Starting phenix.real_space_refine on Mon Dec 30 13:33:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v3u_31684/12_2024/7v3u_31684.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v3u_31684/12_2024/7v3u_31684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v3u_31684/12_2024/7v3u_31684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v3u_31684/12_2024/7v3u_31684.map" model { file = "/net/cci-nas-00/data/ceres_data/7v3u_31684/12_2024/7v3u_31684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v3u_31684/12_2024/7v3u_31684.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 34 5.49 5 Mg 12 5.21 5 S 297 5.16 5 C 39267 2.51 5 N 10931 2.21 5 O 12095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 273 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 62646 Number of models: 1 Model: "" Number of chains: 24 Chain: "2" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "3" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "4" Number of atoms: 5509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5509 Classifications: {'peptide': 692} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5143 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "7" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "B" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "C" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "D" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5323 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5143 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "G" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1302 SG CYS 2 341 93.746 112.830 65.295 1.00 75.28 S ATOM 1325 SG CYS 2 344 97.167 111.084 65.438 1.00 79.22 S ATOM 1483 SG CYS 2 364 95.332 111.588 62.120 1.00 80.80 S ATOM 1504 SG CYS 2 367 94.094 109.062 64.601 1.00 85.84 S ATOM 11586 SG CYS 4 349 52.482 121.748 46.875 1.00 43.84 S ATOM 11607 SG CYS 4 352 50.162 121.050 44.115 1.00 51.06 S ATOM 11754 SG CYS 4 371 48.817 120.506 47.562 1.00 56.66 S ATOM 11796 SG CYS 4 376 51.522 118.155 46.114 1.00 69.30 S ATOM 16779 SG CYS 5 183 85.614 110.847 87.974 1.00 30.85 S ATOM 16804 SG CYS 5 186 87.123 107.147 88.741 1.00 36.10 S ATOM 16991 SG CYS 5 211 88.084 108.984 85.828 1.00 38.53 S ATOM 17109 SG CYS 5 236 84.456 107.895 86.025 1.00 46.83 S ATOM 21857 SG CYS 6 311 71.291 116.989 48.554 1.00 97.48 S ATOM 21879 SG CYS 6 314 71.790 114.417 45.781 1.00101.92 S ATOM 22036 SG CYS 6 333 68.194 115.837 46.355 1.00 99.76 S ATOM 22070 SG CYS 6 338 69.922 113.554 48.776 1.00110.45 S ATOM 27590 SG CYS 7 262 41.029 122.804 73.074 1.00 26.56 S ATOM 27613 SG CYS 7 265 39.123 120.839 75.708 1.00 27.28 S ATOM 27767 SG CYS 7 284 42.872 121.540 76.110 1.00 25.62 S ATOM 27804 SG CYS 7 289 41.632 119.031 73.598 1.00 32.45 S ATOM 32525 SG CYS B 341 61.549 112.483 65.607 1.00 68.84 S ATOM 32548 SG CYS B 344 58.248 114.399 65.440 1.00 72.50 S ATOM 32706 SG CYS B 364 60.199 113.631 62.225 1.00 74.77 S ATOM 32727 SG CYS B 367 61.587 116.129 64.645 1.00 75.83 S ATOM 42623 SG CYS D 349 103.142 103.282 46.814 1.00 61.68 S ATOM 42644 SG CYS D 352 105.361 104.052 43.944 1.00 67.72 S ATOM 42791 SG CYS D 371 106.593 104.585 47.537 1.00 73.61 S ATOM 42833 SG CYS D 376 103.945 106.927 45.940 1.00 81.75 S ATOM 47816 SG CYS E 183 69.948 114.462 88.060 1.00 28.23 S ATOM 47841 SG CYS E 186 68.574 118.240 88.751 1.00 34.13 S ATOM 48028 SG CYS E 211 67.581 116.295 85.862 1.00 38.03 S ATOM 48146 SG CYS E 236 71.213 117.325 86.041 1.00 44.54 S ATOM 52894 SG CYS F 311 84.141 108.278 48.548 1.00 98.82 S ATOM 52916 SG CYS F 314 83.846 110.793 45.627 1.00101.13 S ATOM 53073 SG CYS F 333 87.199 108.853 46.155 1.00100.75 S ATOM 53107 SG CYS F 338 85.882 111.489 48.504 1.00109.55 S ATOM 58627 SG CYS G 262 114.614 102.338 72.963 1.00 27.94 S ATOM 58650 SG CYS G 265 116.503 104.282 75.611 1.00 28.40 S ATOM 58804 SG CYS G 284 112.725 103.591 75.985 1.00 29.52 S ATOM 58841 SG CYS G 289 113.979 106.117 73.530 1.00 36.28 S Time building chain proxies: 28.68, per 1000 atoms: 0.46 Number of scatterers: 62646 At special positions: 0 Unit cell: (156.748, 226.18, 148.332, 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 10 29.99 S 297 16.00 P 34 15.00 Mg 12 11.99 O 12095 8.00 N 10931 7.00 C 39267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.03 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: 11.96 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 22003 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 341 " pdb=" ZN 42003 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 371 " pdb=" ZN 52003 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 186 " pdb=" ZN 62003 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 333 " pdb=" ZN 72003 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 262 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 367 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 364 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 341 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 344 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 349 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 352 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 371 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 376 " pdb=" ZN E2003 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 211 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 236 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 183 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 186 " pdb=" ZN F2003 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 338 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 314 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 311 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 333 " pdb=" ZN G2003 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 284 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 265 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 289 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 262 " Number of angles added : 60 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14996 Finding SS restraints... Secondary structure from input PDB file: 305 helices and 89 sheets defined 44.9% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.17 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 removed outlier: 3.689A pdb=" N ASN 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 removed outlier: 3.823A pdb=" N GLN 2 200 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 200 through 218 Processing helix chain '2' and resid 225 through 238 Processing helix chain '2' and resid 246 through 253 Processing helix chain '2' and resid 253 through 263 Processing helix chain '2' and resid 263 through 283 removed outlier: 4.044A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 290 removed outlier: 4.077A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 305 through 309 removed outlier: 4.100A pdb=" N LEU 2 309 " --> pdb=" O LEU 2 306 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 3.611A pdb=" N ASN 2 313 " --> pdb=" O ARG 2 310 " (cutoff:3.500A) Processing helix chain '2' and resid 411 through 415 removed outlier: 4.069A pdb=" N VAL 2 415 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 489 Processing helix chain '2' and resid 492 through 501 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 removed outlier: 3.507A pdb=" N ILE 2 552 " --> pdb=" O ALA 2 548 " (cutoff:3.500A) Processing helix chain '2' and resid 593 through 599 removed outlier: 3.860A pdb=" N VAL 2 597 " --> pdb=" O GLY 2 593 " (cutoff:3.500A) Processing helix chain '2' and resid 608 through 612 removed outlier: 4.136A pdb=" N MET 2 612 " --> pdb=" O PHE 2 609 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 626 Processing helix chain '2' and resid 652 through 656 removed outlier: 3.793A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 670 through 675 Processing helix chain '2' and resid 688 through 706 Processing helix chain '2' and resid 759 through 774 removed outlier: 3.687A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 779 through 781 No H-bonds generated for 'chain '2' and resid 779 through 781' Processing helix chain '2' and resid 782 through 801 removed outlier: 4.196A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 3.944A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET 2 823 " --> pdb=" O SER 2 819 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 Processing helix chain '2' and resid 850 through 861 removed outlier: 3.585A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG 2 859 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) Processing helix chain '2' and resid 861 through 866 Processing helix chain '3' and resid 18 through 35 Processing helix chain '3' and resid 35 through 59 removed outlier: 4.162A pdb=" N ARG 3 39 " --> pdb=" O PHE 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 136 removed outlier: 3.529A pdb=" N PHE 3 121 " --> pdb=" O GLU 3 117 " (cutoff:3.500A) Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 343 through 355 removed outlier: 3.618A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 366 removed outlier: 3.556A pdb=" N ILE 3 362 " --> pdb=" O ASP 3 358 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER 3 364 " --> pdb=" O PHE 3 360 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 438 through 443 Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 475 through 478 removed outlier: 3.591A pdb=" N MET 3 478 " --> pdb=" O PHE 3 475 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 475 through 478' Processing helix chain '3' and resid 479 through 493 removed outlier: 3.963A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 Processing helix chain '3' and resid 536 through 543 Processing helix chain '3' and resid 554 through 569 Processing helix chain '3' and resid 652 through 666 removed outlier: 3.551A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 688 removed outlier: 3.987A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 716 removed outlier: 4.306A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.595A pdb=" N PHE 3 735 " --> pdb=" O ASN 3 731 " (cutoff:3.500A) Processing helix chain '4' and resid 186 through 200 Processing helix chain '4' and resid 202 through 210 removed outlier: 3.967A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 217 through 222 removed outlier: 3.639A pdb=" N ASP 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU 4 222 " --> pdb=" O ASN 4 218 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 217 through 222' Processing helix chain '4' and resid 224 through 236 Processing helix chain '4' and resid 245 through 251 removed outlier: 3.658A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.552A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 287 removed outlier: 3.937A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 299 removed outlier: 4.084A pdb=" N ILE 4 296 " --> pdb=" O ASP 4 292 " (cutoff:3.500A) Processing helix chain '4' and resid 318 through 322 removed outlier: 3.533A pdb=" N ILE 4 322 " --> pdb=" O PRO 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 422 through 424 No H-bonds generated for 'chain '4' and resid 422 through 424' Processing helix chain '4' and resid 481 through 492 Processing helix chain '4' and resid 502 through 514 removed outlier: 3.572A pdb=" N LEU 4 506 " --> pdb=" O THR 4 502 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 525 Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 597 through 602 removed outlier: 3.739A pdb=" N THR 4 602 " --> pdb=" O ALA 4 598 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 638 through 643 Processing helix chain '4' and resid 644 through 652 removed outlier: 4.249A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 701 removed outlier: 3.863A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 