Starting phenix.real_space_refine on Sat Jan 18 22:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aod_11841/01_2025/7aod_11841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aod_11841/01_2025/7aod_11841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aod_11841/01_2025/7aod_11841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aod_11841/01_2025/7aod_11841.map" model { file = "/net/cci-nas-00/data/ceres_data/7aod_11841/01_2025/7aod_11841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aod_11841/01_2025/7aod_11841.cif" } resolution = 4.5 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1140 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 328 5.16 5 C 37608 2.51 5 N 10240 2.21 5 O 11068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 449 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 59256 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 10976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1384, 10976 Classifications: {'peptide': 1384} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1317} Chain breaks: 13 Chain: "B" Number of atoms: 9127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9127 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 59, 'TRANS': 1096} Chain breaks: 3 Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 195} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1267 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "J" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "L" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 368 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 10976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1384, 10976 Classifications: {'peptide': 1384} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1317} Chain breaks: 13 Chain: "N" Number of atoms: 9127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9127 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 59, 'TRANS': 1096} Chain breaks: 3 Chain: "O" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "P" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "Q" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 195} Chain: "R" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "S" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1267 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Chain: "T" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "U" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "V" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "W" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "X" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 368 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 483 SG CYS A 63 133.861 103.007 104.136 1.00110.95 S ATOM 501 SG CYS A 66 133.326 105.104 100.919 1.00122.56 S ATOM 565 SG CYS A 73 135.418 103.713 101.118 1.00 95.95 S ATOM 809 SG CYS A 103 175.060 113.810 131.338 1.00150.16 S ATOM 1540 SG CYS A 228 176.932 114.201 131.408 1.00162.65 S ATOM 1562 SG CYS A 231 175.736 116.570 134.919 1.00164.31 S ATOM 19527 SG CYS B1089 144.383 118.948 102.596 1.00114.91 S ATOM 19552 SG CYS B1092 145.828 117.220 103.855 1.00115.80 S ATOM 19708 SG CYS B1115 142.861 116.676 104.612 1.00104.03 S ATOM 27567 SG CYS I 10 214.344 46.920 128.526 1.00178.72 S ATOM 27588 SG CYS I 13 211.550 48.141 129.609 1.00194.95 S ATOM 27693 SG CYS I 27 213.434 49.132 131.602 1.00217.33 S ATOM 27716 SG CYS I 30 212.662 47.936 131.051 1.00214.77 S ATOM 28015 SG CYS J 7 154.125 56.517 48.098 1.00 84.28 S ATOM 28038 SG CYS J 10 156.893 56.951 44.991 1.00106.53 S ATOM 28310 SG CYS J 44 158.227 57.557 45.548 1.00100.24 S ATOM 28316 SG CYS J 45 156.326 55.675 45.139 1.00111.55 S ATOM 29303 SG CYS L 24 137.102 40.422 86.091 1.00 99.09 S ATOM 29322 SG CYS L 27 136.834 38.793 85.789 1.00111.53 S ATOM 29429 SG CYS L 41 135.421 39.107 87.376 1.00102.15 S ATOM 29455 SG CYS L 44 137.764 37.602 87.528 1.00105.50 S ATOM 30105 SG CYS M 63 110.764 56.330 104.007 1.00111.02 S ATOM 30123 SG CYS M 66 111.283 54.233 100.788 1.00124.09 S ATOM 30187 SG CYS M 73 109.197 55.633 100.992 1.00 94.01 S ATOM 30431 SG CYS M 103 69.576 45.687 131.289 1.00151.77 S ATOM 31162 SG CYS M 228 67.702 45.303 131.362 1.00165.63 S ATOM 31184 SG CYS M 231 68.895 42.928 134.870 1.00167.14 S ATOM 49149 SG CYS N1089 100.026 40.506 102.573 1.00117.13 S ATOM 49174 SG CYS N1092 98.589 42.240 103.832 1.00117.43 S ATOM 49330 SG CYS N1115 101.558 42.774 104.585 1.00103.25 S ATOM 57189 SG CYS U 10 30.727 111.437 128.324 1.00173.52 S ATOM 57210 SG CYS U 13 33.331 109.949 129.542 1.00186.06 S ATOM 57315 SG CYS U 27 31.253 109.118 131.411 1.00202.39 S ATOM 57338 SG CYS U 30 32.162 110.243 130.923 1.00200.82 S ATOM 57637 SG CYS V 7 90.146 102.506 48.418 1.00 79.08 S ATOM 57660 SG CYS V 10 87.424 102.121 45.264 1.00 98.08 S ATOM 57932 SG CYS V 44 86.062 101.566 45.803 1.00 93.30 S ATOM 57938 SG CYS V 45 88.030 103.380 45.407 1.00103.69 S ATOM 58925 SG CYS X 24 107.250 119.110 85.915 1.00 99.09 S ATOM 58944 SG CYS X 27 107.563 120.727 85.599 1.00104.70 S ATOM 59051 SG CYS X 41 108.968 120.388 87.189 1.00 99.09 S ATOM 59077 SG CYS X 44 106.667 121.959 87.328 1.00100.30 S Time building chain proxies: 24.86, per 1000 atoms: 0.42 Number of scatterers: 59256 At special positions: 0 Unit cell: (245.669, 160.589, 156.