Starting phenix.real_space_refine on Sat Mar 7 08:33:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a6h_11673/03_2026/7a6h_11673.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a6h_11673/03_2026/7a6h_11673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a6h_11673/03_2026/7a6h_11673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a6h_11673/03_2026/7a6h_11673.map" model { file = "/net/cci-nas-00/data/ceres_data/7a6h_11673/03_2026/7a6h_11673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a6h_11673/03_2026/7a6h_11673.cif" } resolution = 3.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 Mg 1 5.21 5 S 276 5.16 5 C 25424 2.51 5 N 6974 2.21 5 O 7530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40216 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 10800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1375, 10800 Classifications: {'peptide': 1375} Link IDs: {'PTRANS': 65, 'TRANS': 1309} Chain breaks: 2 Chain: "B" Number of atoms: 8680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8680 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 2 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: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1001 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} 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: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1509 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 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: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 849 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} 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: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1776 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 13, 'TRANS': 206} Chain breaks: 1 Chain: "N" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1448 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "Q" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 883 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 12, 'TRANS': 91} 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 543 SG CYS A 69 97.330 58.408 122.114 1.00110.77 S ATOM 1245 SG CYS A 156 65.482 89.942 147.952 1.00130.65 S ATOM 19067 SG CYS B1080 80.071 55.632 129.800 1.00 75.80 S ATOM 19086 SG CYS B1083 80.309 59.271 130.089 1.00 75.48 S ATOM 19152 SG CYS B1092 83.340 57.328 129.985 1.00 81.36 S ATOM 19180 SG CYS B1095 80.772 57.554 133.620 1.00 83.97 S ATOM 28295 SG CYS I 5 55.765 141.938 108.776 1.00113.38 S ATOM 28312 SG CYS I 8 58.959 139.919 110.359 1.00116.28 S ATOM 28443 SG CYS I 25 56.190 138.517 112.137 1.00123.41 S ATOM 28464 SG CYS I 28 56.722 142.116 112.170 1.00123.98 S ATOM 29158 SG CYS J 7 91.028 69.264 50.040 1.00 57.24 S ATOM 29182 SG CYS J 10 90.549 66.659 47.510 1.00 56.75 S ATOM 29446 SG CYS J 44 87.846 69.042 47.897 1.00 62.05 S ATOM 29452 SG CYS J 45 91.354 69.508 45.572 1.00 62.77 S ATOM 30541 SG CYS L 19 122.928 85.623 74.017 1.00 85.80 S ATOM 30560 SG CYS L 22 125.026 86.517 71.244 1.00 93.06 S ATOM 30677 SG CYS L 36 126.290 86.778 74.733 1.00100.27 S ATOM 39231 SG CYS P 307 93.785 66.516 152.223 1.00 94.91 S Time building chain proxies: 8.60, per 1000 atoms: 0.21 Number of scatterers: 40216 At special positions: 0 Unit cell: (142.206, 177.552, 205.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 276 16.00 Mg 1 11.99 O 7530 8.00 N 6974 7.00 C 25424 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: 3.52 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" ND1 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 28 " 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 8 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 18 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9516 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 57 sheets defined 39.9% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.573A pdb=" N MET A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.675A pdb=" N GLY A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 135 through 152 removed outlier: 3.664A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 4.039A pdb=" N PHE A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.596A pdb=" N LEU A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.881A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 277 through 297 Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 329 through 333 removed outlier: 4.036A pdb=" N ALA A 333 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.698A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.754A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.649A pdb=" N ASP A 576 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 4.103A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.526A pdb=" N LEU A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 695 removed outlier: 3.560A pdb=" N GLY A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N ASN A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.833A pdb=" N ASN A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.537A pdb=" N VAL A 703 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 733 removed outlier: 3.709A pdb=" N ALA A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 771 removed outlier: 4.063A pdb=" N ARG A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 771 " --> pdb=" O CYS A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 797 removed outlier: 3.546A pdb=" N ILE A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.743A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET A 871 " --> pdb=" O GLU A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.803A pdb=" N MET A 912 " --> pdb=" O PRO A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 954 Processing helix chain 'A' and resid 956 through 960 removed outlier: 3.536A pdb=" N CYS A 960 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 988 removed outlier: 3.567A pdb=" N LEU A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 removed outlier: 3.620A pdb=" N LEU A1003 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1025 Processing helix chain 'A' and resid 1032 through 1043 Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 3.600A pdb=" N ALA A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.634A pdb=" N VAL A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1188 through 1196 Processing helix chain 'A' and resid 1231 through 1238 Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.999A pdb=" N THR A1246 " --> pdb=" O GLY A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1259 removed outlier: 3.573A pdb=" N GLY A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1278 removed outlier: 3.744A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 4.101A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1315 through 1322 removed outlier: 3.665A pdb=" N PHE A1321 " --> pdb=" O MET A1317 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A1322 " --> pdb=" O LEU A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1335 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1355 through 1359 removed outlier: 3.825A pdb=" N LEU A1359 " --> pdb=" O GLY A1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.721A pdb=" N LYS B 26 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 27' Processing helix chain 'B' and resid 28 through 34 Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.609A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.655A pdb=" N CYS B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 273 Proline residue: B 267 - end of helix Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.719A pdb=" N LEU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.746A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 392 removed outlier: 4.364A pdb=" N LEU B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.814A pdb=" N MET B 406 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 444 through 452 removed outlier: 3.559A pdb=" N ALA B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.569A pdb=" N TRP B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 518 removed outlier: 4.274A pdb=" N VAL B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.632A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 533 " --> pdb=" O GLU B 530 " (cutoff:3.500A) 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: 3.537A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.526A pdb=" N LEU B 671 