713 through 727 removed outlier: 3.771A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) Processing helix chain '4' and resid 728 through 730 No H-bonds generated for 'chain '4' and resid 728 through 730' Processing helix chain '4' and resid 743 through 758 Processing helix chain '4' and resid 763 through 781 Processing helix chain '4' and resid 794 through 812 removed outlier: 3.632A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 833 removed outlier: 3.538A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '5' and resid 23 through 38 Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 82 removed outlier: 3.583A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 107 Proline residue: 5 88 - end of helix removed outlier: 3.664A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 5 104 " --> pdb=" O ARG 5 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG 5 106 " --> pdb=" O SER 5 102 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA 5 107 " --> pdb=" O ILE 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 removed outlier: 3.622A pdb=" N LEU 5 151 " --> pdb=" O LEU 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 152 through 156 Processing helix chain '5' and resid 212 through 217 Processing helix chain '5' and resid 281 through 283 No H-bonds generated for 'chain '5' and resid 281 through 283' Processing helix chain '5' and resid 350 through 362 Processing helix chain '5' and resid 365 through 374 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 486 through 499 Processing helix chain '5' and resid 535 through 540 removed outlier: 3.641A pdb=" N ILE 5 540 " --> pdb=" O PRO 5 536 " (cutoff:3.500A) Processing helix chain '5' and resid 544 through 550 removed outlier: 3.596A pdb=" N SER 5 548 " --> pdb=" O THR 5 544 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 578 removed outlier: 3.663A pdb=" N SER 5 567 " --> pdb=" O GLU 5 563 " (cutoff:3.500A) Processing helix chain '5' and resid 578 through 591 Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 641 removed outlier: 3.570A pdb=" N ALA 5 619 " --> pdb=" O SER 5 615 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG 5 630 " --> pdb=" O PHE 5 626 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 667 removed outlier: 3.604A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 695 removed outlier: 3.624A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 122 removed outlier: 3.689A pdb=" N GLU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 147 removed outlier: 3.631A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 160 Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 197 Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 407 through 411 removed outlier: 4.335A pdb=" N GLY 6 411 " --> pdb=" O THR 6 408 " (cutoff:3.500A) Processing helix chain '6' and resid 500 through 506 removed outlier: 3.580A pdb=" N PHE 6 504 " --> pdb=" O ASP 6 500 " (cutoff:3.500A) Processing helix chain '6' and resid 509 through 522 Processing helix chain '6' and resid 524 through 533 Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 removed outlier: 3.950A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 609 Processing helix chain '6' and resid 626 through 631 Processing helix chain '6' and resid 645 through 659 removed outlier: 4.052A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 709 removed outlier: 3.877A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE 6 709 " --> pdb=" O ILE 6 705 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 738 Processing helix chain '6' and resid 739 through 742 Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 766 through 788 removed outlier: 3.715A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 789 through 791 No H-bonds generated for 'chain '6' and resid 789 through 791' Processing helix chain '6' and resid 796 through 814 Processing helix chain '6' and resid 820 through 835 removed outlier: 3.671A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain '7' and resid 15 through 28 Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 82 through 96 Processing helix chain '7' and resid 101 through 109 Processing helix chain '7' and resid 109 through 124 removed outlier: 3.906A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 165 removed outlier: 3.543A pdb=" N ASN 7 165 " --> pdb=" O ILE 7 161 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 189 Processing helix chain '7' and resid 193 through 198 removed outlier: 3.977A pdb=" N ARG 7 198 " --> pdb=" O ASN 7 195 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 215 Processing helix chain '7' and resid 231 through 235 Processing helix chain '7' and resid 286 through 292 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 394 through 408 removed outlier: 3.635A pdb=" N GLU 7 398 " --> pdb=" O THR 7 394 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU 7 399 " --> pdb=" O SER 7 395 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY 7 408 " --> pdb=" O LEU 7 404 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 417 Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 removed outlier: 3.645A pdb=" N LEU 7 469 " --> pdb=" O ALA 7 465 " (cutoff:3.500A) Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 525 through 529 removed outlier: 3.673A pdb=" N MET 7 529 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 544 removed outlier: 4.261A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 584 Processing helix chain '7' and resid 587 through 594 removed outlier: 3.697A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.671A pdb=" N ASP 7 609 " --> pdb=" O SER 7 605 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 648 removed outlier: 3.827A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 674 Processing helix chain '7' and resid 685 through 703 Processing helix chain '7' and resid 709 through 730 removed outlier: 3.557A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 removed outlier: 3.583A pdb=" N ASN B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 removed outlier: 3.597A pdb=" N GLN B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 218 removed outlier: 3.549A pdb=" N TYR B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 263 through 283 removed outlier: 4.157A pdb=" N MET B 267 " --> pdb=" O CYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.974A pdb=" N ILE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.822A pdb=" N LEU B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 411 through 415 removed outlier: 4.127A pdb=" N VAL B 415 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.601A pdb=" N ILE B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 599 removed outlier: 3.878A pdb=" N VAL B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 612 removed outlier: 3.603A pdb=" N LYS B 611 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET B 612 " --> pdb=" O PHE B 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 608 through 612' Processing helix chain 'B' and resid 613 through 626 Processing helix chain 'B' and resid 652 through 656 removed outlier: 4.014A pdb=" N ARG B 656 " --> pdb=" O ASN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.821A pdb=" N ARG B 676 " --> pdb=" O PRO B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 Processing helix chain 'B' and resid 759 through 774 removed outlier: 4.024A pdb=" N LYS B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 781 No H-bonds generated for 'chain 'B' and resid 779 through 781' Processing helix chain 'B' and resid 782 through 801 removed outlier: 4.187A pdb=" N VAL B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 787 " --> pdb=" O MET B 783 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG B 788 " --> pdb=" O ASP B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 824 removed outlier: 3.978A pdb=" N LEU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 824 " --> pdb=" O PHE B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 removed outlier: 3.631A pdb=" N ALA B 848 " --> pdb=" O SER B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 861 removed outlier: 3.743A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'C' and resid 18 through 35 Processing helix chain 'C' and resid 35 through 59 removed outlier: 4.100A pdb=" N ARG C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 117 through 137 removed outlier: 3.583A pdb=" N PHE C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.535A pdb=" N LYS C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 removed outlier: 3.635A pdb=" N GLN C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 414 through 426 removed outlier: 3.512A pdb=" N LEU C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 475 through 478 Processing helix chain 'C' and resid 479 through 493 removed outlier: 3.890A pdb=" N GLU C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 534 Processing helix chain 'C' and resid 536 through 543 Processing helix chain 'C' and resid 554 through 569 Processing helix chain 'C' and resid 652 through 666 Processing helix chain 'C' and resid 672 through 688 removed outlier: 3.810A pdb=" N VAL C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 688 " --> pdb=" O THR C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 716 removed outlier: 4.065A pdb=" N GLU C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 738 removed outlier: 3.529A pdb=" N PHE C 735 " --> pdb=" O ASN C 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.851A pdb=" N ARG D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 237 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 254 through 264 removed outlier: 4.025A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 287 removed outlier: 3.607A pdb=" N SER D 270 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 284 " --> pdb=" O MET D 280 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 4.032A pdb=" N ILE D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.723A pdb=" N ILE D 322 " --> pdb=" O PRO D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.661A pdb=" N LEU D 506 " --> pdb=" O THR D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 525 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 573 through 585 removed outlier: 3.528A pdb=" N ILE D 577 " --> pdb=" O SER D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 633 through 637 Processing helix chain 'D' and resid 638 through 643 Processing helix chain 'D' and resid 644 through 652 removed outlier: 4.323A pdb=" N VAL D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 693 Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 713 through 726 removed outlier: 3.597A pdb=" N ASP D 717 " --> pdb=" O ASP D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 730 removed outlier: 4.054A pdb=" N GLU D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 727 through 730' Processing helix chain 'D' and resid 743 through 758 Processing helix chain 'D' and resid 763 through 781 Processing helix chain 'D' and resid 794 through 812 removed outlier: 3.504A pdb=" N LYS D 812 " --> pdb=" O HIS D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 833 removed outlier: 3.628A pdb=" N ILE D 833 " --> pdb=" O ILE D 829 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 82 through 107 Proline residue: E 88 - end of helix removed outlier: 3.685A pdb=" N ARG E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.585A pdb=" N LEU E 151 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.519A pdb=" N VAL E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 350 through 362 Processing helix chain 'E' and resid 365 through 373 Processing helix chain 'E' and resid 381 through 394 Processing helix chain 'E' and resid 421 through 433 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 486 through 498 Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.614A pdb=" N ILE E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 550 removed outlier: 4.153A pdb=" N LEU E 547 " --> pdb=" O GLN E 543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER E 548 " --> pdb=" O THR E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 578 removed outlier: 3.814A pdb=" N SER E 567 " --> pdb=" O GLU E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 591 Processing helix chain 'E' and resid 595 through 610 Processing helix chain 'E' and resid 615 through 641 removed outlier: 3.599A pdb=" N ALA E 619 " --> pdb=" O SER E 615 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU E 620 " --> pdb=" O PRO E 616 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS E 621 " --> pdb=" O GLN E 617 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 622 " --> pdb=" O ALA E 618 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE E 629 " --> pdb=" O ASN E 625 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG E 630 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 667 removed outlier: 4.167A pdb=" N GLU E 667 " --> pdb=" O LEU E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 695 removed outlier: 3.513A pdb=" N VAL E 677 " --> pdb=" O GLN E 673 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET E 689 " --> pdb=" O GLN E 685 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP E 690 " --> pdb=" O ALA E 686 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 122 removed outlier: 3.659A pdb=" N GLU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 147 Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'F' and resid 173 through 193 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 407 through 411 removed outlier: 4.338A pdb=" N GLY F 411 " --> pdb=" O THR F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.676A pdb=" N PHE F 504 " --> pdb=" O ASP F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 522 removed outlier: 3.531A pdb=" N ASP F 522 " --> pdb=" O GLU F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'F' and resid 540 through 553 Processing helix chain 'F' and resid 580 through 592 removed outlier: 3.813A pdb=" N PHE F 584 " --> pdb=" O SER F 580 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 removed outlier: 3.563A pdb=" N THR F 609 " --> pdb=" O ALA F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 645 through 659 removed outlier: 3.788A pdb=" N ALA F 655 " --> pdb=" O ALA F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 699 Processing helix chain 'F' and resid 702 through 708 removed outlier: 3.759A pdb=" N ARG F 708 " --> pdb=" O PRO F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 738 Processing helix chain 'F' and resid 747 through 759 Processing helix chain 'F' and resid 766 through 788 removed outlier: 3.836A pdb=" N SER F 771 " --> pdb=" O LYS F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 791 No H-bonds generated for 'chain 'F' and resid 789 through 791' Processing helix chain 'F' and resid 796 through 814 Processing helix chain 'F' and resid 820 through 835 removed outlier: 3.618A pdb=" N ILE F 835 " --> pdb=" O LEU F 831 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 28 removed outlier: 3.519A pdb=" N VAL G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 72 Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 109 through 124 removed outlier: 3.923A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 165 Processing helix chain 'G' and resid 174 through 189 Processing helix chain 'G' and resid 193 through 198 removed outlier: 3.843A pdb=" N ARG G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 215 removed outlier: 3.535A pdb=" N TYR G 215 " --> pdb=" O CYS G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 235 Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 394 through 407 removed outlier: 3.741A pdb=" N GLU G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG G 400 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 417 Processing helix chain 'G' and resid 425 through 438 Processing helix chain 'G' and resid 465 through 477 Processing helix chain 'G' and resid 511 through 516 Processing helix chain 'G' and resid 525 through 529 removed outlier: 3.548A pdb=" N MET G 529 " --> pdb=" O PHE G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 544 removed outlier: 4.379A pdb=" N GLU G 542 " --> pdb=" O HIS G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 579 through 584 Processing helix chain 'G' and resid 587 through 594 removed outlier: 3.553A pdb=" N PHE G 594 " --> pdb=" O LEU G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 623 removed outlier: 3.536A pdb=" N GLU G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS G 611 " --> pdb=" O ASP G 607 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 647 removed outlier: 3.633A pdb=" N THR G 647 " --> pdb=" O ALA G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 675 Processing helix chain 'G' and resid 685 through 703 Processing helix chain 'G' and resid 709 through 730 removed outlier: 3.717A pdb=" N VAL G 713 " --> pdb=" O ASP G 709 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS G 724 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER G 726 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU G 727 " --> pdb=" O SER G 723 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 730 " --> pdb=" O SER G 726 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 245 removed outlier: 6.317A pdb=" N LEU 2 242 " --> pdb=" O ARG 2 296 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER 2 298 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL 2 244 " --> pdb=" O SER 2 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 351 through 352 removed outlier: 6.716A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N HIS 2 405 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA 2 448 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG 2 458 " --> pdb=" O GLU 2 423 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU 2 423 " --> pdb=" O ARG 2 458 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 339 through 341 Processing sheet with id=AA4, first strand: chain '2' and resid 525 through 527 Processing sheet with id=AA5, first strand: chain '2' and resid 563 through 567 Processing sheet with id=AA6, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA7, first strand: chain '2' and resid 628 through 633 Processing sheet with id=AA8, first strand: chain '3' and resid 95 through 99 Processing sheet with id=AA9, first strand: chain '3' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 178 through 189 current: chain '3' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 208 through 213 current: chain '3' and resid 273 through 278 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 278 current: chain '3' and resid 318 through 330 Processing sheet with id=AB1, first strand: chain '3' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain '3' and resid 429 through 433 removed outlier: 6.469A pdb=" N ILE 3 430 " --> pdb=" O CYS 3 471 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASP 3 473 " --> pdb=" O ILE 3 430 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 444 through 448 Processing sheet with id=AB4, first strand: chain '3' and resid 494 through 498 Processing sheet with id=AB5, first strand: chain '4' and resid 149 through 151 Processing sheet with id=AB6, first strand: chain '4' and resid 240 through 244 removed outlier: 6.617A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR 4 306 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU 4 243 " --> pdb=" O TYR 4 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '4' and resid 339 through 342 removed outlier: 9.969A pdb=" N SER 4 414 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N VAL 4 461 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER 4 416 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL 4 463 " --> pdb=" O SER 4 416 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N CYS 4 418 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N HIS 4 465 " --> pdb=" O CYS 4 418 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N TYR 4 420 " --> pdb=" O HIS 4 465 " (cutoff:3.500A) removed outlier: 12.981A pdb=" N LYS 4 467 " --> pdb=" O TYR 4 420 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL 4 466 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU 4 434 " --> pdb=" O VAL 4 466 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 355 through 359 Processing sheet with id=AB9, first strand: chain '4' and resid 364 through 367 Processing sheet with id=AC1, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AC2, first strand: chain '4' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain '4' and resid 590 through 591 removed outlier: 6.334A pdb=" N CYS 4 629 " --> pdb=" O LEU 4 672 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER 4 674 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE 4 631 " --> pdb=" O SER 4 674 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 603 through 607 Processing sheet with id=AC5, first strand: chain '4' and resid 653 through 657 Processing sheet with id=AC6, first strand: chain '4' and resid 761 through 762 removed outlier: 6.604A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '5' and resid 8 through 12 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 8 through 12 current: chain 'G' and resid 238 through 248 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 238 through 248 current: chain 'G' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 267 through 272 current: chain 'G' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 336 current: chain 'G' and resid 373 through 383 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '5' and resid 60 through 64 removed outlier: 5.657A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '5' and resid 189 through 193 removed outlier: 5.481A pdb=" N SER 5 174 " --> pdb=" O GLN 5 253 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN 5 253 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA 5 176 " --> pdb=" O ILE 5 251 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE 5 251 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER 5 180 " --> pdb=" O SER 5 247 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER 5 247 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N MET 5 182 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N HIS 5 245 " --> pdb=" O MET 5 182 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR 5 275 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N GLY 5 332 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS 5 158 " --> pdb=" O TYR 5 298 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AD2, first strand: chain '5' and resid 436 through 440 removed outlier: 6.736A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA 5 523 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU 5 414 " --> pdb=" O ALA 5 523 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU 5 413 " --> pdb=" O PHE 5 554 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL 5 556 " --> pdb=" O LEU 5 413 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU 5 415 " --> pdb=" O VAL 5 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain '5' and resid 452 through 455 removed outlier: 3.677A pdb=" N GLY 5 466 " --> pdb=" O SER 5 452 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN 5 454 " --> pdb=" O LEU 5 464 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU 5 464 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '5' and resid 501 through 505 Processing sheet with id=AD5, first strand: chain '5' and resid 613 through 614 removed outlier: 6.683A pdb=" N ARG 5 613 " --> pdb=" O ALA 5 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '6' and resid 124 through 