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 12 29.99 S 328 16.00 O 11068 8.00 N 10240 7.00 C 37608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.98 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 76 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 66 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 63 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 73 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 103 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 231 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 228 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1115 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1089 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 27 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 24 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 27 " pdb=" ZN M1701 " pdb="ZN ZN M1701 " - pdb=" NE2 HIS M 76 " pdb="ZN ZN M1701 " - pdb=" SG CYS M 66 " pdb="ZN ZN M1701 " - pdb=" SG CYS M 63 " pdb="ZN ZN M1701 " - pdb=" SG CYS M 73 " pdb=" ZN M1702 " pdb="ZN ZN M1702 " - pdb=" SG CYS M 103 " pdb="ZN ZN M1702 " - pdb=" SG CYS M 231 " pdb="ZN ZN M1702 " - pdb=" SG CYS M 228 " pdb=" ZN N1301 " pdb="ZN ZN N1301 " - pdb=" SG CYS N1115 " pdb="ZN ZN N1301 " - pdb=" SG CYS N1092 " pdb="ZN ZN N1301 " - pdb=" SG CYS N1089 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 13 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 30 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 10 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 27 " pdb=" ZN V 101 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 10 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 7 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 44 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 44 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 24 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 41 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 27 " Number of angles added : 42 14692 Ramachandran restraints generated. 7346 Oldfield, 0 Emsley, 7346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14004 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 86 sheets defined 37.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.59 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.567A pdb=" N VAL A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 112 through 128 removed outlier: 3.873A pdb=" N TYR A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.705A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.805A pdb=" N PHE A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 4.659A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 386 through 411 Processing helix chain 'A' and resid 422 through 446 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 506 through 513 removed outlier: 3.632A pdb=" N ALA A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 634 through 641 removed outlier: 4.012A pdb=" N ASN A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 666 removed outlier: 3.695A pdb=" N ARG A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 672 Processing helix chain 'A' and resid 686 through 698 Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.876A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 807 through 816 removed outlier: 4.156A pdb=" N SER A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 839 removed outlier: 4.120A pdb=" N ILE A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 865 Processing helix chain 'A' and resid 867 through 878 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 899 through 925 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 1004 through 1022 removed outlier: 3.839A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1035 Processing helix chain 'A' and resid 1069 through 1074 removed outlier: 3.662A pdb=" N LYS A1072 " --> pdb=" O ASP A1069 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A1074 " --> pdb=" O THR A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1085 removed outlier: 3.890A pdb=" N ASN A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1093 removed outlier: 3.534A pdb=" N GLN A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.161A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.857A pdb=" N LYS A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1138 through 1152 removed outlier: 3.774A pdb=" N ASN A1152 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1166 Processing helix chain 'A' and resid 1171 through 1185 Processing helix chain 'A' and resid 1194 through 1209 Proline residue: A1205 - end of helix removed outlier: 4.027A pdb=" N MET A1209 " --> pdb=" O PRO A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1273 through 1276 Processing helix chain 'A' and resid 1305 through 1312 removed outlier: 4.214A pdb=" N GLU A1312 " --> pdb=" O GLU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1344 Processing helix chain 'A' and resid 1504 through 1514 Processing helix chain 'A' and resid 1548 through 1553 Processing helix chain 'A' and resid 1568 through 1575 removed outlier: 3.562A pdb=" N ILE A1572 " --> pdb=" O ASP