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 672 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 removed outlier: 3.675A pdb=" N ASN B 678 " --> pdb=" O PRO B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 690 removed outlier: 3.872A pdb=" N ASN B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 728 removed outlier: 3.535A pdb=" N GLU B 726 " --> pdb=" O THR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 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 933 through 938 removed outlier: 3.701A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 954 removed outlier: 3.977A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 954 " --> pdb=" O LYS B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.823A pdb=" N VAL B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 979 " --> pdb=" O ASP B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1020 removed outlier: 3.507A pdb=" N LYS B1019 " --> pdb=" O MET B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1059 removed outlier: 3.566A pdb=" N GLY B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1069 Processing helix chain 'B' and resid 1108 through 1120 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 removed outlier: 4.237A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.592A pdb=" N LEU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.629A pdb=" N LEU C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.597A pdb=" N GLU C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.883A pdb=" N PHE C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 289 " --> pdb=" O GLU C 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 285 through 289' Processing helix chain 'C' and resid 317 through 344 removed outlier: 3.641A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 removed outlier: 3.730A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.502A pdb=" N LYS D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 109 through 124 removed outlier: 3.785A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 removed outlier: 3.678A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.874A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.989A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 removed outlier: 3.755A pdb=" N ARG E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.523A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.695A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.753A pdb=" N GLN E 169 " --> pdb=" O ARG E 166 " (cutoff:3.500A) 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 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.748A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.559A pdb=" N ALA G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 Processing helix chain 'G' and resid 199 through 201 No H-bonds generated for 'chain 'G' and resid 199 through 201' Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.693A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.850A pdb=" N GLY I 54 " --> pdb=" O ASP I 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 25 Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.708A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.900A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 60 removed outlier: 4.161A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.717A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 128 Processing helix chain 'M' and resid 70 through 82 removed outlier: 4.100A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 154 removed outlier: 3.962A pdb=" N ASP M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 202 removed outlier: 3.752A pdb=" N LEU M 196 " --> pdb=" O SER M 192 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU M 202 " --> pdb=" O LYS M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 223 removed outlier: 3.987A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 226 No H-bonds generated for 'chain 'M' and resid 224 through 226' Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'N' and resid 111 through 124 removed outlier: 3.762A pdb=" N TRP N 123 " --> pdb=" O LYS N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 151 removed outlier: 3.902A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 260 Processing helix chain 'N' and resid 317 through 321 Processing helix chain 'N' and resid 388 through 396 removed outlier: 4.090A pdb=" N LYS N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 18 through 31 removed outlier: 4.645A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 44 removed outlier: 3.582A pdb=" N THR O 43 " --> pdb=" O ILE O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.791A pdb=" N HIS O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 78 through 84 Processing helix chain 'O' and resid 87 through 99 Processing helix chain 'O' and resid 100 through 114 Processing helix chain 'O' and resid 117 through 129 Processing helix chain 'O' and resid 140 through 154 removed outlier: 3.978A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 188 removed outlier: 4.137A pdb=" N MET O 187 " --> pdb=" O GLU O 184 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR O 188 " --> pdb=" O LYS O 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 184 through 188' Processing helix chain 'O' and resid 238 through 259 removed outlier: 3.666A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 274 Processing helix chain 'O' and resid 290 through 296 removed outlier: 3.590A pdb=" N ARG O 295 " --> pdb=" O ASN O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 316 Processing helix chain 'O' and resid 338 through 359 removed outlier: 3.648A pdb=" N VAL O 354 " --> pdb=" O LEU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 372 removed outlier: 3.833A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 385 removed outlier: 4.064A pdb=" N MET O 385 " --> pdb=" O GLU O 381 " (cutoff:3.500A) Processing helix chain 'O' and resid 390 through 400 removed outlier: 3.582A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 416 through 418 No H-bonds generated for 'chain 'O' and resid 416 through 418' Processing helix chain 'O' and resid 427 through 457 removed outlier: 3.547A pdb=" N ALA O 431 " --> pdb=" O ASN O 427 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 473 Processing helix chain 'O' and resid 480 through 490 removed outlier: 4.155A pdb=" N LEU O 484 " --> pdb=" O GLU O 480 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN O 485 " --> pdb=" O GLU O 481 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU O 488 " --> pdb=" O LEU O 484 " (cutoff:3.500A) Processing helix chain 'O' and resid 495 through 516 Processing helix chain 'O' and resid 516 through 530 removed outlier: 3.530A pdb=" N LEU O 522 " --> pdb=" O GLU O 518 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 199 removed outlier: 3.931A pdb=" N LEU P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN P 182 " --> pdb=" O GLU P 178 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE P 185 " --> pdb=" O ASN P 181 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 Processing helix chain 'P' and resid 213 through 224 removed outlier: 3.722A pdb=" N TRP P 217 " --> pdb=" O SER P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 245 removed outlier: 3.794A pdb=" N THR P 237 " --> pdb=" O GLU P 233 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN P 240 " --> pdb=" O GLU P 236 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR P 241 " --> pdb=" O THR P 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.723A pdb=" N CYS P 290 " --> pdb=" O CYS P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 296 Processing helix chain 'P' and resid 303 through 307 removed outlier: 3.910A pdb=" N CYS P 307 " --> pdb=" O PRO P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 314 Processing helix chain 'Q' and resid 15 through 20 removed outlier: 3.666A pdb=" N VAL Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 69 removed outlier: 3.647A pdb=" N MET Q 57 " --> pdb=" O GLY Q 53 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.645A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL G 75 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N PHE G 2 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N SER D 8 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU G 4 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA D 6 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.645A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA G 57 " --> pdb=" O HIS A1364 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU A1362 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1338 through 1339 Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.915A pdb=" N ILE A 34 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASP A 87 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 84 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 88 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N ILE A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.616A pdb=" N LYS A 167 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 175 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488 removed outlier: 6.000A pdb=" N VAL A 380 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS A 481 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 382 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 367 " --> pdb=" O MET A 505 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 395 Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 422 Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 616 through 620 removed outlier: 6.674A pdb=" N THR A 639 " --> pdb=" O MET A 646 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.795A pdb=" N CYS A 883 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 891 " --> pdb=" O CYS A 883 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1085 through 1087 removed outlier: 3.961A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 4.201A pdb=" N GLN A1202 " --> pdb=" O THR A1108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1165 through 1166 removed outlier: 3.754A pdb=" N CYS A1174 " --> pdb=" O ALA A1166 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.573A pdb=" N LEU B 75 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.573A pdb=" N LEU B 75 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (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: 3.715A pdb=" N ILE B 180 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.503A pdb=" N VAL B 203 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 225 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 501 through 502 Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 549 removed outlier: 5.705A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.828A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.828A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) removed outlier: 5.633A 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 927 through 929 removed outlier: 8.550A pdb=" N ILE B 927 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR B 740 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET B 929 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 742 " --> pdb=" O MET B 929 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 755 through 758 removed outlier: 5.702A pdb=" N LEU B 755 " --> pdb=" O CYS B 907 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU B 909 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 911 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.729A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 826 through 828 removed outlier: 3.848A pdb=" N VAL B 828 " --> pdb=" O ILE B 856 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.085A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 13 through 15 removed outlier: 7.229A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 13 through 15 removed outlier: 8.647A pdb=" N ARG C 303 " --> pdb=" O PRO C 237 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N HIS C 305 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 235 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 307 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR C 233 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 173 through 175 removed outlier: 3.563A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.656A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AE2, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.809A pdb=" N THR C 240 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE4, first strand: chain 'E' and resid 62 through 63 removed outlier: 5.759A pdb=" N ASP E 70 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ARG E 101 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 removed outlier: 8.187A pdb=" N GLY E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 4.133A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 83 through 87 removed outlier: 3.777A pdb=" N GLU G 83 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL G 187 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU G 155 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR G 185 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N TYR G 184 " --> pdb=" O PHE G 104 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP G 106 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASP G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU G 101 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 83 through 87 removed outlier: 3.777A pdb=" N GLU G 83 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 128 through 129 removed outlier: 3.595A pdb=" N TRP G 129 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP G 139 " --> pdb=" O TRP G 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.939A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF3, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AF4, first strand: chain 'I' and resid 77 through 82 removed outlier: 3.557A pdb=" N LEU I 82 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR I 92 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 27 through 31 Processing sheet with id=AF6, first strand: chain 'M' and resid 10 through 17 removed outlier: 3.551A pdb=" N HIS M 125 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU N 266 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 25 through 34 removed outlier: 7.380A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU N 357 " --> pdb=" O TYR M 30 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 63 through 67 removed outlier: 3.590A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AG1, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AG2, first strand: chain 'O' and resid 409 through 410 Processing sheet with id=AG3, first strand: chain 'P' and resid 211 through 212 1603 hydrogen bonds defined for protein. 4494 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: 10.86 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 16596 1.43 - 1.64: 23926 1.64 - 1.85: 428 1.85 - 2.06: 0 2.06 - 2.27: 12 Bond restraints: 40962 Sorted by residual: bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.335 1.389 -0.054 9.40e-03 1.13e+04 3.26e+01 bond pdb=" C LYS D 55 " pdb=" N THR D 56 " ideal model delta sigma weight residual 1.329 1.223 0.106 1.86e-02 2.89e+03 3.23e+01 bond pdb=" CA TYR A1187 " pdb=" C TYR A1187 " ideal model delta sigma weight residual 1.523 1.581 -0.058 1.34e-02 5.57e+03 1.87e+01 bond pdb=" C LYS B 820 " pdb=" N VAL B 821 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.42e-02 4.96e+03 1.10e+01 bond pdb=" CA THR B 500 " pdb=" CB THR B 500 " ideal model delta sigma weight residual 1.533 1.494 0.039 1.51e-02 4.39e+03 6.70e+00 ... (remaining 40957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 54008 2.88 - 5.77: 1173 5.77 - 8.65: 105 8.65 - 11.54: 11 11.54 - 14.42: 2 Bond angle restraints: 55299 Sorted by residual: angle pdb=" N ILE A1303 " pdb=" CA ILE A1303 " pdb=" C ILE A1303 " ideal model delta sigma weight residual 112.43 104.32 8.11 9.20e-01 1.18e+00 7.77e+01 angle pdb=" C LEU B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 121.97 136.39 -14.42 1.80e+00 3.09e-01 6.42e+01 angle pdb=" C ASN B 52 " pdb=" N VAL B 53 " pdb=" CA VAL B 53 " ideal model delta sigma weight residual 122.77 116.83 5.94 1.05e+00 9.07e-01 3.20e+01 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 120.91 -11.57 2.08e+00 2.31e-01 3.09e+01 angle pdb=" C ILE A1153 " pdb=" N CYS A1154 " pdb=" CA CYS A1154 " ideal model delta sigma weight residual 122.74 130.23 -7.49 1.44e+00 4.82e-01 2.71e+01 ... (remaining 55294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 24147 17.35 - 34.70: 892 34.70 - 52.05: 148 52.05 - 69.40: 14 69.40 - 86.75: 21 Dihedral angle restraints: 25222 sinusoidal: 10500 harmonic: 14722 Sorted by residual: dihedral pdb=" CA LEU B 39 " pdb=" C LEU B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta harmonic sigma