125 Processing sheet with id=AD7, first strand: chain '6' and resid 150 through 154 Processing sheet with id=AD8, first strand: chain '6' and resid 317 through 322 removed outlier: 3.678A pdb=" N ASN 6 320 " --> pdb=" O ALA 6 307 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU 6 322 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR 6 305 " --> pdb=" O GLU 6 322 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ALA 6 307 " --> pdb=" O ARG 6 350 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N ARG 6 350 " --> pdb=" O ALA 6 307 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N PHE 6 309 " --> pdb=" O VAL 6 348 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N VAL 6 348 " --> pdb=" O PHE 6 309 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N CYS 6 311 " --> pdb=" O LEU 6 346 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N LEU 6 346 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) removed outlier: 14.053A pdb=" N THR 6 376 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ILE 6 452 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASP 6 378 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE 6 454 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG 6 382 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N HIS 6 458 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE 6 452 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL 6 404 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE 6 402 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA 6 456 " --> pdb=" O VAL 6 400 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL 6 400 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 557 through 558 removed outlier: 3.574A pdb=" N LYS 6 557 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '6' and resid 596 through 599 removed outlier: 3.532A pdb=" N VAL 6 596 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA 6 682 " --> pdb=" O ILE 6 571 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL 6 573 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '6' and resid 610 through 614 Processing sheet with id=AE3, first strand: chain '6' and resid 660 through 663 Processing sheet with id=AE4, first strand: chain '6' and resid 764 through 765 removed outlier: 7.094A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AE6, first strand: chain '7' and resid 224 through 225 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 248 current: chain '7' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 267 through 272 current: chain '7' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 373 through 383 Processing sheet with id=AE7, first strand: chain '7' and resid 442 through 443 Processing sheet with id=AE8, first strand: chain '7' and resid 480 through 484 removed outlier: 5.982A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL 7 456 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA 7 567 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU 7 458 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '7' and resid 495 through 500 Processing sheet with id=AF1, first strand: chain '7' and resid 545 through 549 Processing sheet with id=AF2, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.290A pdb=" N LEU B 242 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER B 298 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 244 " --> pdb=" O SER B 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 351 through 352 removed outlier: 6.670A pdb=" N VAL B 381 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N HIS B 405 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE B 451 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU B 407 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 453 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 409 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER B 455 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N THR B 449 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN B 433 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE B 451 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS B 431 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA B 453 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 429 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER B 316 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AF5, first strand: chain 'B' and resid 525 through 527 Processing sheet with id=AF6, first strand: chain 'B' and resid 563 through 567 removed outlier: 6.102A pdb=" N LEU B 540 " --> pdb=" O CYS B 681 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B 683 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 542 " --> pdb=" O VAL B 683 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 579 through 582 Processing sheet with id=AF8, first strand: chain 'B' and resid 628 through 633 Processing sheet with id=AF9, first strand: chain 'C' and resid 95 through 99 Processing sheet with id=AG1, first strand: chain 'C' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 178 through 189 current: chain 'C' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 208 through 213 current: chain 'C' and resid 273 through 278 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 278 current: chain 'C' and resid 318 through 330 Processing sheet with id=AG2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AG3, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.618A pdb=" N ILE C 405 " --> pdb=" O ALA C 514 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ALA C 516 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET C 407 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 406 " --> pdb=" O PHE C 547 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL C 549 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 408 " --> pdb=" O VAL C 549 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 444 through 448 Processing sheet with id=AG5, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AG6, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.563A pdb=" N LEU D 241 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR D 306 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D 243 " --> pdb=" O TYR D 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'D' and resid 339 through 342 removed outlier: 9.838A pdb=" N SER D 414 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N VAL D 461 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER D 416 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL D 463 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS D 418 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N HIS D 465 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N TYR D 420 " --> pdb=" O HIS D 465 " (cutoff:3.500A) removed outlier: 13.045A pdb=" N LYS D 467 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR D 459 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE D 442 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL D 461 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG D 440 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL D 463 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR D 438 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS D 398 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER D 335 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 396 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 355 through 359 Processing sheet with id=AG9, first strand: chain 'D' and resid 364 through 367 Processing sheet with id=AH1, first strand: chain 'D' and resid 453 through 454 Processing sheet with id=AH2, first strand: chain 'D' and resid 550 through 551 Processing sheet with id=AH3, first strand: chain 'D' and resid 589 through 592 removed outlier: 6.235A pdb=" N VAL D 589 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP D 632 " --> pdb=" O VAL D 589 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR D 591 " --> pdb=" O ASP D 632 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS D 629 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER D 674 " --> pdb=" O CYS D 629 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D 631 " --> pdb=" O SER D 674 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE D 564 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA D 675 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU D 566 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU D 565 " --> pdb=" O TYR D 706 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL D 708 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS D 567 " --> pdb=" O VAL D 708 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'D' and resid 603 through 607 Processing sheet with id=AH5, first strand: chain 'D' and resid 653 through 657 Processing sheet with id=AH6, first strand: chain 'D' and resid 761 through 762 removed outlier: 6.569A pdb=" N ILE D 761 " --> pdb=" O VAL D 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'E' and resid 60 through 64 removed outlier: 5.766A pdb=" N LEU E 61 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN E 140 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL E 63 " --> pdb=" O ASN E 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 189 through 193 removed outlier: 5.498A pdb=" N SER E 174 " --> pdb=" O GLN E 253 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN E 253 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA E 176 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE E 251 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER E 180 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER E 247 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N MET E 182 " --> pdb=" O HIS E 245 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N HIS E 245 " --> pdb=" O MET E 182 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N ASN E 273 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ILE E 328 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR E 275 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE E 330 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR E 277 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY E 332 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N ASP E 279 " --> pdb=" O GLY E 332 " (cutoff:3.500A) removed outlier: 12.708A pdb=" N GLN E 334 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR E 301 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE E 328 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER E 299 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE E 330 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS E 158 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 436 through 440 removed outlier: 6.228A pdb=" N VAL E 477 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA E 522 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE E 479 " --> pdb=" O ALA E 522 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 452 through 455 removed outlier: 6.811A pdb=" N SER E 452 " --> pdb=" O GLU E 465 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 501 through 505 Processing sheet with id=AI3, first strand: chain 'E' and resid 613 through 614 removed outlier: 6.997A pdb=" N ARG E 613 " --> pdb=" O ALA E 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AI5, first strand: chain 'F' and resid 150 through 154 Processing sheet with id=AI6, first strand: chain 'F' and resid 287 through 296 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 287 through 296 current: chain 'F' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 317 through 322 current: chain 'F' and resid 377 through 382 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 377 through 382 current: chain 'F' and resid 450 through 460 No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'F' and resid 557 through 558 removed