cc_start: 0.7725 (OUTLIER) cc_final: 0.7496 (p) REVERT: H 123 MET cc_start: 0.8499 (tmm) cc_final: 0.8275 (tmm) REVERT: I 36 ARG cc_start: 0.7295 (ttp-110) cc_final: 0.7075 (tmm-80) REVERT: I 42 LYS cc_start: 0.8764 (tppt) cc_final: 0.8505 (tppt) REVERT: I 91 MET cc_start: 0.7889 (mtp) cc_final: 0.7224 (mmm) REVERT: J 25 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9026 (mm) REVERT: J 54 ASP cc_start: 0.8089 (p0) cc_final: 0.7613 (p0) REVERT: J 57 GLU cc_start: 0.7388 (pm20) cc_final: 0.6754 (pm20) REVERT: K 74 HIS cc_start: 0.7765 (t-90) cc_final: 0.7416 (t-90) REVERT: M 11 GLN cc_start: 0.7937 (mp10) cc_final: 0.7699 (mp10) REVERT: M 62 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7970 (tp) REVERT: M 133 LEU cc_start: 0.8790 (mp) cc_final: 0.8540 (mt) REVERT: M 220 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.7929 (p90) REVERT: M 222 ARG cc_start: 0.8642 (mtp-110) cc_final: 0.8182 (ttt180) REVERT: O 108 GLU cc_start: 0.8286 (tt0) cc_final: 0.8068 (tt0) REVERT: O 133 MET cc_start: 0.4953 (ptp) cc_final: 0.4691 (ptp) REVERT: O 281 SER cc_start: 0.7934 (p) cc_final: 0.7672 (m) REVERT: O 394 MET cc_start: 0.7908 (mmm) cc_final: 0.7598 (mmm) REVERT: O 427 ASN cc_start: 0.8223 (t0) cc_final: 0.7972 (t0) REVERT: P 196 ARG cc_start: 0.8992 (ptm-80) cc_final: 0.8622 (ptm-80) REVERT: P 199 LYS cc_start: 0.7603 (mttt) cc_final: 0.6939 (ttmt) REVERT: P 205 GLN cc_start: 0.4700 (OUTLIER) cc_final: 0.4468 (pp30) REVERT: P 232 MET cc_start: 0.5973 (mmp) cc_final: 0.5329 (mmp) outliers start: 205 outliers final: 129 residues processed: 706 average time/residue: 0.2532 time to fit residues: 295.1816 Evaluate side-chains 636 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 495 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 46 optimal weight: 6.9990 chunk 340 optimal weight: 0.2980 chunk 389 optimal weight: 9.9990 chunk 287 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 623 GLN A 962 GLN A1190 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN M 149 HIS M 220 HIS N 278 GLN O 457 ASN Q 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.089090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066233 restraints weight = 129996.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.068691 restraints weight = 64346.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.070288 restraints weight = 41013.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.071325 restraints weight = 30544.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.072014 restraints weight = 25215.798| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 40315 Z= 0.307 Angle : 0.862 67.277 54627 Z= 0.410 Chirality : 0.048 0.400 6150 Planarity : 0.006 0.086 6872 Dihedral : 11.171 150.699 5845 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.74 % Favored : 94.18 % Rotamer: Outliers : 5.81 % Allowed : 21.87 % Favored : 72.32 % 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: -0.72 (0.12), residues: 4791 helix: 0.47 (0.12), residues: 1707 sheet: -0.37 (0.19), residues: 650 loop : -1.19 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 85 TYR 0.033 0.002 TYR D 14 PHE 0.024 0.002 PHE B 91 TRP 0.021 0.002 TRP G 200 HIS 0.019 0.002 HIS M 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.31 (40293) covalent geometry : angle 0.78715 / 0.41 (54600) hydrogen bonds : bond 0.04914 / 3.30 ( 1542) hydrogen bonds : angle 5.32358 / 3.82 ( 4338) metal coordination : bond 0.01423 / 0.79 ( 22) metal coordination : angle 15.86081 / 8.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 506 time to evaluate : 1.632 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: A 66 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7487 (p0) REVERT: A 99 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7596 (mmm160) REVERT: A 107 MET cc_start: 0.8862 (tpp) cc_final: 0.8548 (tpp) REVERT: A 128 TYR cc_start: 0.8558 (t80) cc_final: 0.8314 (t80) REVERT: A 307 MET cc_start: 0.8700 (mmm) cc_final: 0.8328 (mmm) REVERT: A 339 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8326 (ptm-80) REVERT: A 370 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.9043 (m) REVERT: A 513 GLU cc_start: 0.8045 (mp0) cc_final: 0.7766 (mm-30) REVERT: A 896 ASP cc_start: 0.7743 (t0) cc_final: 0.7335 (p0) REVERT: A 1051 LYS cc_start: 0.5763 (OUTLIER) cc_final: 0.5240 (tptm) REVERT: A 1189 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 1236 MET cc_start: 0.8790 (ptm) cc_final: 0.8444 (ptp) REVERT: A 1322 GLU cc_start: 0.8185 (mp0) cc_final: 0.7846 (mt-10) REVERT: B 94 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8041 (p) REVERT: B 432 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7134 (t70) REVERT: B 460 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 750 ASP cc_start: 0.8050 (p0) cc_final: 