weight residual -180.00 -128.75 -51.25 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA LYS A 74 " pdb=" C LYS A 74 " pdb=" N ASN A 75 " pdb=" CA ASN A 75 " ideal model delta harmonic sigma weight residual -180.00 -138.05 -41.95 0 5.00e+00 4.00e-02 7.04e+01 dihedral pdb=" CA CYS A 69 " pdb=" C CYS A 69 " pdb=" N GLU A 70 " pdb=" CA GLU A 70 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 25219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4839 0.070 - 0.140: 1205 0.140 - 0.210: 140 0.210 - 0.279: 19 0.279 - 0.349: 4 Chirality restraints: 6207 Sorted by residual: chirality pdb=" CA ALA G 137 " pdb=" N ALA G 137 " pdb=" C ALA G 137 " pdb=" CB ALA G 137 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB ILE A 473 " pdb=" CA ILE A 473 " pdb=" CG1 ILE A 473 " pdb=" CG2 ILE A 473 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB ILE J 3 " pdb=" CA ILE J 3 " pdb=" CG1 ILE J 3 " pdb=" CG2 ILE J 3 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 6204 not shown) Planarity restraints: 7139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 411 " 0.064 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO A 412 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1009 " 0.028 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR B1009 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B1009 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B1009 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B1009 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B1009 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B1009 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1009 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 749 " 0.019 2.00e-02 2.50e+03 2.09e-02 8.73e+00 pdb=" CG TYR B 749 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 749 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 749 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 749 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 749 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 749 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 749 " 0.003 2.00e-02 2.50e+03 ... (remaining 7136 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 120 2.46 - 3.07: 24741 3.07 - 3.68: 58341 3.68 - 4.29: 85142 4.29 - 4.90: 143715 Nonbonded interactions: 312059 Sorted by model distance: nonbonded pdb=" OD2 ASP A 499 " pdb="MG MG A1403 " model vdw 1.851 2.170 nonbonded pdb=" N HIS A 157 " pdb="ZN ZN A1402 " model vdw 2.156 2.310 nonbonded pdb=" O ILE O 409 " pdb=" OG1 THR O 420 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU B 521 " pdb=" OG1 THR N 352 " model vdw 2.223 3.040 nonbonded pdb=" O ILE D 53 " pdb=" OG1 THR D 56 " model vdw 2.271 3.040 ... (remaining 312054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.720 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: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 47.850 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.013 0.792 40984 Z= 0.497 Angle : 1.145 44.838 55329 Z= 0.590 Chirality : 0.060 0.349 6207 Planarity : 0.008 0.097 7139 Dihedral : 10.132 86.750 15706 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.71 % Rotamer: Outliers : 0.27 % Allowed : 2.84 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.66 (0.09), residues: 5005 helix: -2.58 (0.09), residues: 1724 sheet: -2.35 (0.17), residues: 668 loop : -2.31 (0.10), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 900 TYR 0.061 0.004 TYR B1009 PHE 0.039 0.003 PHE B 897 TRP 0.032 0.003 TRP B 424 HIS 0.019 0.003 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00991 (40962) covalent geometry : angle 1.03683 (55299) hydrogen bonds : bond 0.19884 ( 1566) hydrogen bonds : angle 7.46648 ( 4494) metal coordination : bond 0.36183 ( 22) metal coordination : angle 20.84984 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 370 time to evaluate : 1.647 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: A 312 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: D 100 MET cc_start: 0.9369 (mtt) cc_final: 0.9163 (mtp) REVERT: G 141 TYR cc_start: 0.8489 (m-10) cc_final: 0.8264 (m-80) outliers start: 12 outliers final: 1 residues processed: 382 average time/residue: 0.2878 time to fit residues: 173.0395 Evaluate side-chains 230 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain B residue 27 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 33 HIS A 176 HIS A 217 ASN A 374 ASN A 476 HIS A 616 ASN A 662 ASN A 927 ASN A1180 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 HIS A1385 HIS B 183 GLN B 208 HIS B 320 HIS B 501 HIS B 602 GLN B 683 ASN B 716 GLN B 738 ASN B 758 ASN B 901 HIS B 903 GLN B 932 HIS B1100 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 290 ASN D 76 HIS D 88 ASN D 98 GLN E 98 ASN H 76 ASN ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN K 81 ASN K 85 GLN K 129 ASN ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 HIS N 106 HIS N 111 GLN O 34 GLN O 59 GLN O 155 HIS O 158 GLN P 181 ASN P 297 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.041110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.029065 restraints weight = 266651.005| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.57 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40984 Z= 0.150 Angle : 0.668 22.473 55329 Z= 0.327 Chirality : 0.043 0.270 6207 Planarity : 0.005 0.061 7139 Dihedral : 5.372 53.716 5506 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 0.94 % Allowed : 5.60 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.11), residues: 5005 helix: -0.63 (0.12), residues: 1780 sheet: -1.77 (0.18), residues: 693 loop : -1.65 (0.11), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 128 TYR 0.021 0.001 TYR B1009 PHE 0.016 0.001 PHE P 176 TRP 0.013 0.001 TRP B 27 HIS 0.008 0.001 HIS P 214 Details of bonding type rmsd covalent geometry : bond 0.00324 (40962) covalent geometry : angle 0.62588 (55299) hydrogen bonds : bond 0.04419 ( 1566) hydrogen bonds : angle 5.22159 ( 4494) metal coordination : bond 0.00837 ( 22) metal coordination : angle 10.07912 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9230 (tp) REVERT: A 505 MET cc_start: 0.8733 (mtp) cc_final: 0.8116 (mmm) REVERT: A 795 MET cc_start: 0.9443 (ptt) cc_final: 0.9242 (ptm) REVERT: A 912 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: B 72 MET cc_start: 0.8536 (mpp) cc_final: 0.8191 (ppp) REVERT: B 216 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8571 (mmm) REVERT: B 452 MET cc_start: 0.9015 (mmm) cc_final: 0.8403 (mmm) REVERT: B 478 MET cc_start: 0.9227 (mmp) cc_final: 0.8922 (mmp) REVERT: B 499 MET cc_start: 0.8672 (ttp) cc_final: 0.8431 (ttp) REVERT: B 506 MET cc_start: 0.8654 (mpp) cc_final: 0.8193 (mpp) REVERT: B 870 MET cc_start: 0.8544 (tmm) cc_final: 0.8043 (tmm) REVERT: B 1069 MET cc_start: 0.8734 (ttm) cc_final: 0.8483 (ttt) REVERT: C 56 MET cc_start: 0.8463 (tmm) cc_final: 0.8231 (tmm) REVERT: C 87 MET cc_start: 0.9177 (mmm) cc_final: 0.8798 (mmm) REVERT: C 330 MET cc_start: 0.8790 (ttm) cc_final: 0.8586 (ttm) REVERT: D 100 MET cc_start: 0.9580 (mtt) cc_final: 0.9304 (mtp) REVERT: E 94 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7673 (ppp) REVERT: E 121 MET cc_start: 0.9080 (mtt) cc_final: 0.8760 (ptp) REVERT: G 45 CYS cc_start: 0.9343 (m) cc_final: 0.8994 (t) REVERT: G 141 TYR cc_start: 0.9179 (m-10) cc_final: 0.8267 (m-80) REVERT: H 37 MET cc_start: 0.8918 (mmt) cc_final: 0.8639 (mmm) REVERT: I 91 MET cc_start: 0.5783 (mtm) cc_final: 0.5464 (mtp) REVERT: I 106 TRP cc_start: 0.5327 (m100) cc_final: 0.5126 (m100) REVERT: J 1 MET cc_start: 0.8891 (ttp) cc_final: 0.8429 (ttp) REVERT: K 64 GLU cc_start: 0.8772 (mp0) cc_final: 0.8531 (mp0) REVERT: K 104 MET cc_start: 0.9286 (ttm) cc_final: 0.8936 (ttm) REVERT: L 15 MET cc_start: 0.7358 (tpp) cc_final: 0.6971 (tpp) REVERT: L 23 HIS cc_start: 0.8456 (t-170) cc_final: 0.8204 (t-170) REVERT: L 44 MET cc_start: 0.9094 (mmm) cc_final: 0.8847 (mmm) REVERT: M 17 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8858 (tm) REVERT: M 60 MET cc_start: 0.8023 (mtp) cc_final: 0.7197 (mmm) REVERT: N 109 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5203 (t80) REVERT: N 373 MET cc_start: 0.8922 (tmm) cc_final: 0.8614 (ppp) REVERT: O 85 MET cc_start: 0.9150 (ttm) cc_final: 0.8770 (ttt) REVERT: O 139 MET cc_start: 0.8188 (mmp) cc_final: 0.7701 (mmp) REVERT: P 200 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8373 (pm20) outliers start: 42 outliers