outlier: 3.570A pdb=" N LYS F 557 " --> pdb=" O LEU F 565 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 596 through 599 removed outlier: 6.437A pdb=" N ILE F 571 " --> pdb=" O ALA F 680 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA F 682 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL F 573 " --> pdb=" O ALA F 682 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS F 572 " --> pdb=" O PHE F 713 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE F 715 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL F 574 " --> pdb=" O ILE F 715 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 610 through 614 Processing sheet with id=AJ1, first strand: chain 'F' and resid 660 through 663 Processing sheet with id=AJ2, first strand: chain 'F' and resid 764 through 765 removed outlier: 6.840A pdb=" N ILE F 764 " --> pdb=" O ILE F 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'G' and resid 77 through 81 Processing sheet with id=AJ4, first strand: chain 'G' and resid 442 through 443 Processing sheet with id=AJ5, first strand: chain 'G' and resid 481 through 484 removed outlier: 6.168A pdb=" N VAL G 481 " --> pdb=" O CYS G 522 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP G 524 " --> pdb=" O VAL G 481 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR G 483 " --> pdb=" O ASP G 524 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N CYS G 521 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA G 566 " --> pdb=" O CYS G 521 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE G 523 " --> pdb=" O ALA G 566 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL G 456 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA G 567 " --> pdb=" O VAL G 456 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU G 458 " --> pdb=" O ALA G 567 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'G' and resid 495 through 500 Processing sheet with id=AJ7, first strand: chain 'G' and resid 545 through 549 Processing sheet with id=AJ8, first strand: chain 'G' and resid 651 through 652 removed outlier: 7.109A pdb=" N VAL G 651 " --> pdb=" O VAL G 708 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ8 2633 hydrogen bonds defined for protein. 7641 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: 27.21 Time building geometry restraints manager: 14.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 21235 1.37 - 1.51: 18196 1.51 - 1.66: 23726 1.66 - 1.80: 374 1.80 - 1.95: 100 Bond restraints: 63631 Sorted by residual: bond pdb=" CB PRO E 647 " pdb=" CG PRO E 647 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.99e+00 bond pdb=" CB PRO 2 524 " pdb=" CG PRO 2 524 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.23e+00 bond pdb=" CG GLU 3 563 " pdb=" CD GLU 3 563 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.15e+00 bond pdb=" CG1 ILE E 251 " pdb=" CD1 ILE E 251 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.91e+00 bond pdb=" C PRO D 696 " pdb=" N PRO D 697 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.22e+00 ... (remaining 63626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 85458 2.97 - 5.94: 575 5.94 - 8.92: 61 8.92 - 11.89: 11 11.89 - 14.86: 4 Bond angle restraints: 86109 Sorted by residual: angle pdb=" CA PRO E 647 " pdb=" N PRO E 647 " pdb=" CD PRO E 647 " ideal model delta sigma weight residual 112.00 103.77 8.23 1.40e+00 5.10e-01 3.46e+01 angle pdb=" CA GLU 3 563 " pdb=" CB GLU 3 563 " pdb=" CG GLU 3 563 " ideal model delta sigma weight residual 114.10 125.04 -10.94 2.00e+00 2.50e-01 2.99e+01 angle pdb=" N GLU 3 563 " pdb=" CA GLU 3 563 " pdb=" CB GLU 3 563 " ideal model delta sigma weight residual 110.28 118.54 -8.26 1.55e+00 4.16e-01 2.84e+01 angle pdb=" C ILE 6 819 " pdb=" N THR 6 820 " pdb=" CA THR 6 820 " ideal model delta sigma weight residual 120.69 135.55 -14.86 2.95e+00 1.15e-01 2.54e+01 angle pdb=" C ILE F 819 " pdb=" N THR F 820 " pdb=" CA THR F 820 " ideal model delta sigma weight residual 120.69 134.36 -13.67 2.95e+00 1.15e-01 2.15e+01 ... (remaining 86104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.51: 37898 30.51 - 61.03: 1254 61.03 - 91.54: 119 91.54 - 122.05: 2 122.05 - 152.56: 4 Dihedral angle restraints: 39277 sinusoidal: 16176 harmonic: 23101 Sorted by residual: dihedral pdb=" O2A ADP C2001 " pdb=" O3A ADP C2001 " pdb=" PA ADP C2001 " pdb=" PB ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 68.57 -128.57 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O2A ADP 32001 " pdb=" O3A ADP 32001 " pdb=" PA ADP 32001 " pdb=" PB ADP 32001 " ideal model delta sinusoidal sigma weight residual -60.00 65.66 -125.65 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" O1B ADP C2001 " pdb=" O3A ADP C2001 " pdb=" PB ADP C2001 " pdb=" PA ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 -168.52 108.52 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 39274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 8512 0.067 - 0.133: 1405 0.133 - 0.200: 66 0.200 - 0.267: 5 0.267 - 0.333: 3 Chirality restraints: 9991 Sorted by residual: chirality pdb=" CB ILE E 646 " pdb=" CA ILE E 646 " pdb=" CG1 ILE E 646 " pdb=" CG2 ILE E 646 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE 5 646 " pdb=" CA ILE 5 646 " pdb=" CG1 ILE 5 646 " pdb=" CG2 ILE 5 646 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB VAL 6 403 " pdb=" CA VAL 6 403 " pdb=" CG1 VAL 6 403 " pdb=" CG2 VAL 6 403 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 9988 not shown) Planarity restraints: 11074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU 4 378 " -0.067 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO 4 379 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO 4 379 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO 4 379 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 5 535 " -0.048 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO 5 536 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO 5 536 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO 5 536 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG 3 559 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ARG 3 559 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG 3 559 " -0.017 2.00e-02 2.50e+03 pdb=" N SER 3 560 " -0.015 2.00e-02 2.50e+03 ... (remaining 11071 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 505 2.59 - 3.17: 49767 3.17 - 3.74: 97106 3.74 - 4.32: 137104 4.32 - 4.90: 228358 Nonbonded interactions: 512840 Sorted by model distance: nonbonded pdb=" O2G AGS 62001 " pdb="MG MG 62002 " model vdw 2.009 2.170 nonbonded pdb=" OG SER 6 582 " pdb="MG MG 62002 " model vdw 2.025 2.170 nonbonded pdb=" OG SER 4 575 " pdb="MG MG 42002 " model vdw 2.033 2.170 nonbonded pdb=" O2G AGS 72001 " pdb="MG MG 72002 " model vdw 2.053 2.170 nonbonded pdb=" OG SER 7 467 " pdb="MG MG 72002 " model vdw 2.057 2.170 ... (remaining 512835 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 Found NCS groups: ncs_group { reference = chain '2' selection = chain 'B' } ncs_group { reference = chain '3' selection = chain 'C' } ncs_group { reference = (chain '4' and (resid 176 through 853 or resid 2001 through 2003)) selection = chain 'D' } ncs_group { reference = chain '5' selection = chain 'E' } ncs_group { reference = chain '6' selection = chain 'F' } ncs_group { reference = chain '7' selection = chain 'G' } 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: 3.070 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: 0.060 Extract box with map and model: 1.800 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 123.210 Find NCS groups from input model: 4.620 Set up NCS constraints: 0.400 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: 0.020 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.004 0.141 63631 Z= 0.248 Angle : 0.694 14.862 86109 Z= 0.370 Chirality : 0.047 0.333 9991 Planarity : 0.006 0.099 11074 Dihedral : 14.709 152.564 24278 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.09), residues: 7808 helix: 0.07 (0.09), residues: 3128 sheet: -0.09 (0.13), residues: 1493 loop : -0.41 (0.10), residues: 3187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 343 HIS 0.018 0.001 HIS 7 538 PHE 0.040 0.002 PHE E 197 TYR 0.042 0.001 TYR 6 828 ARG 0.017 0.001 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 971 time to evaluate : 5.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 788 ARG cc_start: 0.7384 (mmm160) cc_final: 0.7099 (mmm160) REVERT: 2 847 ASP cc_start: 0.7148 (m-30) cc_final: 0.6858 (m-30) REVERT: 3 346 ASP cc_start: 0.7213 (m-30) cc_final: 0.6939 (m-30) REVERT: 3 576 TYR cc_start: 0.7713 (m-80) cc_final: 0.7425 (m-80) REVERT: 5 572 VAL cc_start: 0.9390 (t) cc_final: 0.9184 (t) REVERT: 6 521 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7945 (mmtm) REVERT: 6 561 GLU cc_start: 0.7808 (mp0) cc_final: 0.7384 (mm-30) REVERT: 6 658 GLN cc_start: 0.8224 (mp10) cc_final: 0.7972 (mm-40) REVERT: 6 829 ASP cc_start: 0.7944 (m-30) cc_final: 0.7534 (m-30) REVERT: 7 177 MET cc_start: 0.6257 (tpt) cc_final: 0.5894 (tpt) REVERT: B 272 ASP cc_start: 0.7133 (m-30) cc_final: 0.6732 (m-30) REVERT: B 671 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6260 (mm-30) REVERT: B 681 CYS cc_start: 0.7800 (m) cc_final: 0.7550 (m) REVERT: B 843 ASP cc_start: 0.7048 (m-30) cc_final: 0.6735 (m-30) REVERT: C 55 ASN cc_start: 0.5539 (m-40) cc_final: 0.4959 (t0) REVERT: E 5 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7500 (ttm170) REVERT: E 267 VAL cc_start: 0.7873 (m) cc_final: 0.7642 (t) REVERT: G 27 THR cc_start: 0.8127 (m) cc_final: 0.7909 (m) REVERT: G 670 ASP cc_start: 0.7670 (m-30) cc_final: 0.7068 (m-30) outliers start: 2 outliers final: 2 residues processed: 973 average time/residue: 0.6395 time to fit residues: 1044.0165 Evaluate side-chains 720 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 718 time to evaluate : 5.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain E residue 339 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 660 optimal weight: 0.4980 chunk 592 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 399 optimal weight: 1.9990 chunk 316 optimal weight: 0.8980 chunk 612 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 372 optimal weight: 1.9990 chunk 456 optimal weight: 0.9990 chunk 710 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 290 HIS 2 353 GLN 2 653 ASN 2 779 HIS 3 151 HIS 3 324 ASN 4 240 ASN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 646 HIS 5 576 HIS 6 264 GLN 6 550 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 90 ASN 7 297 GLN D 386 HIS ** E 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN F 347 ASN F 506 ASN G 19 ASN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 63631 Z= 0.203 Angle : 0.523 9.242 86109 Z= 0.273 Chirality : 0.043 0.150 9991 Planarity : 0.004 0.060 11074 Dihedral : 7.026 153.200 8855 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 6.28 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.09), residues: 7808 helix: 0.95 (0.09), residues: 3175 sheet: -0.24 (0.13), residues: 1559 loop : -0.14 (0.11), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 153 HIS 0.011 0.001 HIS F 653 PHE 0.017 0.001 PHE C 421 TYR 0.027 0.001 TYR G 618 ARG 0.023 0.000 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 780 time to evaluate : 5.