A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1595 removed outlier: 3.752A pdb=" N ALA A1581 " --> pdb=" O GLY A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1613 removed outlier: 3.855A pdb=" N LEU A1605 " --> pdb=" O ASP A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 Processing helix chain 'A' and resid 1633 through 1638 Processing helix chain 'A' and resid 1640 through 1652 removed outlier: 4.053A pdb=" N PHE A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A1651 " --> pdb=" O GLU A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1666 removed outlier: 3.538A pdb=" N VAL A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1676 Processing helix chain 'B' and resid 4 through 13 Processing helix chain 'B' and resid 22 through 41 removed outlier: 3.707A pdb=" N GLN B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.535A pdb=" N ALA B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 199 through 202 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 299 through 312 removed outlier: 3.708A pdb=" N THR B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.563A pdb=" N GLY B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 361 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 409 removed outlier: 3.883A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 468 through 478 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.637A pdb=" N ALA B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.594A pdb=" N ASN B 596 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.739A pdb=" N ASN B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 746 through 750 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 935 through 939 removed outlier: 3.681A pdb=" N PHE B 939 " --> pdb=" O PRO B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 961 removed outlier: 3.967A pdb=" N PHE B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 959 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 989 Processing helix chain 'B' and resid 1059 through 1068 Processing helix chain 'B' and resid 1069 through 1078 Processing helix chain 'B' and resid 1152 through 1164 removed outlier: 3.631A pdb=" N ASN B1156 " --> pdb=" O PRO B1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.538A pdb=" N ALA C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.616A pdb=" N VAL C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 4.101A pdb=" N GLU C 184 " --> pdb=" O GLY C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.513A pdb=" N PHE C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.626A pdb=" N ILE C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 33 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 83 through 88 Processing helix chain 'E' and resid 88 through 97 removed outlier: 4.083A pdb=" N HIS E 92 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.774A pdb=" N LYS E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 76 through 93 removed outlier: 4.103A pdb=" N ALA F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.706A pdb=" N GLN F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 removed outlier: 4.531A pdb=" N ARG G 23 " --> pdb=" O GLY G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 removed outlier: 4.070A pdb=" N ALA G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 71 Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'J' and resid 14 through 17 Processing helix chain 'J' and resid 18 through 26 removed outlier: 4.422A pdb=" N LEU J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 39 removed outlier: 3.888A pdb=" N LYS J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 52 removed outlier: 4.756A pdb=" N ILE J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 43 through 55 removed outlier: 4.596A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 removed outlier: 3.594A pdb=" N VAL K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 28 removed outlier: 3.566A pdb=" N VAL M 24 " --> pdb=" O ASP M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 101 Processing helix chain 'M' and resid 112 through 128 removed outlier: 3.873A pdb=" N TYR M 128 " --> pdb=" O LYS M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 136 Processing helix chain 'M' and resid 137 through 139 No H-bonds generated for 'chain 'M' and resid 137 through 139' Processing helix chain 'M' and resid 173 through 195 removed outlier: 3.705A pdb=" N GLN M 195 " --> pdb=" O ALA M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 223 Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.807A pdb=" N PHE M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 339 removed outlier: 4.658A pdb=" N VAL M 328 " --> pdb=" O THR M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 347 Processing helix chain 'M' and resid 357 through 359 No H-bonds generated for 'chain 'M' and resid 357 through 359' Processing helix chain 'M' and resid 386 through 411 Processing helix chain 'M' and resid 422 through 446 Processing helix chain 'M' and resid 463 through 469 Processing helix chain 'M' and resid 506 through 513 removed outlier: 3.632A pdb=" N ALA M 510 " --> pdb=" O PRO M 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 523 through 534 Processing helix chain 