final: 12 residues processed: 278 average time/residue: 0.2535 time to fit residues: 116.8713 Evaluate side-chains 239 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 71 LYS Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain O residue 490 MET Chi-restraints excluded: chain P residue 200 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 366 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 334 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 420 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 248 optimal weight: 0.5980 chunk 343 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 114 HIS A 163 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN I 10 ASN ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 339 HIS O 377 GLN O 475 GLN P 182 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.040220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.028213 restraints weight = 270748.035| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.42 r_work: 0.2656 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 2.062 40984 Z= 0.408 Angle : 0.657 21.304 55329 Z= 0.320 Chirality : 0.043 0.187 6207 Planarity : 0.004 0.063 7139 Dihedral : 4.971 57.360 5504 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.86 % Rotamer: Outliers : 1.25 % Allowed : 6.18 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.11), residues: 5005 helix: 0.31 (0.12), residues: 1794 sheet: -1.37 (0.18), residues: 687 loop : -1.24 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 76 TYR 0.019 0.002 TYR I 78 PHE 0.015 0.001 PHE O 148 TRP 0.017 0.001 TRP Q 103 HIS 0.011 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00497 (40962) covalent geometry : angle 0.62630 (55299) hydrogen bonds : bond 0.03711 ( 1566) hydrogen bonds : angle 4.76609 ( 4494) metal coordination : bond 0.43970 ( 22) metal coordination : angle 8.61448 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7661 (mmm) cc_final: 0.7057 (mmm) REVERT: A 505 MET cc_start: 0.9067 (mtp) cc_final: 0.8569 (mmm) REVERT: A 871 MET cc_start: 0.8821 (tmm) cc_final: 0.8568 (tmm) REVERT: A 912 MET cc_start: 0.9474 (OUTLIER) cc_final: 0.9096 (mmm) REVERT: A 1308 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8238 (tp) REVERT: A 1311 MET cc_start: 0.8719 (mtt) cc_final: 0.8330 (mtm) REVERT: B 72 MET cc_start: 0.8739 (mpp) cc_final: 0.8486 (ppp) REVERT: B 139 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8809 (ttt) REVERT: B 216 MET cc_start: 0.8941 (mmm) cc_final: 0.8734 (mmm) REVERT: B 452 MET cc_start: 0.9324 (mmm) cc_final: 0.9019 (mmm) REVERT: B 499 MET cc_start: 0.9152 (ttp) cc_final: 0.8894 (ttp) REVERT: B 506 MET cc_start: 0.9012 (mpp) cc_final: 0.8543 (mpp) REVERT: B 649 THR cc_start: 0.9730 (OUTLIER) cc_final: 0.9530 (p) REVERT: B 755 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9419 (pp) REVERT: B 870 MET cc_start: 0.9053 (tmm) cc_final: 0.8832 (tmm) REVERT: C 56 MET cc_start: 0.8975 (tmm) cc_final: 0.8738 (tmm) REVERT: C 87 MET cc_start: 0.9362 (mmm) cc_final: 0.9030 (mmm) REVERT: E 54 ARG cc_start: 0.7983 (mmt180) cc_final: 0.7048 (mmp-170) REVERT: G 141 TYR cc_start: 0.9227 (m-10) cc_final: 0.8146 (m-80) REVERT: H 37 MET cc_start: 0.9103 (mmt) cc_final: 0.8829 (mmm) REVERT: I 42 LYS cc_start: 0.9422 (mmmt) cc_final: 0.8978 (mmtm) REVERT: I 45 LYS cc_start: 0.9372 (mmmm) cc_final: 0.9060 (mmmm) REVERT: I 85 ARG cc_start: 0.9127 (mmt90) cc_final: 0.8925 (mpp80) REVERT: K 64 GLU cc_start: 0.9050 (mp0) cc_final: 0.8837 (mp0) REVERT: K 104 MET cc_start: 0.9646 (ttm) cc_final: 0.9250 (ttm) REVERT: K 119 LYS cc_start: 0.9520 (tptt) cc_final: 0.9013 (tptp) REVERT: K 120 ASP cc_start: 0.9431 (t0) cc_final: 0.9028 (t0) REVERT: K 124 GLN cc_start: 0.9477 (mm110) cc_final: 0.9215 (mm-40) REVERT: L 23 HIS cc_start: 0.8786 (t-170) cc_final: 0.8574 (t-170) REVERT: L 44 MET cc_start: 0.9250 (mmm) cc_final: 0.8843 (mmm) REVERT: N 103 ILE cc_start: 0.8117 (mt) cc_final: 0.7578 (mm) REVERT: N 109 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.4883 (t80) REVERT: N 139 ASN cc_start: 0.9155 (p0) cc_final: 0.8927 (p0) REVERT: N 373 MET cc_start: 0.9025 (tmm) cc_final: 0.8702 (ppp) REVERT: O 85 MET cc_start: 0.9208 (ttm) cc_final: 0.8902 (ttt) REVERT: O 133 MET cc_start: 0.5246 (ptt) cc_final: 0.5033 (ptt) REVERT: O 139 MET cc_start: 0.8563 (mmp) cc_final: 0.8199 (mmp) REVERT: P 200 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: Q 111 MET cc_start: 0.8967 (mmm) cc_final: 0.8619 (mmm) outliers start: 56 outliers final: 21 residues processed: 265 average time/residue: 0.2461 time to fit residues: 109.1263 Evaluate side-chains 243 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 71 LYS Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 490 MET Chi-restraints excluded: chain P residue 200 GLN Chi-restraints excluded: chain Q residue 42 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 69 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 491 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 260 optimal weight: 10.0000 chunk 432 optimal weight: 20.0000 chunk 437 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 488 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN N 122 ASN ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.039765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.027886 restraints weight = 273522.174| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 4.34 r_work: 0.2649 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 40984 Z= 0.246 Angle : 0.654 21.486 55329 Z= 0.318 Chirality : 0.043 0.144 6207 Planarity : 0.004 0.053 7139 Dihedral : 4.826 59.629 5504 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 1.59 % Allowed : 6.49 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.12), residues: 5005 helix: 0.76 (0.13), residues: 1802 sheet: -1.13 (0.19), residues: 697 loop : -1.04 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 398 TYR 0.030 0.002 TYR K 70 PHE 0.012 0.001 PHE B 897 TRP 0.011 0.001 TRP I 106 HIS 0.011 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00540 (40962) covalent geometry : angle 0.62607 (55299) hydrogen bonds : bond 0.03505 ( 1566) hydrogen bonds : angle 4.60042 ( 4494) metal coordination : bond 0.01572 ( 22) metal coordination : angle 8.14306 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7714 (mmm) cc_final: 0.7207 (mmm) REVERT: A 871 MET cc_start: 0.8897 (tmm) cc_final: 0.8567 (tmm) REVERT: A 912 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9211 (mmm) REVERT: A 1288 MET cc_start: 0.9063 (mtm) cc_final: 0.8832 (mtp) REVERT: B 452 MET cc_start: 0.9380 (mmm) cc_final: 0.9111 (mmm) REVERT: B 478 MET cc_start: 0.9527 (mmp) cc_final: 0.9316 (mmm) REVERT: B 499 MET cc_start: 0.9248 (ttp) cc_final: 0.8957 (ttp) REVERT: B 506 MET cc_start: 0.9034 (mpp) cc_final: 0.8526 (mpp) REVERT: B 755 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9257 (pp) REVERT: B 870 MET cc_start: 0.9010 (tmm) cc_final: 0.8784 (tmm) REVERT: C 56 MET cc_start: 0.9032 (tmm) cc_final: 0.8709 (tmm) REVERT: C 87 MET cc_start: 0.9362 (mmm) cc_final: 0.9005 (mmm) REVERT: E 54 ARG cc_start: 0.8083 (mmt180) cc_final: 0.7219 (mmp-170) REVERT: G 45 CYS cc_start: 0.9530 (OUTLIER) cc_final: 0.9232 (t) REVERT: G 141 TYR cc_start: 0.9256 (m-10) cc_final: 0.8322 (m-80) REVERT: H 37 MET cc_start: 0.9070 (mmt) cc_final: 0.8799 (mmm) REVERT: I 42 LYS cc_start: 0.9432 (mmmt) cc_final: 0.8973 (mmtm) REVERT: I 45 LYS cc_start: 0.9365 (mmmm) cc_final: 0.9095 (mmmm) REVERT: K 64 GLU cc_start: 0.9041 (mp0) cc_final: 0.8827 (mp0) REVERT: K 104 MET cc_start: 0.9670 (ttm) cc_final: 0.9157 (ttm) REVERT: L 44 MET cc_start: 0.9233 (mmm) cc_final: 0.8750 (mmm) REVERT: M 60 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8961 (mmp) REVERT: N 109 PHE cc_start: 0.5684 (t80) cc_final: 0.4803 (t80) REVERT: N 139 ASN cc_start: 0.9173 (p0) cc_final: 0.8966 (p0) REVERT: O 139 MET cc_start: 0.8702 (mmp) cc_final: 0.8349 (mmp) REVERT: O 333 MET cc_start: 0.8748 (tpp) cc_final: 0.8511 (tpp) REVERT: O 520 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9492 (pt) outliers start: 71 outliers final: 31 residues processed: 272 average time/residue: 0.2482 time to fit residues: 113.1794 Evaluate side-chains 247 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 71 LYS Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 475 GLN Chi-restraints excluded: chain O residue 490 MET Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain Q residue 42 