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 779 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.6024 (p-80) REVERT: 2 847 ASP cc_start: 0.7100 (m-30) cc_final: 0.6767 (m-30) REVERT: 3 346 ASP cc_start: 0.7198 (m-30) cc_final: 0.6916 (m-30) REVERT: 3 576 TYR cc_start: 0.7721 (m-80) cc_final: 0.7404 (m-80) REVERT: 4 772 ARG cc_start: 0.7988 (tmm-80) cc_final: 0.7375 (ttm-80) REVERT: 6 313 MET cc_start: 0.6315 (mtm) cc_final: 0.6075 (ptp) REVERT: 6 561 GLU cc_start: 0.7779 (mp0) cc_final: 0.7546 (mm-30) REVERT: 6 829 ASP cc_start: 0.8009 (m-30) cc_final: 0.7574 (m-30) REVERT: 7 177 MET cc_start: 0.6243 (tpt) cc_final: 0.5870 (tpt) REVERT: B 272 ASP cc_start: 0.7107 (m-30) cc_final: 0.6707 (m-30) REVERT: B 354 ASP cc_start: 0.6472 (p0) cc_final: 0.6261 (p0) REVERT: B 671 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6268 (mm-30) REVERT: B 681 CYS cc_start: 0.7840 (m) cc_final: 0.7588 (m) REVERT: B 843 ASP cc_start: 0.6985 (m-30) cc_final: 0.6719 (m-30) REVERT: C 55 ASN cc_start: 0.5762 (m-40) cc_final: 0.5085 (t0) REVERT: D 273 ASP cc_start: 0.7460 (m-30) cc_final: 0.7117 (m-30) REVERT: D 649 MET cc_start: 0.9012 (mtp) cc_final: 0.8713 (mtp) REVERT: E 69 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8031 (mm) REVERT: F 313 MET cc_start: 0.7243 (mpp) cc_final: 0.7017 (ptp) REVERT: G 543 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: G 670 ASP cc_start: 0.7627 (m-30) cc_final: 0.7310 (m-30) outliers start: 63 outliers final: 40 residues processed: 815 average time/residue: 0.5900 time to fit residues: 812.0429 Evaluate side-chains 748 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 705 time to evaluate : 5.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 653 ASN Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 223 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 651 VAL Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 108 GLN Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 394 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 591 optimal weight: 4.9990 chunk 483 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 711 optimal weight: 0.5980 chunk 768 optimal weight: 0.7980 chunk 633 optimal weight: 10.0000 chunk 705 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 570 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 391 GLN 2 526 ASN 3 417 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 90 ASN 7 264 GLN ** E 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 HIS ** E 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 750 GLN G 95 GLN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 63631 Z= 0.195 Angle : 0.496 9.502 86109 Z= 0.258 Chirality : 0.042 0.147 9991 Planarity : 0.004 0.054 11074 Dihedral : 6.781 152.489 8853 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.28 % Allowed : 8.71 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 7808 helix: 1.33 (0.09), residues: 3194 sheet: -0.30 (0.13), residues: 1501 loop : -0.08 (0.11), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 356 HIS 0.018 0.001 HIS 2 779 PHE 0.017 0.001 PHE 7 113 TYR 0.022 0.001 TYR 2 769 ARG 0.005 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 764 time to evaluate : 5.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 764 MET cc_start: 0.8126 (mtp) cc_final: 0.7907 (mtm) REVERT: 2 779 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.6104 (p90) REVERT: 2 847 ASP cc_start: 0.7009 (m-30) cc_final: 0.6705 (m-30) REVERT: 3 346 ASP cc_start: 0.7179 (m-30) cc_final: 0.6891 (m-30) REVERT: 3 576 TYR cc_start: 0.7805 (m-80) cc_final: 0.7448 (m-80) REVERT: 4 772 ARG cc_start: 0.8039 (tmm-80) cc_final: 0.7454 (ttm-80) REVERT: 6 313 MET cc_start: 0.6346 (mtm) cc_final: 0.6067 (mtm) REVERT: 6 561 GLU cc_start: 0.7762 (mp0) cc_final: 0.7542 (mm-30) REVERT: 6 829 ASP cc_start: 0.8015 (m-30) cc_final: 0.7580 (m-30) REVERT: 7 101 ASP cc_start: 0.8478 (t0) cc_final: 0.8263 (t0) REVERT: 7 177 MET cc_start: 0.6280 (tpt) cc_final: 0.5818 (tpt) REVERT: B 272 ASP cc_start: 0.7108 (m-30) cc_final: 0.6692 (m-30) REVERT: B 551 GLN cc_start: 0.7613 (mp10) cc_final: 0.7302 (mp10) REVERT: B 671 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6279 (mm-30) REVERT: B 681 CYS cc_start: 0.7874 (m) cc_final: 0.7616 (m) REVERT: B 843 ASP cc_start: 0.6952 (m-30) cc_final: 0.6687 (m-30) REVERT: C 55 ASN cc_start: 0.5754 (m-40) cc_final: 0.5134 (t0) REVERT: D 417 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8815 (pp) REVERT: E 69 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8251 (mm) REVERT: E 358 LEU cc_start: 0.8637 (mp) cc_final: 0.8358 (mp) REVERT: F 313 MET cc_start: 0.7209 (mpp) cc_final: 0.6976 (ptp) REVERT: G 177 MET cc_start: 0.4854 (ptt) cc_final: 0.4499 (ptt) REVERT: G 543 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: G 683 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.6830 (tm-30) outliers start: 89 outliers final: 65 residues processed: 814 average time/residue: 0.6104 time to fit residues: 837.7561 Evaluate side-chains 780 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 710 time to evaluate : 5.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 223 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 651 VAL Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 108 GLN Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 157 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 560 HIS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 683 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 702 optimal weight: 4.9990 chunk 534 optimal weight: 1.9990 chunk 369 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 477 optimal weight: 0.4980 chunk 713 optimal weight: 1.9990 chunk 755 optimal weight: 3.9990 chunk 373 optimal weight: 3.9990 chunk 676 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 405 HIS 2 779 HIS 3 293 ASN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 673 ASN 7 89 GLN 7 112 HIS 7 159 ASN B 366 ASN C 210 HIS E 334 GLN E 344 ASN E 560 HIS ** E 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 63631 Z= 0.328 Angle : 0.556 9.890 86109 Z= 0.287 Chirality : 0.044 0.191 9991 Planarity : 0.004 0.076 11074 Dihedral : 6.778 151.573 8853 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.95 % Allowed : 10.32 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.09), residues: 7808 helix: 1.33 (0.09), residues: 3219 sheet: -0.40 (0.13), residues: 1478 loop : -0.15 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 153 HIS 0.021 0.001 HIS E 560 PHE 0.025 0.002 PHE 7 113 TYR 0.019 0.001 TYR 6 136 ARG 0.009 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 751 time to evaluate : 5.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 764 MET cc_start: 0.8184 (mtp) cc_final: 0.7942 (mtm) REVERT: 2 779 HIS cc_start: 0.6293 (OUTLIER) cc_final: 0.5959 (p-80) REVERT: 2 847 ASP cc_start: 0.7239 (m-30) cc_final: 0.6946 (m-30) REVERT: 3 386 MET cc_start: 0.9102 (mmt) cc_final: 0.8438 (mmt) REVERT: 3 576 TYR cc_start: 0.7887 (m-80) cc_final: 0.7621 (m-80) REVERT: 4 772 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7464 (ttm-80) REVERT: 4 799 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: 5 541 ASP cc_start: 0.5828 (t0) cc_final: 0.5476 (t0) REVERT: 6 121 ASP cc_start: 0.6494 (m-30) cc_final: 0.6237 (m-30) REVERT: 6 313 MET cc_start: 0.6499 (mtm) cc_final: 0.5999 (mpp) REVERT: 6 658 GLN cc_start: 0.8208 (mp10) cc_final: 0.8007 (mp10) REVERT: 6 833 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7695 (mm-40) REVERT: 7 177 MET cc_start: 0.6299 (tpt) cc_final: 0.5821 (tpt) REVERT: B 272 ASP cc_start: 0.7172 (m-30) cc_final: 0.6793 (m-30) REVERT: B 681 CYS cc_start: 0.7911 (m) cc_final: 0.7662 (m) REVERT: B 843 ASP cc_start: 0.6988 (m-30) cc_final: 0.6738 (m-30) REVERT: C 55 ASN cc_start: 0.5605 (m-40) cc_final: 0.5005 (t0) REVERT: C 320 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8811 (pp) REVERT: C 458 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6273 (mp0) REVERT: D 417 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8936 (pp) REVERT: D 637 MET cc_start: 0.8877 (ttm) cc_final: 0.8519 (mtp) REVERT: F 370 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7794 (t) REVERT: F 658 GLN cc_start: 0.8229 (mt0) cc_final: 0.7912 (mt0) REVERT: G 543 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: G 683 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7056 (tm-30) outliers start: 136 outliers final: 90 residues processed: 842 average time/residue: 0.5907 time to fit residues: 839.8164 Evaluate side-chains 797 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 700 time to evaluate : 5.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 239 SER Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 577 THR Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 223 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 464 LEU Chi-restraints excluded: chain 3 residue 651 VAL Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 799 GLU Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 157 SER Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 345 THR Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 653 SER Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 683 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 629 optimal weight: 4.9990 chunk 429 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 562 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 645 optimal weight: 0.6980 chunk 522 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 385 optimal weight: 0.9990 chunk 678 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 209 GLN B 551 GLN D 386 HIS ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 63631 Z= 0.219 Angle : 0.507 10.239 86109 Z= 0.263 Chirality : 0.043 0.298 9991 Planarity : 0.004 0.061 11074 Dihedral : 6.675 151.073 8853 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.89 % Allowed : 11.58 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.09), residues: 7808 helix: 1.51 (0.09), residues: 3209 sheet: -0.43 (0.13), residues: 1502 loop : -0.10 (0.11), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 356 HIS 0.012 0.001 HIS F 653 PHE 0.018 0.001 PHE 7 113 TYR 0.018 0.001 TYR 6 136 ARG 0.005 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 748 time to evaluate : 5.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 656 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7038 (tpp-160) REVERT: 2 764 MET cc_start: 0.8137 (mtp) cc_final: 0.7882 (mtm) REVERT: 2 779 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.5823 (p90) REVERT: 2 847 ASP cc_start: 0.7232 (m-30) cc_final: 0.6945 (m-30) REVERT: 3 320 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8714 (pp) REVERT: 3 346 ASP cc_start: 0.7133 (m-30) cc_final: 0.6852 (m-30) REVERT: 3 576 TYR cc_start: 0.7872 (m-80) cc_final: 0.7588 (m-80) REVERT: 4 200 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8763 (p) REVERT: 4 772 ARG cc_start: 0.8037 (tmm-80) cc_final: 0.7488 (ttm-80) REVERT: 4 799 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: 5 695 ASP cc_start: 0.7042 (t70) cc_final: 0.6306 (p0) REVERT: 6 121 ASP cc_start: 0.6471 (m-30) cc_final: 0.6210 (m-30) REVERT: 6 313 MET cc_start: 0.6505 (mtm) cc_final: 0.5952 (mpp) REVERT: 6 521 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7966 (mmtm) REVERT: 6 658 GLN cc_start: 0.8153 (mp10) cc_final: 0.7952 (mp10) REVERT: 6 733 ASP cc_start: 0.7505 (m-30) cc_final: 0.7290 (m-30) REVERT: 6 829 ASP cc_start: 0.8018 (m-30) cc_final: 0.7584 (m-30) REVERT: 7 177 MET cc_start: 0.6256 (tpt) cc_final: 0.5805 (tpt) REVERT: 7 297 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: B 272 ASP cc_start: 0.7153 (m-30) cc_final: 0.6762 (m-30) REVERT: B 354 ASP cc_start: 0.6661 (p0) cc_final: 0.6450 (p0) REVERT: B 681 CYS cc_start: 0.7914 (m) cc_final: 0.7641 (m) REVERT: B 822 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8281 (mttt) REVERT: B 843 ASP cc_start: 0.6940 (m-30) cc_final: 0.6684 (m-30) REVERT: C 55 ASN cc_start: 0.5642 (m-40) cc_final: 0.5090 (t0) REVERT: C 320 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8833 (pp) REVERT: C 458 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6270 (mp0) REVERT: D 417 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8863 (pp) REVERT: D 637 MET cc_start: 0.8893 (ttm) cc_final: 0.8567 (mtp) REVERT: F 658 GLN cc_start: 0.8224 (mt0) cc_final: 0.7894 (mt0) REVERT: G 347 ASP cc_start: 0.7541 (m-30) cc_final: 0.7319 (m-30) REVERT: G 543 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7852 (mp10) outliers start: 132 outliers final: 89 residues processed: 829 average time/residue: 0.6151 time to fit residues: 862.0283 Evaluate side-chains 808 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 710 time to evaluate : 5.