0.7771 (p0) REVERT: C 98 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9150 (p) REVERT: E 2 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7242 (p0) REVERT: E 130 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.6838 (m-80) REVERT: F 64 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8378 (tpp80) REVERT: F 82 GLU cc_start: 0.8956 (pp20) cc_final: 0.8744 (pp20) REVERT: F 84 GLU cc_start: 0.8479 (pm20) cc_final: 0.8135 (pm20) REVERT: G 24 ASP cc_start: 0.8875 (t0) cc_final: 0.8646 (t0) REVERT: G 32 LYS cc_start: 0.7055 (mmtt) cc_final: 0.6611 (mmtt) REVERT: G 82 ASP cc_start: 0.5131 (t0) cc_final: 0.4637 (t0) REVERT: G 86 ILE cc_start: 0.6956 (mp) cc_final: 0.6679 (pt) REVERT: H 123 MET cc_start: 0.8584 (tmm) cc_final: 0.8318 (tmm) REVERT: H 145 MET cc_start: 0.8430 (tpp) cc_final: 0.7256 (tpp) REVERT: I 36 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.6751 (tmm-80) REVERT: I 91 MET cc_start: 0.7993 (mtp) cc_final: 0.7108 (ttt) REVERT: J 25 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8934 (mm) REVERT: J 48 MET cc_start: 0.8705 (mmm) cc_final: 0.8483 (mmt) REVERT: J 54 ASP cc_start: 0.8224 (p0) cc_final: 0.7995 (p0) REVERT: K 74 HIS cc_start: 0.7946 (t-90) cc_final: 0.7716 (t-90) REVERT: L 56 ASP cc_start: 0.7779 (t0) cc_final: 0.7575 (t0) REVERT: M 11 GLN cc_start: 0.7665 (mp10) cc_final: 0.7423 (mp10) REVERT: M 37 MET cc_start: 0.8642 (pmm) cc_final: 0.8417 (pmm) REVERT: M 87 ASP cc_start: 0.7506 (m-30) cc_final: 0.7043 (t70) REVERT: M 150 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8432 (mmm160) REVERT: M 222 ARG cc_start: 0.8671 (mtp-110) cc_final: 0.8447 (ttp-170) REVERT: N 248 ASP cc_start: 0.8145 (t0) cc_final: 0.7587 (t0) REVERT: O 9 CYS cc_start: 0.8862 (m) cc_final: 0.8508 (m) REVERT: O 133 MET cc_start: 0.4997 (ptp) cc_final: 0.4745 (ptp) REVERT: O 281 SER cc_start: 0.8066 (p) cc_final: 0.7764 (m) REVERT: O 394 MET cc_start: 0.7862 (mmm) cc_final: 0.7627 (mmm) REVERT: O 415 HIS cc_start: 0.8354 (m90) cc_final: 0.7940 (m90) REVERT: O 427 ASN cc_start: 0.8444 (t0) cc_final: 0.8167 (t0) REVERT: P 196 ARG cc_start: 0.8982 (ptm-80) cc_final: 0.8622 (ptm-80) REVERT: P 199 LYS cc_start: 0.7785 (mttt) cc_final: 0.7291 (ttmt) REVERT: P 205 GLN cc_start: 0.5129 (OUTLIER) cc_final: 0.4759 (pp30) REVERT: P 232 MET cc_start: 0.6267 (mmp) cc_final: 0.5639 (mmp) outliers start: 248 outliers final: 176 residues processed: 693 average time/residue: 0.2502 time to fit residues: 286.5790 Evaluate side-chains 649 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 460 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 904 LYS Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 527 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 402 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 317 optimal weight: 7.9990 chunk 412 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 528 ASN A1039 GLN B 692 GLN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS O 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.089753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.067024 restraints weight = 128342.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.069493 restraints weight = 63715.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071102 restraints weight = 40551.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.072140 restraints weight = 30157.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.072719 restraints weight = 24846.641| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 40315 Z= 0.208 Angle : 0.802 65.905 54627 Z= 0.375 Chirality : 0.046 0.312 6150 Planarity : 0.005 0.075 6872 Dihedral : 11.015 150.688 5838 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 4.85 % Allowed : 23.14 % Favored : 72.01 % 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: -0.61 (0.12), residues: 4791 helix: 0.62 (0.12), residues: 1715 sheet: -0.44 (0.19), residues: 661 loop : -1.13 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 113 TYR 0.027 0.002 TYR L 41 PHE 0.025 0.002 PHE P 210 TRP 0.058 0.002 TRP G 127 HIS 0.009 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (40293) covalent geometry : angle 0.72487 / 0.37 (54600) hydrogen bonds : bond 0.04405 / 2.96 ( 1542) hydrogen bonds : angle 5.11067 / 3.68 ( 4338) metal coordination : bond 0.01070 / 0.60 ( 22) metal coordination : angle 15.41325 / 8.26 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 500 time to evaluate : 1.653 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: symmetry clash REVERT: A 6 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.5624 (m-80) REVERT: A 66 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7479 (p0) REVERT: A 99 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7494 (mmm160) REVERT: A 107 MET cc_start: 0.8869 (tpp) cc_final: 0.8346 (tpp) REVERT: A 116 MET cc_start: 0.8551 (mpp) cc_final: 0.8212 (mpp) REVERT: A 513 GLU cc_start: 0.7981 (mp0) cc_final: 0.7705 (mm-30) REVERT: A 572 LEU cc_start: 0.9162 (mt) cc_final: 0.8941 (mp) REVERT: A 896 ASP cc_start: 0.7727 (t0) cc_final: 0.7236 (p0) REVERT: A 920 GLU cc_start: 0.7645 (tp30) cc_final: 0.6805 (tm-30) REVERT: A 1051 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5547 (tptm) REVERT: A 1196 LEU cc_start: 0.9467 (tp) cc_final: 0.9044 (mt) REVERT: A 1236 MET cc_start: 0.8772 (ptm) cc_final: 0.8439 (ptp) REVERT: A 1322 GLU cc_start: 0.8037 (mp0) cc_final: 0.7774 (mp0) REVERT: B 369 LEU cc_start: 0.9067 (mm) cc_final: 0.8819 (mm) REVERT: B 384 MET cc_start: 0.8216 (mmp) cc_final: 0.7892 (mmt) REVERT: B 460 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: B 750 ASP cc_start: 0.7912 (p0) cc_final: 0.7647 (p0) REVERT: C 98 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9127 (p) REVERT: C 311 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6876 (tm-30) REVERT: D 5 ASP cc_start: 0.7625 (t0) cc_final: 0.7419 (t0) REVERT: E 2 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7074 (p0) REVERT: E 130 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: G 24 ASP cc_start: 0.8799 (t0) cc_final: 0.8519 (t0) REVERT: G 32 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6755 (mmtt) REVERT: G 82 ASP cc_start: 0.5300 (t0) cc_final: 0.5069 (t0) REVERT: G 159 ASP cc_start: 0.7950 (t0) cc_final: 0.7723 (t0) REVERT: H 123 MET cc_start: 0.8646 (tmm) cc_final: 0.8388 (tmm) REVERT: H 145 MET cc_start: 0.8387 (tpp) cc_final: 0.7191 (tpp) REVERT: I 36 ARG cc_start: 0.7454 (ttp-110) cc_final: 0.6785 (tmm-80) REVERT: I 91 MET cc_start: 0.7978 (mtp) cc_final: 0.7059 (ttt) REVERT: J 54 ASP cc_start: 0.8190 (p0) cc_final: 0.7963 (p0) REVERT: M 11 GLN cc_start: 0.7747 (mp10) cc_final: 0.7239 (mp10) REVERT: M 37 MET cc_start: 0.8651 (pmm) cc_final: 0.8321 (pmm) REVERT: M 87 ASP cc_start: 0.7620 (m-30) cc_final: 0.7279 (t0) REVERT: M 150 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8485 (mmm160) REVERT: M 220 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8273 (p90) REVERT: O 9 CYS cc_start: 0.8430 (m) cc_final: 0.8062 (m) REVERT: O 281 SER cc_start: 0.8028 (p) cc_final: 0.7772 (m) REVERT: O 394 MET cc_start: 0.8030 (mmm) cc_final: 0.7785 (mmm) REVERT: O 415 HIS cc_start: 0.8280 (m90) cc_final: 0.7843 (m90) REVERT: O 427 ASN cc_start: 0.8512 (t0) cc_final: 0.8224 (t0) REVERT: P 196 ARG cc_start: 0.8978 (ptm-80) cc_final: 0.8634 (ptm-80) REVERT: P 199 LYS cc_start: 0.7779 (mttt) cc_final: 0.7380 (ttmt) REVERT: P 205 GLN cc_start: 0.5155 (OUTLIER) cc_final: 0.4774 (pp30) REVERT: P 232 MET cc_start: 0.6185 (mmp) cc_final: 0.5585 (mmp) outliers start: 207 outliers final: 153 residues processed: 661 average time/residue: 0.2467 time to fit residues: 272.2210 Evaluate side-chains 623 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 461 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 527 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 310 MET Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 324 optimal weight: 0.1980 chunk 82 optimal weight: 0.0670 chunk 419 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 37 optimal weight: 0.0470 chunk 357 optimal weight: 0.7980 chunk 371 optimal weight: 3.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 HIS M 220 HIS N 139 ASN O 60 HIS ** P 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.095764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073914 restraints weight = 130878.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076404 restraints weight = 63361.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.077990 restraints weight = 39497.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079021 restraints weight = 29038.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079643 restraints weight = 23737.193| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40315 Z= 0.132 Angle : 0.769 61.303 54627 Z= 0.358 Chirality : 0.045 0.512 6150 Planarity : 0.005 0.088 6872 Dihedral : 10.759 150.644 5834 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 3.82 % Allowed : 24.00 % Favored : 72.18 % 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: -0.41 (0.12), residues: 4791 helix: 0.80 (0.12), residues: 1724 sheet: -0.25 (0.19), residues: 659 loop : -1.05 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 222 TYR 0.023 0.001 TYR D 52 PHE 0.044 0.001 PHE D 17 TRP 0.038 0.002 TRP G 127 HIS 0.010 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (40293) covalent geometry : angle 0.70346 / 0.36 (54600) hydrogen bonds : bond 0.03911 / 2.62 ( 1542) hydrogen bonds : angle 4.86601 / 3.50 ( 4338) metal coordination : bond 0.00494 / 0.30 ( 22) metal coordination : angle 14.03914 / 7.44 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 523 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7461 (mmm160) REVERT: A 107 MET cc_start: 0.8820 (tpp) cc_final: 0.8468 (tpp) REVERT: A 339 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8386 (ptm-80) REVERT: A 504 GLU cc_start: 0.7662 (mp0) cc_final: 0.7290 (mp0) REVERT: A 578 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8512 (mmmt) REVERT: A 646 MET cc_start: 0.8093 (mmm) cc_final: 0.7848 (mmm) REVERT: A 896 ASP cc_start: 0.7652 (t0) cc_final: 0.7206 (p0) REVERT: A 919 LEU cc_start: 0.8205 (mm) cc_final: 0.7987 (mm) REVERT: A 920 GLU cc_start: 0.7503 (tp30) cc_final: 0.6788 (tm-30) REVERT: A 1048 MET cc_start: 0.5055 (mmt) cc_final: 0.3759 (mmm) REVERT: A 1051 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5758 (tptm) REVERT: A 1072 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8176 (mt-10) REVERT: A 1196 LEU cc_start: 0.9410 (tp) cc_final: 0.9030 (mt) REVERT: A 1236 MET cc_start: 0.8633 (ptm) cc_final: 0.8399 (ptp) REVERT: B 262 MET cc_start: 0.8330 (ppp) cc_final: 0.8082 (ppp) REVERT: B 384 MET cc_start: 0.8257 (mmp) cc_final: 0.7778 (tpp) REVERT: B 618 TYR cc_start: 0.8106 (m-10) cc_final: 0.7835 (m-10) REVERT: B 697 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8988 (mp) REVERT: B 750 ASP cc_start: 0.7699 (p0) cc_final: 0.7363 (p0) REVERT: B 800 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7828 (tpp-160) REVERT: C 98 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9089 (p) REVERT: C 311 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6944 (tm-30) REVERT: D 5 ASP cc_start: 0.7672 (t0) cc_final: 0.7356 (t0) REVERT: E 2 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6762 (p0) REVERT: E 130 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.6805 (m-80) REVERT: F 90 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8956 (tt) REVERT: G 82 ASP cc_start: 0.5358 (t0) cc_final: 0.5062 (t0) REVERT: G 115 GLN cc_start: 0.2973 (tp-100) cc_final: 0.2571 (tp40) REVERT: G 159 ASP cc_start: 0.7933 (t0) cc_final: 0.7701 (t0) REVERT: H 123 MET cc_start: 0.8638 (tmm) cc_final: 0.8394 (tmm) REVERT: I 36 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.6844 (tmm-80) REVERT: I 85 ARG cc_start: 0.7688 (mmm160) cc_final: 0.7124 (tpp-160) REVERT: I 91 MET cc_start: 0.7903 (mtp) cc_final: 0.7107 (mmm) REVERT: I 94 PHE cc_start: 0.8552 (m-10) cc_final: 0.8233 (m-80) REVERT: K 94 GLU cc_start: 0.7670 (tp30) cc_final: 0.7124 (tp30) REVERT: K 98 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8333 (ttp-170) REVERT: L 46 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7651 (mtpt) REVERT: M 11 GLN cc_start: 0.7577 (mp10) cc_final: 0.6930 (mp10) REVERT: M 87 ASP cc_start: 0.7404 (m-30) cc_final: 0.7176 (t70) REVERT: N 247 LYS cc_start: 0.8335 (pptt) cc_final: 0.8047 (pptt) REVERT: O 85 MET cc_start: 0.9284 (mmm) cc_final: 0.8475 (mmm) REVERT: O 133 MET cc_start: 0.3740 (ptp) cc_final: 0.2093 (ppp) REVERT: O 281 SER cc_start: 0.8082 (p) cc_final: 0.7843 (m) REVERT: O 394 MET cc_start: 0.7831 (mmm) cc_final: 0.7618 (mmm) REVERT: O 415 HIS cc_start: 0.8085 (m90) cc_final: 0.7635 (m-70) REVERT: O 427 ASN cc_start: 0.8416 (t0) cc_final: 0.8143 (t0) REVERT: P 199 LYS cc_start: 0.7842 (mttt) cc_final: 0.7157 (ttmt) REVERT: P 205 GLN cc_start: 0.4923 (OUTLIER) cc_final: 0.4581 (pp30) REVERT: P 232 MET cc_start: 0.5846 (mmp) cc_final: 0.5308 (mmp) outliers start: 163 outliers final: 107 residues processed: 645 average time/residue: 0.2500 time to fit residues: 268.0576 Evaluate side-chains 598 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 481 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 54 optimal weight: 6.9990 chunk 369 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 475 optimal weight: 10.0000 chunk 432 optimal weight: 0.4980 chunk 171 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 HIS ** P 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.090813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068030 restraints weight = 127790.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070578 restraints weight = 62415.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.072215 restraints weight = 39388.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.073287 restraints weight = 29112.