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 4 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 384 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN B 346 GLN B 544 ASN ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN I 81 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.039703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.027782 restraints weight = 275222.398| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 4.35 r_work: 0.2648 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 40984 Z= 0.227 Angle : 0.641 22.290 55329 Z= 0.308 Chirality : 0.043 0.158 6207 Planarity : 0.004 0.053 7139 Dihedral : 4.720 58.220 5504 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 1.61 % Allowed : 7.10 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 5005 helix: 1.03 (0.13), residues: 1804 sheet: -1.05 (0.19), residues: 695 loop : -0.92 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 398 TYR 0.024 0.001 TYR K 70 PHE 0.015 0.001 PHE A 462 TRP 0.011 0.001 TRP C 40 HIS 0.010 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00498 (40962) covalent geometry : angle 0.61284 (55299) hydrogen bonds : bond 0.03326 ( 1566) hydrogen bonds : angle 4.49793 ( 4494) metal coordination : bond 0.01508 ( 22) metal coordination : angle 8.12945 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 213 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7867 (mmm) cc_final: 0.7296 (mmm) REVERT: A 871 MET cc_start: 0.8941 (tmm) cc_final: 0.8622 (tmm) REVERT: A 912 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.9256 (mmm) REVERT: A 1288 MET cc_start: 0.9120 (mtm) cc_final: 0.8870 (mtp) REVERT: B 72 MET cc_start: 0.8656 (mpp) cc_final: 0.8023 (ppp) REVERT: B 216 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: B 499 MET cc_start: 0.9117 (ttp) cc_final: 0.8899 (ttp) REVERT: B 506 MET cc_start: 0.9083 (mpp) cc_final: 0.8630 (mpp) REVERT: B 649 THR cc_start: 0.9726 (OUTLIER) cc_final: 0.9511 (p) REVERT: B 755 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9262 (pp) REVERT: C 56 MET cc_start: 0.9010 (tmm) cc_final: 0.8694 (tmm) REVERT: C 87 MET cc_start: 0.9339 (mmm) cc_final: 0.9055 (mmm) REVERT: E 54 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7218 (mmp-170) REVERT: E 121 MET cc_start: 0.9048 (ptp) cc_final: 0.8702 (mtt) REVERT: G 45 CYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9241 (t) REVERT: G 141 TYR cc_start: 0.9218 (m-10) cc_final: 0.8228 (m-80) REVERT: G 143 ASP cc_start: 0.8734 (m-30) cc_final: 0.8304 (p0) REVERT: H 37 MET cc_start: 0.9019 (mmt) cc_final: 0.8774 (mmm) REVERT: I 42 LYS cc_start: 0.9410 (mmmt) cc_final: 0.8992 (mmtm) REVERT: K 66 GLU cc_start: 0.9100 (pt0) cc_final: 0.8887 (pm20) REVERT: K 104 MET cc_start: 0.9574 (ttm) cc_final: 0.9212 (ttm) REVERT: L 44 MET cc_start: 0.9234 (mmm) cc_final: 0.8833 (mmm) REVERT: M 60 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8857 (mmp) REVERT: M 99 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8738 (ptpt) REVERT: N 103 ILE cc_start: 0.8160 (mt) cc_final: 0.7592 (mm) REVERT: N 109 PHE cc_start: 0.5651 (t80) cc_final: 0.4730 (t80) REVERT: N 139 ASN cc_start: 0.9121 (p0) cc_final: 0.8861 (p0) REVERT: O 133 MET cc_start: 0.5677 (ptt) cc_final: 0.5415 (ptt) REVERT: O 333 MET cc_start: 0.8848 (tpp) cc_final: 0.8619 (tpp) REVERT: P 294 ASP cc_start: 0.9246 (p0) cc_final: 0.8710 (p0) REVERT: Q 111 MET cc_start: 0.9080 (mmm) cc_final: 0.8760 (mmm) outliers start: 72 outliers final: 37 residues processed: 270 average time/residue: 0.2451 time to fit residues: 110.9287 Evaluate side-chains 252 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 71 LYS Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 475 GLN Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 3 optimal weight: 6.9990 chunk 351 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 chunk 390 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 446 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 716 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.039701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.027818 restraints weight = 276040.651| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 4.36 r_work: 0.2651 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40984 Z= 0.192 Angle : 0.618 22.132 55329 Z= 0.297 Chirality : 0.042 0.143 6207 Planarity : 0.004 0.053 7139 Dihedral : 4.618 56.072 5504 Min Nonbonded Distance : 1.475 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 1.37 % Allowed : 7.68 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.12), residues: 5005 helix: 1.18 (0.13), residues: 1818 sheet: -1.01 (0.19), residues: 694 loop : -0.86 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 70 TYR 0.019 0.001 TYR K 70 PHE 0.018 0.001 PHE A 462 TRP 0.010 0.001 TRP C 40 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00423 (40962) covalent geometry : angle 0.59075 (55299) hydrogen bonds : bond 0.03164 ( 1566) hydrogen bonds : angle 4.42563 ( 4494) metal coordination : bond 0.01264 ( 22) metal coordination : angle 7.83460 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7648 (mmm) cc_final: 0.7373 (mmm) REVERT: A 332 MET cc_start: 0.8934 (mmm) cc_final: 0.8611 (mmm) REVERT: A 505 MET cc_start: 0.9310 (mmm) cc_final: 0.8960 (tpt) REVERT: A 871 MET cc_start: 0.8954 (tmm) cc_final: 0.8622 (tmm) REVERT: A 912 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9207 (mmm) REVERT: A 1288 MET cc_start: 0.9111 (mtm) cc_final: 0.8873 (mtp) REVERT: B 72 MET cc_start: 0.8690 (mpp) cc_final: 0.8014 (ppp) REVERT: B 216 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8363 (mtm) REVERT: B 499 MET cc_start: 0.9176 (ttp) cc_final: 0.8925 (ttp) REVERT: B 506 MET cc_start: 0.9061 (mpp) cc_final: 0.8575 (mpp) REVERT: B 649 THR cc_start: 0.9720 (OUTLIER) cc_final: 0.9510 (p) REVERT: B 755 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9387 (pp) REVERT: C 56 MET cc_start: 0.9025 (tmm) cc_final: 0.8693 (tmm) REVERT: C 87 MET cc_start: 0.9346 (mmm) cc_final: 0.9065 (mmm) REVERT: E 54 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7293 (mmp-170) REVERT: G 45 CYS cc_start: 0.9545 (OUTLIER) cc_final: 0.9227 (t) REVERT: G 141 TYR cc_start: 0.9201 (m-10) cc_final: 0.8269 (m-80) REVERT: G 143 ASP cc_start: 0.8735 (m-30) cc_final: 0.8293 (p0) REVERT: H 37 MET cc_start: 0.9021 (mmt) cc_final: 0.8769 (mmm) REVERT: K 64 GLU cc_start: 0.8887 (mp0) cc_final: 0.8599 (pm20) REVERT: K 104 MET cc_start: 0.9588 (ttm) cc_final: 0.9224 (ttm) REVERT: K 120 ASP cc_start: 0.9457 (t0) cc_final: 0.8973 (t0) REVERT: K 124 GLN cc_start: 0.9520 (mm110) cc_final: 0.9173 (mm-40) REVERT: L 44 MET cc_start: 0.9266 (mmm) cc_final: 0.8847 (mmm) REVERT: M 99 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8780 (ttmt) REVERT: N 103 ILE cc_start: 0.8212 (mt) cc_final: 0.7666 (mm) REVERT: N 109 PHE cc_start: 0.5654 (t80) cc_final: 0.4876 (t80) REVERT: N 139 ASN cc_start: 0.9104 (p0) cc_final: 0.8820 (p0) REVERT: O 85 MET cc_start: 0.9197 (ttm) cc_final: 0.8912 (ttt) REVERT: O 270 MET cc_start: 0.8920 (ppp) cc_final: 0.8691 (ppp) REVERT: O 273 MET cc_start: 0.8885 (mmp) cc_final: 0.8590 (mpp) REVERT: O 333 MET cc_start: 0.8871 (tpp) cc_final: 0.8647 (tpp) REVERT: O 520 ILE cc_start: 0.9695 (OUTLIER) cc_final: 0.9494 (pt) REVERT: P 294 ASP cc_start: 0.9269 (p0) cc_final: 0.8868 (p0) REVERT: Q 111 MET cc_start: 0.9112 (mmm) cc_final: 0.8808 (mmm) outliers start: 61 outliers final: 38 residues processed: 256 average time/residue: 0.2440 time to fit residues: 105.9015 Evaluate side-chains 251 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 71 LYS Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 475 GLN Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 490 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 253 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 365 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 296 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 448 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 282 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.040163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.028280 restraints weight = 273281.415| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 4.37 r_work: 0.2671 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40984 Z= 0.128 Angle : 0.583 19.773 55329 Z= 0.280 Chirality : 0.041 0.148 6207 Planarity : 0.003 0.054 7139 Dihedral : 4.488 55.476 5504 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 