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 4 residue 498 VAL Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 799 GLU Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 157 SER Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 653 SER Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 822 LYS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 636 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 254 optimal weight: 10.0000 chunk 680 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 443 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 756 optimal weight: 0.5980 chunk 628 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 250 optimal weight: 8.9990 chunk 397 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 651 GLN 5 560 HIS 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 209 GLN B 353 GLN ** E 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 HIS ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 63631 Z= 0.198 Angle : 0.494 10.572 86109 Z= 0.256 Chirality : 0.042 0.190 9991 Planarity : 0.004 0.059 11074 Dihedral : 6.584 150.769 8853 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.06 % Allowed : 12.16 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 7808 helix: 1.61 (0.09), residues: 3208 sheet: -0.48 (0.13), residues: 1521 loop : -0.04 (0.11), residues: 3079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 356 HIS 0.012 0.001 HIS 6 653 PHE 0.021 0.001 PHE C 735 TYR 0.017 0.001 TYR 6 136 ARG 0.007 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 745 time to evaluate : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 656 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7051 (tpp-160) REVERT: 2 764 MET cc_start: 0.8116 (mtp) cc_final: 0.7870 (mtm) REVERT: 2 847 ASP cc_start: 0.7204 (m-30) cc_final: 0.6923 (m-30) REVERT: 3 320 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8681 (pp) REVERT: 3 346 ASP cc_start: 0.7117 (m-30) cc_final: 0.6829 (m-30) REVERT: 3 561 ILE cc_start: 0.8548 (mm) cc_final: 0.8218 (mm) REVERT: 3 576 TYR cc_start: 0.7871 (m-80) cc_final: 0.7573 (m-80) REVERT: 4 199 MET cc_start: 0.8102 (mmt) cc_final: 0.7768 (mmp) REVERT: 4 772 ARG cc_start: 0.8022 (tmm-80) cc_final: 0.7490 (ttm-80) REVERT: 4 799 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: 5 541 ASP cc_start: 0.5653 (t0) cc_final: 0.5375 (t0) REVERT: 5 695 ASP cc_start: 0.7069 (t70) cc_final: 0.6648 (t0) REVERT: 6 121 ASP cc_start: 0.6467 (m-30) cc_final: 0.6201 (m-30) REVERT: 6 313 MET cc_start: 0.6521 (mtm) cc_final: 0.6231 (mpp) REVERT: 6 658 GLN cc_start: 0.8118 (mp10) cc_final: 0.7911 (mp10) REVERT: 6 733 ASP cc_start: 0.7486 (m-30) cc_final: 0.7270 (m-30) REVERT: 7 177 MET cc_start: 0.6370 (tpt) cc_final: 0.5909 (tpt) REVERT: 7 297 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: B 272 ASP cc_start: 0.7123 (m-30) cc_final: 0.6733 (m-30) REVERT: B 681 CYS cc_start: 0.7907 (m) cc_final: 0.7642 (m) REVERT: B 822 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8278 (mttt) REVERT: B 843 ASP cc_start: 0.6963 (m-30) cc_final: 0.6721 (m-30) REVERT: C 55 ASN cc_start: 0.5773 (m-40) cc_final: 0.5143 (t0) REVERT: C 320 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8821 (pp) REVERT: C 546 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8760 (tt) REVERT: D 417 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8851 (pp) REVERT: D 637 MET cc_start: 0.8879 (ttm) cc_final: 0.8513 (mtp) REVERT: D 724 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8870 (mp) REVERT: F 672 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8761 (mt) REVERT: G 94 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7794 (mp) REVERT: G 167 MET cc_start: 0.4814 (mtp) cc_final: 0.4294 (mtt) REVERT: G 177 MET cc_start: 0.5042 (ptt) cc_final: 0.4643 (ptt) REVERT: G 347 ASP cc_start: 0.7493 (m-30) cc_final: 0.7264 (m-30) REVERT: G 543 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7805 (mp10) outliers start: 144 outliers final: 100 residues processed: 831 average time/residue: 0.6055 time to fit residues: 853.3037 Evaluate side-chains 813 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 702 time to evaluate : 5.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 498 VAL Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 799 GLU Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 157 SER Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 5 residue 560 HIS Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 653 SER Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 822 LYS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 560 HIS Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 671 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 729 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 431 optimal weight: 0.8980 chunk 552 optimal weight: 4.9990 chunk 428 optimal weight: 5.9990 chunk 636 optimal weight: 8.9990 chunk 422 optimal weight: 4.9990 chunk 753 optimal weight: 2.9990 chunk 471 optimal weight: 0.1980 chunk 459 optimal weight: 3.9990 chunk 347 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 682 ASN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN 7 209 GLN B 658 ASN ** E 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 63631 Z= 0.162 Angle : 0.484 10.204 86109 Z= 0.251 Chirality : 0.042 0.169 9991 Planarity : 0.004 0.057 11074 Dihedral : 6.506 150.596 8853 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.93 % Allowed : 12.92 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.10), residues: 7808 helix: 1.71 (0.09), residues: 3208 sheet: -0.45 (0.13), residues: 1513 loop : -0.02 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 344 HIS 0.029 0.001 HIS 5 560 PHE 0.022 0.001 PHE C 735 TYR 0.016 0.001 TYR 6 136 ARG 0.006 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 740 time to evaluate : 5.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 656 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7049 (tpp-160) REVERT: 2 764 MET cc_start: 0.8097 (mtp) cc_final: 0.7862 (mtm) REVERT: 2 847 ASP cc_start: 0.7131 (m-30) cc_final: 0.6850 (m-30) REVERT: 3 320 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8653 (pp) REVERT: 3 346 ASP cc_start: 0.7095 (m-30) cc_final: 0.6788 (m-30) REVERT: 3 576 TYR cc_start: 0.7857 (m-80) cc_final: 0.7531 (m-80) REVERT: 4 199 MET cc_start: 0.8106 (mmt) cc_final: 0.7706 (mmp) REVERT: 4 772 ARG cc_start: 0.8002 (tmm-80) cc_final: 0.7485 (ttm-80) REVERT: 4 799 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: 5 695 ASP cc_start: 0.6996 (t70) cc_final: 0.6606 (t0) REVERT: 6 121 ASP cc_start: 0.6451 (m-30) cc_final: 0.6187 (m-30) REVERT: 6 313 MET cc_start: 0.6548 (mtm) cc_final: 0.6205 (mpp) REVERT: 6 658 GLN cc_start: 0.8115 (mp10) cc_final: 0.7907 (mp10) REVERT: 6 733 ASP cc_start: 0.7521 (m-30) cc_final: 0.7278 (m-30) REVERT: 6 829 ASP cc_start: 0.7957 (m-30) cc_final: 0.7577 (m-30) REVERT: 7 177 MET cc_start: 0.6436 (tpt) cc_final: 0.5964 (tpt) REVERT: 7 297 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: 7 621 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8205 (ptt) REVERT: B 272 ASP cc_start: 0.6997 (m-30) cc_final: 0.6540 (m-30) REVERT: B 681 CYS cc_start: 0.7897 (m) cc_final: 0.7629 (m) REVERT: B 843 ASP cc_start: 0.6958 (m-30) cc_final: 0.6722 (m-30) REVERT: C 55 ASN cc_start: 0.5791 (m-40) cc_final: 0.5204 (t0) REVERT: C 320 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8803 (pp) REVERT: C 474 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 546 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8779 (tt) REVERT: C 719 LYS cc_start: 0.8107 (tppt) cc_final: 0.7752 (mmtt) REVERT: D 417 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8832 (pp) REVERT: D 637 MET cc_start: 0.8844 (ttm) cc_final: 0.8477 (mtp) REVERT: D 724 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8877 (mp) REVERT: F 672 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8739 (mt) REVERT: G 94 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7776 (mp) REVERT: G 167 MET cc_start: 0.4903 (mtp) cc_final: 0.4340 (mtt) REVERT: G 543 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7754 (mp10) outliers start: 135 outliers final: 97 residues processed: 825 average time/residue: 0.5874 time to fit residues: 823.3567 Evaluate side-chains 814 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 706 time to evaluate : 5.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 799 GLU Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 105 SER Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 157 SER Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 300 ILE Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 671 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 466 optimal weight: 2.9990 chunk 300 optimal weight: 8.9990 chunk 450 optimal weight: 0.0060 chunk 227 optimal weight: 0.0970 chunk 148 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 479 optimal weight: 10.0000 chunk 513 optimal weight: 1.9990 chunk 372 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 592 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 560 HIS 6 264 GLN 7 209 GLN 7 669 GLN B 658 ASN D 386 HIS ** E 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN F 506 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 63631 Z= 0.184 Angle : 0.490 10.289 86109 Z= 0.253 Chirality : 0.042 0.210 9991 Planarity : 0.004 0.057 11074 Dihedral : 6.473 150.371 8853 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.96 % Allowed : 13.27 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 7808 helix: 1.74 (0.09), residues: 3215 sheet: -0.45 (0.13), residues: 1511 loop : -0.01 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 344 HIS 0.013 0.001 HIS 6 653 PHE 0.028 0.001 PHE C 735 TYR 0.016 0.001 TYR 6 136 ARG 0.007 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 731 time to evaluate : 5.