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.073927 restraints weight = 23886.013| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40315 Z= 0.165 Angle : 0.774 59.796 54627 Z= 0.361 Chirality : 0.044 0.274 6150 Planarity : 0.005 0.075 6872 Dihedral : 10.668 150.858 5828 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 3.45 % Allowed : 24.89 % Favored : 71.66 % 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: -0.39 (0.12), residues: 4791 helix: 0.78 (0.12), residues: 1732 sheet: -0.25 (0.19), residues: 668 loop : -1.02 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 9 TYR 0.026 0.001 TYR L 41 PHE 0.023 0.001 PHE P 293 TRP 0.035 0.002 TRP G 201 HIS 0.016 0.001 HIS M 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (40293) covalent geometry : angle 0.70571 / 0.36 (54600) hydrogen bonds : bond 0.03937 / 2.65 ( 1542) hydrogen bonds : angle 4.88226 / 3.50 ( 4338) metal coordination : bond 0.00769 / 0.46 ( 22) metal coordination : angle 14.36091 / 7.59 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 498 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7495 (mmm160) REVERT: A 107 MET cc_start: 0.8896 (tpp) cc_final: 0.8538 (tpp) REVERT: A 339 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8390 (ptm-80) REVERT: A 504 GLU cc_start: 0.7735 (mp0) cc_final: 0.7336 (mp0) REVERT: A 513 GLU cc_start: 0.7864 (mp0) cc_final: 0.7501 (mm-30) REVERT: A 578 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8533 (mmmt) REVERT: A 896 ASP cc_start: 0.7792 (t0) cc_final: 0.7141 (p0) REVERT: A 919 LEU cc_start: 0.8348 (mm) cc_final: 0.8146 (mm) REVERT: A 920 GLU cc_start: 0.7607 (tp30) cc_final: 0.6839 (tm-30) REVERT: A 1048 MET cc_start: 0.5349 (mmt) cc_final: 0.4093 (mmm) REVERT: A 1051 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5765 (tptm) REVERT: A 1157 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8599 (tptp) REVERT: A 1196 LEU cc_start: 0.9432 (tp) cc_final: 0.9019 (mt) REVERT: A 1236 MET cc_start: 0.8805 (ptm) cc_final: 0.8478 (ptp) REVERT: A 1313 GLU cc_start: 0.8527 (pm20) cc_final: 0.8128 (pm20) REVERT: B 262 MET cc_start: 0.8423 (ppp) cc_final: 0.8193 (ppp) REVERT: B 384 MET cc_start: 0.8278 (mmp) cc_final: 0.7830 (tpp) REVERT: B 460 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: B 697 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9058 (mp) REVERT: B 750 ASP cc_start: 0.7857 (p0) cc_final: 0.7531 (p0) REVERT: B 800 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7797 (tpp-160) REVERT: C 98 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9104 (p) REVERT: C 311 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6895 (tm-30) REVERT: D 5 ASP cc_start: 0.7724 (t0) cc_final: 0.7399 (t0) REVERT: D 67 ARG cc_start: 0.7777 (tpm170) cc_final: 0.7551 (tpm170) REVERT: E 2 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6810 (p0) REVERT: E 130 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: F 64 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8323 (tpp80) REVERT: F 90 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9035 (tt) REVERT: G 24 ASP cc_start: 0.8754 (t0) cc_final: 0.8397 (t0) REVERT: G 32 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6835 (mmtt) REVERT: G 82 ASP cc_start: 0.5381 (t0) cc_final: 0.5135 (t0) REVERT: G 115 GLN cc_start: 0.3351 (tp-100) cc_final: 0.3005 (tp40) REVERT: G 159 ASP cc_start: 0.7962 (t0) cc_final: 0.7689 (t0) REVERT: H 7 GLU cc_start: 0.8132 (tp30) cc_final: 0.7094 (tp30) REVERT: H 89 GLU cc_start: 0.7297 (mp0) cc_final: 0.6748 (mp0) REVERT: H 123 MET cc_start: 0.8689 (tmm) cc_final: 0.8411 (tmm) REVERT: I 36 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.6838 (tmm-80) REVERT: I 85 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7301 (tpp-160) REVERT: I 91 MET cc_start: 0.7924 (mtp) cc_final: 0.7030 (ttt) REVERT: I 94 PHE cc_start: 0.8552 (m-10) cc_final: 0.8234 (m-80) REVERT: J 54 ASP cc_start: 0.8124 (p0) cc_final: 0.7859 (p0) REVERT: J 57 GLU cc_start: 0.7539 (pm20) cc_final: 0.7289 (pm20) REVERT: K 74 HIS cc_start: 0.8018 (t-90) cc_final: 0.7787 (t-90) REVERT: K 94 GLU cc_start: 0.7843 (tp30) cc_final: 0.7347 (tp30) REVERT: K 98 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8448 (ttp-170) REVERT: L 43 ILE cc_start: 0.9015 (pt) cc_final: 0.8680 (mt) REVERT: M 11 GLN cc_start: 0.7755 (mt0) cc_final: 0.7123 (mp10) REVERT: M 87 ASP cc_start: 0.7677 (m-30) cc_final: 0.7316 (t70) REVERT: M 220 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8147 (p90) REVERT: N 247 LYS cc_start: 0.8414 (pptt) cc_final: 0.8103 (pptt) REVERT: N 347 ASP cc_start: 0.7442 (t70) cc_final: 0.7127 (t0) REVERT: O 85 MET cc_start: 0.9327 (mmm) cc_final: 0.8531 (mmm) REVERT: O 139 MET cc_start: 0.1353 (ptt) cc_final: 0.0283 (mtm) REVERT: O 281 SER cc_start: 0.8116 (p) cc_final: 0.7863 (m) REVERT: O 415 HIS cc_start: 0.8189 (m90) cc_final: 0.7893 (m-70) REVERT: O 427 ASN cc_start: 0.8534 (t0) cc_final: 0.8222 (t0) REVERT: P 196 ARG cc_start: 0.8885 (mtm110) cc_final: 0.8392 (mtm110) REVERT: P 199 LYS cc_start: 0.7953 (mttt) cc_final: 0.7269 (ttmt) REVERT: P 205 GLN cc_start: 0.4917 (OUTLIER) cc_final: 0.4599 (pp30) REVERT: P 232 MET cc_start: 0.5858 (mmp) cc_final: 0.5344 (mmp) REVERT: P 293 PHE cc_start: 