1.30 % Allowed : 8.29 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 5005 helix: 1.37 (0.13), residues: 1810 sheet: -0.90 (0.19), residues: 705 loop : -0.77 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 70 TYR 0.017 0.001 TYR K 70 PHE 0.018 0.001 PHE A 462 TRP 0.010 0.001 TRP G 16 HIS 0.006 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00284 (40962) covalent geometry : angle 0.56088 (55299) hydrogen bonds : bond 0.02973 ( 1566) hydrogen bonds : angle 4.30301 ( 4494) metal coordination : bond 0.00947 ( 22) metal coordination : angle 6.84470 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7634 (mmm) cc_final: 0.7136 (mmm) REVERT: A 332 MET cc_start: 0.8903 (mmm) cc_final: 0.8587 (mmm) REVERT: A 505 MET cc_start: 0.9349 (mmm) cc_final: 0.8899 (tpt) REVERT: A 871 MET cc_start: 0.8957 (tmm) cc_final: 0.8603 (tmm) REVERT: A 912 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9153 (mmm) REVERT: A 1288 MET cc_start: 0.9065 (mtm) cc_final: 0.8851 (mtp) REVERT: B 72 MET cc_start: 0.8653 (mpp) cc_final: 0.8000 (ppp) REVERT: B 139 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8921 (ttp) REVERT: B 216 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: B 499 MET cc_start: 0.9126 (ttp) cc_final: 0.8860 (ttp) REVERT: B 506 MET cc_start: 0.9076 (mpp) cc_final: 0.8599 (mpp) REVERT: B 649 THR cc_start: 0.9721 (OUTLIER) cc_final: 0.9518 (p) REVERT: B 755 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9364 (pp) REVERT: C 56 MET cc_start: 0.8992 (tmm) cc_final: 0.8665 (tmm) REVERT: C 87 MET cc_start: 0.9350 (mmm) cc_final: 0.9047 (mmm) REVERT: E 54 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7289 (mmp-170) REVERT: E 94 MET cc_start: 0.8601 (ttt) cc_final: 0.8027 (tmm) REVERT: G 45 CYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9212 (t) REVERT: G 141 TYR cc_start: 0.9186 (m-10) cc_final: 0.8279 (m-80) REVERT: G 143 ASP cc_start: 0.8671 (m-30) cc_final: 0.8215 (p0) REVERT: H 37 MET cc_start: 0.8959 (mmt) cc_final: 0.8673 (mmm) REVERT: I 42 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8877 (mmtm) REVERT: K 64 GLU cc_start: 0.8888 (mp0) cc_final: 0.8653 (pm20) REVERT: K 104 MET cc_start: 0.9579 (ttm) cc_final: 0.9229 (ttm) REVERT: K 120 ASP cc_start: 0.9450 (t0) cc_final: 0.9112 (t0) REVERT: K 124 GLN cc_start: 0.9520 (mm110) cc_final: 0.9186 (mm110) REVERT: L 44 MET cc_start: 0.9242 (mmm) cc_final: 0.8831 (mmm) REVERT: M 99 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8725 (ttmt) REVERT: N 103 ILE cc_start: 0.8133 (mt) cc_final: 0.7617 (mm) REVERT: N 109 PHE cc_start: 0.5760 (t80) cc_final: 0.4888 (t80) REVERT: N 132 MET cc_start: 0.8728 (ptm) cc_final: 0.8527 (ppp) REVERT: N 139 ASN cc_start: 0.9147 (p0) cc_final: 0.8863 (p0) REVERT: O 118 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.9172 (tpt) REVERT: O 333 MET cc_start: 0.8857 (tpp) cc_final: 0.8639 (tpp) REVERT: P 196 ARG cc_start: 0.9348 (ttm110) cc_final: 0.9118 (ptp-110) REVERT: P 294 ASP cc_start: 0.9251 (p0) cc_final: 0.8843 (p0) REVERT: Q 57 MET cc_start: 0.9083 (mtt) cc_final: 0.8722 (mmt) REVERT: Q 111 MET cc_start: 0.9108 (mmm) cc_final: 0.8812 (mmm) outliers start: 58 outliers final: 32 residues processed: 256 average time/residue: 0.2420 time to fit residues: 104.7779 Evaluate side-chains 248 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 475 GLN Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 382 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN B 260 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN O 534 GLN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.039757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.027971 restraints weight = 274917.037| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.33 r_work: 0.2660 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40984 Z= 0.182 Angle : 0.613 16.659 55329 Z= 0.296 Chirality : 0.042 0.165 6207 Planarity : 0.004 0.050 7139 Dihedral : 4.460 54.095 5504 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 1.30 % Allowed : 8.60 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 5005 helix: 1.40 (0.13), residues: 1813 sheet: -0.83 (0.19), residues: 698 loop : -0.71 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 70 TYR 0.014 0.001 TYR K 70 PHE 0.017 0.001 PHE A 462 TRP 0.010 0.001 TRP G 16 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00403 (40962) covalent geometry : angle 0.59474 (55299) hydrogen bonds : bond 0.03049 ( 1566) hydrogen bonds : angle 4.31543 ( 4494) metal coordination : bond 0.01227 ( 22) metal coordination : angle 6.48558 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7638 (mmm) cc_final: 0.7225 (mmm) REVERT: A 332 MET cc_start: 0.8923 (mmm) cc_final: 0.8584 (mmm) REVERT: A 505 MET cc_start: 0.9369 (mmm) cc_final: 0.8846 (tpt) REVERT: A 871 MET cc_start: 0.8987 (tmm) cc_final: 0.8636 (tmm) REVERT: A 912 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.9135 (mmm) REVERT: A 1288 MET cc_start: 0.9115 (mtm) cc_final: 0.8905 (mtp) REVERT: B 72 MET cc_start: 0.8624 (mpp) cc_final: 0.7996 (ppp) REVERT: B 139 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8731 (ttt) REVERT: B 216 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8304 (mtm) REVERT: B 499 MET cc_start: 0.9102 (ttp) cc_final: 0.8863 (ttp) REVERT: B 506 MET cc_start: 0.9085 (mpp) cc_final: 0.8621 (mpp) REVERT: B 649 THR cc_start: 0.9721 (OUTLIER) cc_final: 0.9520 (p) REVERT: B 755 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9352 (pp) REVERT: C 56 MET cc_start: 0.9025 (tmm) cc_final: 0.8694 (tmm) REVERT: C 87 MET cc_start: 0.9327 (mmm) cc_final: 0.9072 (mmm) REVERT: D 58 CYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7957 (p) REVERT: E 54 ARG cc_start: 0.7952 (mmt180) cc_final: 0.7243 (mmp-170) REVERT: E 94 MET cc_start: 0.8630 (ttt) cc_final: 0.8072 (tmm) REVERT: G 45 CYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9259 (t) REVERT: G 141 TYR cc_start: 0.9180 (m-10) cc_final: 0.8273 (m-80) REVERT: G 143 ASP cc_start: 0.8708 (m-30) cc_final: 0.8266 (p0) REVERT: H 37 MET cc_start: 0.8964 (mmt) cc_final: 0.8692 (mmm) REVERT: I 42 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8971 (mmtm) REVERT: K 64 GLU cc_start: 0.8874 (mp0) cc_final: 0.8672 (pm20) REVERT: K 104 MET cc_start: 0.9589 (ttm) cc_final: 0.9261 (ttm) REVERT: K 120 ASP cc_start: 0.9450 (t0) cc_final: 0.9100 (t0) REVERT: K 124 GLN cc_start: 0.9523 (mm110) cc_final: 0.9190 (mm110) REVERT: L 44 MET cc_start: 0.9248 (mmm) cc_final: 0.8782 (mmm) REVERT: M 99 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8702 (ttmt) REVERT: N 103 ILE cc_start: 0.8154 (mt) cc_final: 0.7640 (mm) REVERT: N 109 PHE cc_start: 0.5665 (t80) cc_final: 0.4785 (t80) REVERT: N 139 ASN cc_start: 0.9133 (p0) cc_final: 0.8843 (p0) REVERT: O 85 MET cc_start: 0.9177 (ttm) cc_final: 0.8897 (ttt) REVERT: O 273 MET cc_start: 0.8908 (mmp) cc_final: 0.8591 (mpp) REVERT: O 333 MET cc_start: 0.8862 (tpp) cc_final: 0.8652 (tpp) REVERT: O 531 MET cc_start: 0.8792 (mmm) cc_final: 0.8195 (mmm) REVERT: P 196 ARG cc_start: 0.9347 (ttm110) cc_final: 0.9119 (ptp-110) REVERT: P 294 ASP cc_start: 0.9234 (p0) cc_final: 0.8843 (p0) REVERT: Q 57 MET cc_start: 0.9075 (mtt) cc_final: 0.8790 (mmt) REVERT: Q 111 MET cc_start: 0.9080 (mmm) cc_final: 0.8779 (mmm) outliers start: 58 outliers final: 37 residues processed: 253 average time/residue: 0.2513 time to fit residues: 108.1051 Evaluate side-chains 253 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 475 GLN Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 161 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 408 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 385 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.039676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.027933 restraints weight = 274724.936| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 4.32 r_work: 0.2658 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40984 Z= 0.189 Angle : 0.621 15.512 55329 Z= 0.299 Chirality : 0.042 0.163 6207 Planarity : 0.004 0.048 7139 Dihedral : 4.462 53.176 5504 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 1.16 % Allowed : 8.73 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 5005 helix: 1.45 (0.13), residues: 1815 sheet: -0.87 (0.19), residues: 718 loop : -0.66 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 70 TYR 0.014 0.001 TYR K 70 PHE 0.017 0.001 PHE A 462 TRP 0.010 0.001 TRP G 16 