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 656 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7058 (tpp-160) REVERT: 2 764 MET cc_start: 0.8101 (mtp) cc_final: 0.7869 (mtm) REVERT: 2 847 ASP cc_start: 0.7176 (m-30) cc_final: 0.6898 (m-30) REVERT: 3 320 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8668 (pp) REVERT: 3 346 ASP cc_start: 0.7085 (m-30) cc_final: 0.6781 (m-30) REVERT: 3 576 TYR cc_start: 0.7866 (m-80) cc_final: 0.7537 (m-80) REVERT: 4 133 MET cc_start: 0.6542 (pmm) cc_final: 0.6325 (pmm) REVERT: 4 212 ARG cc_start: 0.7002 (mtm180) cc_final: 0.6705 (mtm180) REVERT: 4 772 ARG cc_start: 0.7991 (tmm-80) cc_final: 0.7482 (ttm-80) REVERT: 4 799 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: 5 541 ASP cc_start: 0.5581 (t0) cc_final: 0.5293 (t0) REVERT: 5 695 ASP cc_start: 0.6992 (t70) cc_final: 0.6608 (t0) REVERT: 6 121 ASP cc_start: 0.6455 (m-30) cc_final: 0.6189 (m-30) REVERT: 6 313 MET cc_start: 0.6615 (mtm) cc_final: 0.6240 (mpp) REVERT: 6 658 GLN cc_start: 0.8115 (mp10) cc_final: 0.7886 (mp10) REVERT: 6 733 ASP cc_start: 0.7523 (m-30) cc_final: 0.7286 (m-30) REVERT: 6 829 ASP cc_start: 0.7965 (m-30) cc_final: 0.7583 (m-30) REVERT: 7 177 MET cc_start: 0.6384 (tpt) cc_final: 0.6133 (tpt) REVERT: 7 297 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: B 272 ASP cc_start: 0.6976 (m-30) cc_final: 0.6523 (m-30) REVERT: B 681 CYS cc_start: 0.7904 (m) cc_final: 0.7637 (m) REVERT: B 843 ASP cc_start: 0.6961 (m-30) cc_final: 0.6718 (m-30) REVERT: C 55 ASN cc_start: 0.5804 (m-40) cc_final: 0.5191 (t0) REVERT: C 320 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8804 (pp) REVERT: C 474 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7526 (mt-10) REVERT: C 546 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8768 (tt) REVERT: D 417 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8838 (pp) REVERT: D 637 MET cc_start: 0.8857 (ttm) cc_final: 0.8431 (mtp) REVERT: D 724 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8912 (mp) REVERT: E 625 ASN cc_start: 0.8261 (t0) cc_final: 0.7887 (t0) REVERT: F 672 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8746 (mt) REVERT: G 94 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7803 (mp) REVERT: G 167 MET cc_start: 0.4777 (mtp) cc_final: 0.4322 (mtt) REVERT: G 543 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7717 (mp10) outliers start: 137 outliers final: 104 residues processed: 815 average time/residue: 0.6469 time to fit residues: 901.7316 Evaluate side-chains 816 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 702 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 239 SER Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 799 GLU Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 105 SER Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 157 SER Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 300 ILE Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 653 SER Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 671 SER Chi-restraints excluded: chain G residue 673 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 685 optimal weight: 0.8980 chunk 722 optimal weight: 3.9990 chunk 658 optimal weight: 0.0470 chunk 702 optimal weight: 3.9990 chunk 721 optimal weight: 0.6980 chunk 422 optimal weight: 5.9990 chunk 305 optimal weight: 0.9980 chunk 551 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 634 optimal weight: 2.9990 chunk 664 optimal weight: 9.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 417 GLN 4 240 ASN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN 7 209 GLN 7 669 GLN B 658 ASN D 380 ASN ** E 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 63631 Z= 0.161 Angle : 0.482 11.086 86109 Z= 0.249 Chirality : 0.041 0.166 9991 Planarity : 0.004 0.056 11074 Dihedral : 6.423 150.171 8853 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.75 % Allowed : 13.60 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.10), residues: 7808 helix: 1.81 (0.09), residues: 3209 sheet: -0.45 (0.13), residues: 1518 loop : 0.00 (0.11), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 344 HIS 0.013 0.001 HIS 6 653 PHE 0.024 0.001 PHE C 421 TYR 0.015 0.001 TYR F 136 ARG 0.006 0.000 ARG 3 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 736 time to evaluate : 5.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 656 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7033 (tpp-160) REVERT: 2 764 MET cc_start: 0.8084 (mtp) cc_final: 0.7852 (mtm) REVERT: 2 847 ASP cc_start: 0.7126 (m-30) cc_final: 0.6846 (m-30) REVERT: 3 320 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8674 (pp) REVERT: 3 346 ASP cc_start: 0.7067 (m-30) cc_final: 0.6765 (m-30) REVERT: 3 576 TYR cc_start: 0.7861 (m-80) cc_final: 0.7540 (m-80) REVERT: 4 133 MET cc_start: 0.6594 (pmm) cc_final: 0.6350 (pmm) REVERT: 4 772 ARG cc_start: 0.8053 (tmm-80) cc_final: 0.7533 (ttm-80) REVERT: 4 799 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: 5 695 ASP cc_start: 0.6936 (t70) cc_final: 0.6589 (t0) REVERT: 6 121 ASP cc_start: 0.6440 (m-30) cc_final: 0.6173 (m-30) REVERT: 6 313 MET cc_start: 0.6562 (mtm) cc_final: 0.6197 (mpp) REVERT: 6 658 GLN cc_start: 0.8091 (mp10) cc_final: 0.7849 (mp10) REVERT: 6 696 ARG cc_start: 0.7821 (mmm160) cc_final: 0.7428 (tpt90) REVERT: 6 733 ASP cc_start: 0.7510 (m-30) cc_final: 0.7271 (m-30) REVERT: 6 829 ASP cc_start: 0.7946 (m-30) cc_final: 0.7568 (m-30) REVERT: 7 177 MET cc_start: 0.6372 (tpt) cc_final: 0.6121 (tpt) REVERT: 7 297 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: B 272 ASP cc_start: 0.6984 (m-30) cc_final: 0.6507 (m-30) REVERT: B 681 CYS cc_start: 0.7897 (m) cc_final: 0.7635 (m) REVERT: B 843 ASP cc_start: 0.6958 (m-30) cc_final: 0.6717 (m-30) REVERT: C 55 ASN cc_start: 0.5802 (m-40) cc_final: 0.5192 (t0) REVERT: C 320 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8796 (pp) REVERT: C 474 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 546 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8794 (tt) REVERT: D 417 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8820 (pp) REVERT: D 637 MET cc_start: 0.8833 (ttm) cc_final: 0.8419 (mtp) REVERT: D 724 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8895 (mp) REVERT: E 625 ASN cc_start: 0.8210 (t0) cc_final: 0.7918 (t0) REVERT: F 102 LYS cc_start: 0.7846 (mttt) cc_final: 0.7440 (mptt) REVERT: F 672 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8744 (mt) REVERT: G 94 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7766 (mp) REVERT: G 167 MET cc_start: 0.4846 (mtp) cc_final: 0.4395 (mtt) REVERT: G 543 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: G 673 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6709 (ttp-110) outliers start: 122 outliers final: 97 residues processed: 814 average time/residue: 0.6027 time to fit residues: 833.8215 Evaluate side-chains 812 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 704 time to evaluate : 5.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 799 GLU Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 105 SER Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 157 SER Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 300 ILE Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 168 MET Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain F residue 838 VAL Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 671 SER Chi-restraints excluded: chain G residue 673 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 699 optimal weight: 0.8980 chunk 461 optimal weight: 0.9990 chunk 742 optimal weight: 0.0670 chunk 453 optimal weight: 2.9990 chunk 352 optimal weight: 0.5980 chunk 516 optimal weight: 4.9990 chunk 779 optimal weight: 2.9990 chunk 717 optimal weight: 3.9990 chunk 620 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 479 optimal weight: 8.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 145 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 209 GLN 7 669 GLN B 658 ASN C 340 GLN ** E 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 63631 Z= 0.180 Angle : 0.493 11.739 86109 Z= 0.253 Chirality : 0.042 0.226 9991 Planarity : 0.004 0.056 11074 Dihedral : 6.416 149.870 8853 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.76 % Allowed : 13.71 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.10), residues: 7808 helix: 1.79 (0.09), residues: 3217 sheet: -0.51 (0.13), residues: 1496 loop : 0.01 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 356 HIS 0.013 0.001 HIS 6 653 PHE 0.024 0.001 PHE C 421 TYR 0.015 0.001 TYR 6 136 ARG 0.007 0.000 ARG E 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 714 time to evaluate : 5.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.8372 (mmt) cc_final: 0.8022 (mmt) REVERT: 2 656 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7038 (tpp-160) REVERT: 2 764 MET cc_start: 0.8100 (mtp) cc_final: 0.7878 (mtm) REVERT: 2 847 ASP cc_start: 0.7146 (m-30) cc_final: 0.6858 (m-30) REVERT: 3 320 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8650 (pp) REVERT: 3 346 ASP cc_start: 0.7069 (m-30) cc_final: 0.6770 (m-30) REVERT: 3 576 TYR cc_start: 0.7866 (m-80) cc_final: 0.7547 (m-80) REVERT: 4 133 MET cc_start: 0.6480 (pmm) cc_final: 0.6247 (pmm) REVERT: 4 772 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7519 (ttm-80) REVERT: 4 799 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: 5 152 ASP cc_start: 0.7003 (t70) cc_final: 0.6756 (t70) REVERT: 5 541 ASP cc_start: 0.5490 (t0) cc_final: 0.5217 (t0) REVERT: 5 695 ASP cc_start: 0.6959 (t70) cc_final: 0.6614 (t0) REVERT: 6 121 ASP cc_start: 0.6376 (m-30) cc_final: 0.6104 (m-30) REVERT: 6 313 MET cc_start: 0.6517 (mtm) cc_final: 0.6180 (mpp) REVERT: 6 360 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7702 (ttt180) REVERT: 6 696 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7419 (tpt90) REVERT: 6 733 ASP cc_start: 0.7520 (m-30) cc_final: 0.7278 (m-30) REVERT: 7 177 MET cc_start: 0.6370 (tpt) cc_final: 0.6123 (tpt) REVERT: 7 297 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: B 268 LEU cc_start: 0.8470 (mt) cc_final: 0.7554 (mt) REVERT: B 272 ASP cc_start: 0.6999 (m-30) cc_final: 0.6521 (m-30) REVERT: B 681 CYS cc_start: 0.7896 (m) cc_final: 0.7650 (m) REVERT: B 843 ASP cc_start: 0.6919 (m-30) cc_final: 0.6675 (m-30) REVERT: C 55 ASN cc_start: 0.5799 (m-40) cc_final: 0.5192 (t0) REVERT: C 320 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8800 (pp) REVERT: C 474 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 546 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8810 (tt) REVERT: D 417 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8833 (pp) REVERT: E 625 ASN cc_start: 0.8341 (t0) cc_final: 0.8130 (t0) REVERT: F 579 THR cc_start: 0.8955 (p) cc_final: 0.8718 (p) REVERT: F 672 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8752 (mt) REVERT: G 94 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7785 (mp) REVERT: G 167 MET cc_start: 0.4653 (mtp) cc_final: 0.4331 (mtt) REVERT: G 543 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7697 (mp10) outliers start: 123 outliers final: 108 residues processed: 794 average time/residue: 0.5984 time to fit residues: 807.9919 Evaluate side-chains 821 residues out of total 6986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 704 time to evaluate : 5.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 239 SER Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 799 GLU Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 105 SER Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 157 SER Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 300 ILE Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 168 MET Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 653 SER Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 580 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain F residue 838 VAL Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 671 SER Chi-restraints excluded: chain G residue 673 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 380 optimal weight: 0.1980 chunk 492 optimal weight: 10.0000 chunk 660 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 572 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 621 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 638 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 209 GLN 7 669 GLN B 658 ASN C 340 GLN ** E 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 662 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112580 restraints weight = 81138.590| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.89 r_work: 0.3055 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.198 63631 Z= 0.220 Angle : 0.560 59.198 86109 Z= 0.301 Chirality : 0.042 0.489 9991 Planarity : 0.004 0.056 11074 Dihedral : 6.415 149.875 8853 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.75 % Allowed : 13.83 % Favored : 84.43 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 7808 helix: 1.79 (0.09), residues: 3217 sheet: -0.52 (0.13), residues: 1500 loop : 0.01 (0.11), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 356 HIS 0.013 0.001 HIS 6 653 PHE 0.021 0.001 PHE C 421 TYR 0.015 0.001 TYR 6 136 ARG 0.006 0.000 ARG E 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13950.49 seconds wall clock time: 245 minutes 31.00 seconds (14731.00 seconds total)