0.4825 (m-80) cc_final: 0.4498 (t80) outliers start: 147 outliers final: 114 residues processed: 613 average time/residue: 0.2483 time to fit residues: 253.3160 Evaluate side-chains 597 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 470 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 527 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 307 optimal weight: 0.6980 chunk 320 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 387 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 226 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 chunk 375 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS M 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.091220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068842 restraints weight = 127910.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.071298 restraints weight = 64030.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.072874 restraints weight = 40874.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.073895 restraints weight = 30495.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.074527 restraints weight = 25173.413| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.6567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40315 Z= 0.154 Angle : 0.778 58.294 54627 Z= 0.361 Chirality : 0.044 0.275 6150 Planarity : 0.005 0.077 6872 Dihedral : 10.589 150.572 5824 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 3.42 % Allowed : 25.04 % Favored : 71.54 % 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: 4791 helix: 0.80 (0.12), residues: 1736 sheet: -0.19 (0.19), residues: 658 loop : -0.99 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 256 TYR 0.034 0.001 TYR E 8 PHE 0.018 0.001 PHE P 210 TRP 0.059 0.002 TRP G 127 HIS 0.012 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (40293) covalent geometry : angle 0.71124 / 0.36 (54600) hydrogen bonds : bond 0.03847 / 2.58 ( 1542) hydrogen bonds : angle 4.83851 / 3.47 ( 4338) metal coordination : bond 0.00679 / 0.40 ( 22) metal coordination : angle 14.20549 / 7.50 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 483 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7779 (mmm160) cc_final: 0.7535 (mmm160) REVERT: A 107 MET cc_start: 0.8928 (tpp) cc_final: 0.8667 (tpp) REVERT: A 339 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8397 (ptm-80) REVERT: A 504 GLU cc_start: 0.7694 (mp0) cc_final: 0.7315 (mp0) REVERT: A 513 GLU cc_start: 0.7837 (mp0) cc_final: 0.7465 (mm-30) REVERT: A 896 ASP cc_start: 0.7737 (t0) cc_final: 0.7153 (p0) REVERT: A 919 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8143 (mm) REVERT: A 920 GLU cc_start: 0.7590 (tp30) cc_final: 0.6875 (tm-30) REVERT: A 1048 MET cc_start: 0.5355 (mmt) cc_final: 0.4133 (mmm) REVERT: A 1051 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5797 (tptm) REVERT: A 1157 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8575 (tptp) REVERT: A 1196 LEU cc_start: 0.9451 (tp) cc_final: 0.9007 (mt) REVERT: A 1236 MET cc_start: 0.8743 (ptm) cc_final: 0.8417 (ptp) REVERT: A 1313 GLU cc_start: 0.8509 (pm20) cc_final: 0.8210 (pm20) REVERT: B 384 MET cc_start: 0.8288 (mmp) cc_final: 0.7809 (tpp) REVERT: B 460 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: B 616 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7965 (mm-40) REVERT: B 697 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9073 (mp) REVERT: B 750 ASP cc_start: 0.7784 (p0) cc_final: 0.7435 (p0) REVERT: B 800 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7789 (tpp-160) REVERT: C 98 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9108 (p) REVERT: C 151 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7494 (p90) REVERT: C 311 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6898 (tm-30) REVERT: C 330 MET cc_start: 0.8551 (mmm) cc_final: 0.8331 (mmt) REVERT: D 5 ASP cc_start: 0.7740 (t0) cc_final: 0.7454 (t0) REVERT: D 67 ARG cc_start: 0.7738 (tpm170) cc_final: 0.7518 (tpm170) REVERT: E 2 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6719 (p0) REVERT: E 130 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.6887 (m-80) REVERT: F 64 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8253 (tpt90) REVERT: G 32 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6867 (mmtt) REVERT: G 82 ASP cc_start: 0.5526 (t0) cc_final: 0.5163 (t0) REVERT: G 115 GLN cc_start: 0.3488 (tp-100) cc_final: 0.2879 (tp40) REVERT: G 159 ASP cc_start: 0.7944 (t0) cc_final: 0.7642 (t0) REVERT: H 7 GLU cc_start: 0.8089 (tp30) cc_final: 0.7114 (tp30) REVERT: H 89 GLU cc_start: 0.7245 (mp0) cc_final: 0.6790 (mp0) REVERT: H 123 MET cc_start: 0.8713 (tmm) cc_final: 0.8450 (tmm) REVERT: H 145 MET cc_start: 0.8427 (tpp) cc_final: 0.7094 (tpp) REVERT: I 36 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.6818 (tmm-80) REVERT: I 85 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7501 (tpp-160) REVERT: I 91 MET cc_start: 0.7926 (mtp) cc_final: 0.7014 (ttt) REVERT: I 94 PHE cc_start: 0.8530 (m-10) cc_final: 0.8243 (m-80) REVERT: J 54 ASP cc_start: 0.8106 (p0) cc_final: 0.7796 (p0) REVERT: J 57 GLU cc_start: 0.7607 (pm20) cc_final: 0.7323 (pm20) REVERT: M 11 GLN cc_start: 0.7755 (mt0) cc_final: 0.7096 (mp10) REVERT: M 87 ASP cc_start: 0.7717 (m-30) cc_final: 0.7312 (t70) REVERT: N 247 LYS cc_start: 0.8309 (pptt) cc_final: 0.7910 (pptt) REVERT: N 347 ASP cc_start: 0.7397 (t70) cc_final: 0.7087 (t0) REVERT: O 85 MET cc_start: 0.9326 (mmm) cc_final: 0.8458 (mmm) REVERT: O 281 SER cc_start: 0.8157 (p) cc_final: 0.7933 (m) REVERT: O 415 HIS cc_start: 0.8225 (m90) cc_final: 0.7907 (m-70) REVERT: O 427 ASN cc_start: 0.8528 (t0) cc_final: 0.8205 (t0) REVERT: P 196 ARG cc_start: 0.8867 (mtm110) cc_final: 0.8515 (mtm110) REVERT: P 199 LYS cc_start: 0.7908 (mttt) cc_final: 0.7285 (ttmt) REVERT: P 205 GLN cc_start: 0.5053 (OUTLIER) cc_final: 0.4761 (pp30) REVERT: P 232 MET cc_start: 0.5889 (mmp) cc_final: 0.5384 (mmp) REVERT: P 293 PHE cc_start: 0.4863 (m-80) cc_final: 0.4501 (t80) REVERT: Q 113 ARG cc_start: 0.7464 (mmm160) cc_final: 0.6925 (mmm160) outliers start: 146 outliers final: 121 residues processed: 596 average time/residue: 0.2482 time to fit residues: 246.6663 Evaluate side-chains 600 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 467 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 527 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 405 optimal weight: 0.9990 chunk 234 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 299 optimal weight: 0.9990 chunk 402 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 399 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 457 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.094917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073896 restraints weight = 130926.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076279 restraints weight = 63212.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077819 restraints weight = 39242.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078804 restraints weight = 28683.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079333 restraints weight = 23412.226| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40315 Z= 0.140 Angle : 0.780 56.286 54627 Z= 0.361 Chirality : 0.044 0.264 6150 Planarity : 0.005 0.072 6872 Dihedral : 10.528 150.478 5824 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 3.31 % Allowed : 25.18 % Favored : 71.52 % 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: -0.29 (0.12), residues: 4791 helix: 0.83 (0.12), residues: 1737 sheet: -0.14 (0.19), residues: 656 loop : -0.95 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 9 TYR 0.022 0.001 TYR A 179 PHE 0.044 0.001 PHE A1321 TRP 0.059 0.002 TRP G 127 HIS 0.009 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (40293) covalent geometry : angle 0.71603 / 0.36 (54600) hydrogen bonds : bond 0.03744 / 2.51 ( 1542) hydrogen bonds : angle 4.81516 / 3.46 ( 4338) metal coordination : bond 0.00582 / 0.35 ( 22) metal coordination : angle 13.91466 / 7.34 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 494 time to evaluate : 1.389 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: A 99 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7533 (mmm160) REVERT: A 107 MET cc_start: 0.8906 (tpp) cc_final: 0.8645 (tpp) REVERT: A 339 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8461 (ptm-80) REVERT: A 504 GLU cc_start: 0.7662 (mp0) cc_final: 0.7302 (mp0) REVERT: A 513 GLU cc_start: 0.7767 (mp0) cc_final: 0.7455 (mm-30) REVERT: A 896 ASP cc_start: 0.7690 (t0) cc_final: 0.7284 (p0) REVERT: A 919 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 920 GLU cc_start: 0.7563 (tp30) cc_final: 0.6873 (tm-30) REVERT: A 1048 MET cc_start: 0.5270 (mmt) cc_final: 0.4082 (mmm) REVERT: A 1051 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5927 (tptm) REVERT: A 1072 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8195 (mt-10) REVERT: A 1157 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8574 (tptp) REVERT: A 1196 LEU cc_start: 0.9449 (tp) cc_final: 0.9013 (mt) REVERT: A 1236 MET cc_start: 0.8676 (ptm) cc_final: 0.8411 (ptp) REVERT: A 1313 GLU cc_start: 0.8462 (pm20) cc_final: 0.8228 (pm20) REVERT: B 384 MET cc_start: 0.8281 (mmp) cc_final: 0.7820 (tpp) REVERT: B 460 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: B 616 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7986 (mm-40) REVERT: B 697 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9004 (mp) REVERT: B 750 ASP cc_start: 0.7709 (p0) cc_final: 0.7349 (p0) REVERT: B 800 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7867 (mmm160) REVERT: C 98 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.9093 (p) REVERT: C 151 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7479 (p90) REVERT: C 311 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6929 (tm-30) REVERT: C 330 MET cc_start: 0.8466 (mmm) cc_final: 0.8238 (mmt) REVERT: D 5 ASP cc_start: 0.7644 (t0) cc_final: 0.7370 (t0) REVERT: D 67 ARG cc_start: 0.7716 (tpm170) cc_final: 0.7500 (tpm170) REVERT: E 2 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6788 (p0) REVERT: E 130 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: F 64 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8213 (tpt90) REVERT: G 82 ASP cc_start: 0.5559 (t0) cc_final: 0.5220 (t0) REVERT: G 115 GLN cc_start: 0.3409 (tp-100) cc_final: 0.2810 (tp40) REVERT: G 116 GLN cc_start: 0.1407 (OUTLIER) cc_final: 0.0448 (pt0) REVERT: G 159 ASP cc_start: 0.7920 (t0) cc_final: 0.7591 (t0) REVERT: H 7 GLU cc_start: 0.8071 (tp30) cc_final: 0.7088 (tp30) REVERT: H 89 GLU cc_start: 0.7169 (mp0) cc_final: 0.6739 (mp0) REVERT: H 123 MET cc_start: 0.8715 (tmm) cc_final: 0.8465 (tmm) REVERT: H 145 MET cc_start: 0.8410 (tpp) cc_final: 0.7112 (tpp) REVERT: I 36 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.6831 (tmm-80) REVERT: I 85 ARG cc_start: 0.7934 (mmm160) cc_final: 0.7561 (tpp-160) REVERT: I 91 MET cc_start: 0.7827 (mtp) cc_final: 0.7125 (mmm) REVERT: I 94 PHE cc_start: 0.8463 (m-10) cc_final: 0.8189 (m-80) REVERT: J 54 ASP cc_start: 0.8114 (p0) cc_final: 0.7755 (p0) REVERT: J 57 GLU cc_start: 0.7598 (pm20) cc_final: 0.7245 (pm20) REVERT: M 11 GLN cc_start: 0.7759 (mt0) cc_final: 0.7087 (mp10) REVERT: M 87 ASP cc_start: 0.7658 (m-30) cc_final: 0.7322 (t70) REVERT: M 220 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8052 (p90) REVERT: N 347 ASP cc_start: 0.7371 (t70) cc_final: 0.7063 (t0) REVERT: O 139 MET cc_start: 0.1284 (ptt) cc_final: 0.0045 (mpp) REVERT: O 281 SER cc_start: 0.8144 (p) cc_final: 0.7923 (m) REVERT: O 411 LYS cc_start: 0.5527 (OUTLIER) cc_final: 0.4609 (pttt) REVERT: O 415 HIS cc_start: 0.8130 (m90) cc_final: 0.7867 (m-70) REVERT: O 427 ASN cc_start: 0.8503 (t0) cc_final: 0.8187 (t0) REVERT: P 196 ARG cc_start: 0.8860 (mtm110) cc_final: 0.8504 (mtm110) REVERT: P 199 LYS cc_start: 0.7894 (mttt) cc_final: 0.7279 (ttmt) REVERT: P 205 GLN cc_start: 0.5131 (OUTLIER) cc_final: 0.4887 (pp30) REVERT: P 232 MET cc_start: 0.5902 (mmp) cc_final: 0.5403 (mmp) REVERT: P 293 PHE cc_start: 0.4760 (m-80) cc_final: 0.4419 (t80) REVERT: Q 113 ARG cc_start: 0.7297 (mmm160) cc_final: 0.6849 (mmm160) outliers start: 141 outliers final: 114 residues processed: 603 average time/residue: 0.2404 time to fit residues: 241.8055 Evaluate side-chains 603 residues out of total 4275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 474 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 272 optimal weight: 1.9990 chunk 433 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 243 optimal weight: 0.8980 chunk 368 optimal weight: 0.7980 chunk 133 optimal weight: 0.2980 chunk 20 optimal weight: 0.0170 chunk 476 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN G 116 GLN M 149 HIS O 34 GLN O 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.095671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074907 restraints weight = 131780.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078109 restraints weight = 63092.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078977 restraints weight = 34212.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079418 restraints weight = 26589.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079519 restraints weight = 25175.406| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.6746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40315 Z= 0.133 Angle : 0.780 54.211 54627 Z= 0.362 Chirality : 0.044 0.256 6150 Planarity : 0.005 0.066 6872 Dihedral : 10.469 150.497 5824 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 3.28 % Allowed : 25.06 % Favored : 71.66 % 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: -0.26 (0.12), residues: 4791 helix: 0.88 (0.13), residues: 1727 sheet: -0.12 (0.19), residues: 658 loop : -0.95 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 9 TYR 0.035 0.001 TYR A 179 PHE 0.036 0.001 PHE A1321 TRP 0.055 0.002 TRP G 127 HIS 0.012 0.001 HIS M 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (40293) covalent geometry : angle 0.72054 / 0.36 (54600) hydrogen bonds : bond 0.03639 / 2.44 ( 1542) hydrogen bonds : angle 4.76856 / 3.42 ( 4338) metal coordination : bond 0.00523 / 0.33 ( 22) metal coordination : angle 13.48554 / 7.10 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8927.50 seconds wall clock time: 154 minutes 53.65 seconds (9293.65 seconds total)