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00419 (40962) covalent geometry : angle 0.60274 (55299) hydrogen bonds : bond 0.03036 ( 1566) hydrogen bonds : angle 4.32105 ( 4494) metal coordination : bond 0.01240 ( 22) metal coordination : angle 6.52800 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7599 (mmm) cc_final: 0.7202 (mmm) REVERT: A 332 MET cc_start: 0.8920 (mmm) cc_final: 0.8560 (mmm) REVERT: A 505 MET cc_start: 0.9393 (mmm) cc_final: 0.8865 (tpt) REVERT: A 871 MET cc_start: 0.9017 (tmm) cc_final: 0.8672 (tmm) REVERT: A 912 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.9151 (mmm) REVERT: A 1288 MET cc_start: 0.9121 (mtm) cc_final: 0.8910 (mtp) REVERT: A 1353 MET cc_start: 0.8928 (ptt) cc_final: 0.8664 (ptt) REVERT: B 72 MET cc_start: 0.8637 (mpp) cc_final: 0.7986 (ppp) REVERT: B 216 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8334 (mtm) REVERT: B 499 MET cc_start: 0.9120 (ttp) cc_final: 0.8891 (ttp) REVERT: B 506 MET cc_start: 0.9054 (mpp) cc_final: 0.8637 (mpp) REVERT: B 649 THR cc_start: 0.9719 (OUTLIER) cc_final: 0.9518 (p) REVERT: B 755 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9348 (pp) REVERT: C 56 MET cc_start: 0.9011 (tmm) cc_final: 0.8677 (tmm) REVERT: C 87 MET cc_start: 0.9317 (mmm) cc_final: 0.9065 (mmm) REVERT: D 58 CYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8010 (p) REVERT: E 54 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7223 (mmp-170) REVERT: E 94 MET cc_start: 0.8622 (ttt) cc_final: 0.8279 (tmm) REVERT: G 45 CYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9258 (t) REVERT: G 141 TYR cc_start: 0.9182 (m-10) cc_final: 0.8265 (m-80) REVERT: G 143 ASP cc_start: 0.8720 (m-30) cc_final: 0.8271 (p0) REVERT: G 144 THR cc_start: 0.9104 (p) cc_final: 0.8896 (p) REVERT: K 104 MET cc_start: 0.9591 (ttm) cc_final: 0.9263 (ttm) REVERT: K 120 ASP cc_start: 0.9460 (t0) cc_final: 0.9102 (t0) REVERT: K 124 GLN cc_start: 0.9526 (mm110) cc_final: 0.9191 (mm110) REVERT: L 44 MET cc_start: 0.9255 (mmm) cc_final: 0.8783 (mmm) REVERT: M 99 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8739 (ttmt) REVERT: N 103 ILE cc_start: 0.8187 (mt) cc_final: 0.7684 (mm) REVERT: N 109 PHE cc_start: 0.5689 (t80) cc_final: 0.4813 (t80) REVERT: N 139 ASN cc_start: 0.9137 (p0) cc_final: 0.8840 (p0) REVERT: O 85 MET cc_start: 0.9173 (ttm) cc_final: 0.8892 (ttt) REVERT: O 273 MET cc_start: 0.8911 (mmp) cc_final: 0.8590 (mpp) REVERT: O 333 MET cc_start: 0.8867 (tpp) cc_final: 0.8659 (tpp) REVERT: P 196 ARG cc_start: 0.9353 (ttm110) cc_final: 0.9120 (ptp-110) REVERT: P 294 ASP cc_start: 0.9236 (p0) cc_final: 0.8855 (p0) REVERT: Q 57 MET cc_start: 0.9066 (mtt) cc_final: 0.8778 (mmt) REVERT: Q 111 MET cc_start: 0.9080 (mmm) cc_final: 0.8780 (mmm) outliers start: 52 outliers final: 38 residues processed: 250 average time/residue: 0.2383 time to fit residues: 101.7007 Evaluate side-chains 249 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 475 GLN Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 134 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 316 optimal weight: 8.9990 chunk 441 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 405 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 282 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN O 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.039238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.027378 restraints weight = 278508.947| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 4.32 r_work: 0.2634 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 40984 Z= 0.272 Angle : 0.691 17.545 55329 Z= 0.332 Chirality : 0.043 0.171 6207 Planarity : 0.004 0.049 7139 Dihedral : 4.611 51.837 5504 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 1.16 % Allowed : 8.69 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 5005 helix: 1.36 (0.13), residues: 1838 sheet: -0.92 (0.19), residues: 708 loop : -0.69 (0.13), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 70 TYR 0.020 0.002 TYR B 357 PHE 0.027 0.001 PHE O 148 TRP 0.011 0.001 TRP A 337 HIS 0.012 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00597 (40962) covalent geometry : angle 0.67051 (55299) hydrogen bonds : bond 0.03255 ( 1566) hydrogen bonds : angle 4.45086 ( 4494) metal coordination : bond 0.01660 ( 22) metal coordination : angle 7.22145 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10010 Ramachandran restraints generated. 5005 Oldfield, 0 Emsley, 5005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7603 (mmm) cc_final: 0.7237 (mmm) REVERT: A 332 MET cc_start: 0.8968 (mmm) cc_final: 0.8611 (mmm) REVERT: A 505 MET cc_start: 0.9401 (mmm) cc_final: 0.8862 (tpt) REVERT: A 871 MET cc_start: 0.9021 (tmm) cc_final: 0.8678 (tmm) REVERT: A 912 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.9121 (mmm) REVERT: A 1288 MET cc_start: 0.9183 (mtm) cc_final: 0.8899 (mtp) REVERT: B 72 MET cc_start: 0.8673 (mpp) cc_final: 0.7990 (ppp) REVERT: B 216 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: B 478 MET cc_start: 0.9514 (mmp) cc_final: 0.9266 (mmm) REVERT: B 499 MET cc_start: 0.9147 (ttp) cc_final: 0.8940 (ttp) REVERT: B 506 MET cc_start: 0.9032 (mpp) cc_final: 0.8388 (mpp) REVERT: B 649 THR cc_start: 0.9711 (OUTLIER) cc_final: 0.9507 (p) REVERT: B 755 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9244 (pp) REVERT: C 56 MET cc_start: 0.9044 (tmm) cc_final: 0.8701 (tmm) REVERT: C 87 MET cc_start: 0.9320 (mmm) cc_final: 0.9024 (mmm) REVERT: D 58 CYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8029 (p) REVERT: E 54 ARG cc_start: 0.7977 (mmt180) cc_final: 0.7329 (mmp-170) REVERT: G 45 CYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9280 (t) REVERT: G 141 TYR cc_start: 0.9188 (m-10) cc_final: 0.8226 (m-80) REVERT: G 143 ASP cc_start: 0.8679 (m-30) cc_final: 0.8225 (p0) REVERT: G 144 THR cc_start: 0.9086 (p) cc_final: 0.8824 (p) REVERT: K 104 MET cc_start: 0.9623 (ttm) cc_final: 0.9291 (ttm) REVERT: K 120 ASP cc_start: 0.9443 (t0) cc_final: 0.9054 (t0) REVERT: K 124 GLN cc_start: 0.9518 (mm110) cc_final: 0.9166 (mm110) REVERT: L 44 MET cc_start: 0.9295 (mmm) cc_final: 0.8783 (mmm) REVERT: M 99 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8771 (ttmt) REVERT: N 103 ILE cc_start: 0.8310 (mt) cc_final: 0.7804 (mm) REVERT: N 109 PHE cc_start: 0.5602 (t80) cc_final: 0.4710 (t80) REVERT: N 139 ASN cc_start: 0.9141 (p0) cc_final: 0.8839 (p0) REVERT: O 273 MET cc_start: 0.8933 (mmp) cc_final: 0.8614 (mpp) REVERT: O 531 MET cc_start: 0.8772 (mmm) cc_final: 0.8104 (mmm) REVERT: P 196 ARG cc_start: 0.9300 (ttm110) cc_final: 0.9082 (ptp-110) REVERT: P 294 ASP cc_start: 0.9256 (p0) cc_final: 0.8898 (p0) REVERT: Q 57 MET cc_start: 0.9067 (mtt) cc_final: 0.8758 (mmt) REVERT: Q 111 MET cc_start: 0.9102 (mmm) cc_final: 0.8821 (mmm) outliers start: 52 outliers final: 38 residues processed: 247 average time/residue: 0.2308 time to fit residues: 98.1972 Evaluate side-chains 251 residues out of total 4465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 475 GLN Chi-restraints excluded: chain P residue 250 MET Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 416 optimal weight: 1.9990 chunk 492 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 404 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 197 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.039809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.028085 restraints weight = 273389.548| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 4.30 r_work: 0.2666 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40984 Z= 0.144 Angle : 0.618 16.211 55329 Z= 0.295 Chirality : 0.042 0.185 6207 Planarity : 0.003 0.051 7139 Dihedral : 4.496 53.069 5504 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 1.05 % Allowed : 9.05 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 5005 helix: 1.49 (0.13), residues: 1830 sheet: -0.87 (0.19), residues: 713 loop : -0.61 (0.13), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 70 TYR 0.023 0.001 TYR K 70 PHE 0.021 0.001 PHE O 148 TRP 0.010 0.001 TRP O 235 HIS 0.007 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00322 (40962) covalent geometry : angle 0.59709 (55299) hydrogen bonds : bond 0.02980 ( 1566) hydrogen bonds : angle 4.31789 ( 4494) metal coordination : bond 0.00997 ( 22) metal coordination : angle 6.87310 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10529.19 seconds wall clock time: 181 minutes 39.30 seconds (10899.30 seconds total)