'M' and resid 558 through 568 Processing helix chain 'M' and resid 585 through 589 Processing helix chain 'M' and resid 612 through 614 No H-bonds generated for 'chain 'M' and resid 612 through 614' Processing helix chain 'M' and resid 634 through 641 removed outlier: 4.011A pdb=" N ASN M 638 " --> pdb=" O TYR M 634 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER M 639 " --> pdb=" O ALA M 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 656 through 666 removed outlier: 3.695A pdb=" N ARG M 660 " --> pdb=" O SER M 656 " (cutoff:3.500A) Processing helix chain 'M' and resid 668 through 672 Processing helix chain 'M' and resid 686 through 698 Processing helix chain 'M' and resid 704 through 717 Processing helix chain 'M' and resid 717 through 722 removed outlier: 3.875A pdb=" N THR M 721 " --> pdb=" O LYS M 717 " (cutoff:3.500A) Processing helix chain 'M' and resid 742 through 754 Processing helix chain 'M' and resid 771 through 775 Processing helix chain 'M' and resid 807 through 816 removed outlier: 4.156A pdb=" N SER M 811 " --> pdb=" O GLY M 807 " (cutoff:3.500A) Processing helix chain 'M' and resid 816 through 839 removed outlier: 4.121A pdb=" N ILE M 820 " --> pdb=" O TYR M 816 " (cutoff:3.500A) Processing helix chain 'M' and resid 851 through 865 Processing helix chain 'M' and resid 867 through 878 Processing helix chain 'M' and resid 884 through 896 Processing helix chain 'M' and resid 899 through 925 Processing helix chain 'M' and resid 936 through 944 Processing helix chain 'M' and resid 949 through 958 Processing helix chain 'M' and resid 988 through 992 Processing helix chain 'M' and resid 1004 through 1022 removed outlier: 3.839A pdb=" N PHE M1010 " --> pdb=" O GLN M1006 " (cutoff:3.500A) Processing helix chain 'M' and resid 1030 through 1035 Processing helix chain 'M' and resid 1069 through 1074 removed outlier: 3.662A pdb=" N LYS M1072 " --> pdb=" O ASP M1069 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS M1074 " --> pdb=" O THR M1071 " (cutoff:3.500A) Processing helix chain 'M' and resid 1078 through 1085 removed outlier: 3.891A pdb=" N ASN M1085 " --> pdb=" O PHE M1081 " (cutoff:3.500A) Processing helix chain 'M' and resid 1086 through 1093 removed outlier: 3.534A pdb=" N GLN M1091 " --> pdb=" O LYS M1087 " (cutoff:3.500A) Processing helix chain 'M' and resid 1094 through 1102 removed outlier: 4.161A pdb=" N SER M1100 " --> pdb=" O LYS M1096 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA M1101 " --> pdb=" O SER M1097 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL M1102 " --> pdb=" O VAL M1098 " (cutoff:3.500A) Processing helix chain 'M' and resid 1104 through 1116 removed outlier: 3.856A pdb=" N LYS M1112 " --> pdb=" O SER M1108 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS M1113 " --> pdb=" O SER M1109 " (cutoff:3.500A) Processing helix chain 'M' and resid 1123 through 1128 Processing helix chain 'M' and resid 1138 through 1152 removed outlier: 3.774A pdb=" N ASN M1152 " --> pdb=" O TYR M1148 " (cutoff:3.500A) Processing helix chain 'M' and resid 1162 through 1166 Processing helix chain 'M' and resid 1171 through 1185 Processing helix chain 'M' and resid 1194 through 1209 Proline residue: M1205 - end of helix removed outlier: 4.026A pdb=" N MET M1209 " --> pdb=" O PRO M1205 " (cutoff:3.500A) Processing helix chain 'M' and resid 1227 through 1236 Processing helix chain 'M' and resid 1256 through 1268 Processing helix chain 'M' and resid 1273 through 1276 Processing helix chain 'M' and resid 1305 through 1312 removed outlier: 4.214A pdb=" N GLU M1312 " --> pdb=" O GLU M1308 " (cutoff:3.500A) Processing helix chain 'M' and resid 1316 through 1344 Processing helix chain 'M' and resid 1504 through 1514 Processing helix chain 'M' and resid 1548 through 1553 Processing helix chain 'M' and resid 1568 through 1575 removed outlier: 3.562A pdb=" N ILE M1572 " --> pdb=" O ASP M1568 " (cutoff:3.500A) Processing helix chain 'M' and resid 1577 through 1595 removed outlier: 3.753A pdb=" N ALA M1581 " --> pdb=" O GLY M1577 " (cutoff:3.500A) Processing helix chain 'M' and resid 1601 through 1613 removed outlier: 3.856A pdb=" N LEU M1605 " --> pdb=" O ASP M1601 " (cutoff:3.500A) Processing helix chain 'M' and resid 1622 through 1627 Processing helix chain 'M' and resid 1633 through 1638 Processing helix chain 'M' and resid 1640 through 1652 removed outlier: 4.054A pdb=" N PHE M1644 " --> pdb=" O THR M1640 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG M1651 " --> pdb=" O GLU M1647 " (cutoff:3.500A) Processing helix chain 'M' and resid 1659 through 1666 removed outlier: 3.539A pdb=" N VAL M1666 " --> pdb=" O SER M1662 " (cutoff:3.500A) Processing helix chain 'M' and resid 1672 through 1676 Processing helix chain 'N' and resid 4 through 13 Processing helix chain 'N' and resid 22 through 41 removed outlier: 3.707A pdb=" N GLN N 26 " --> pdb=" O PHE N 22 " (cutoff:3.500A) Proline residue: N 31 - end of helix Processing helix chain 'N' and resid 43 through 51 Processing helix chain 'N' and resid 102 through 109 removed outlier: 3.536A pdb=" N ALA N 106 " --> pdb=" O TYR N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 162 Processing helix chain 'N' and resid 199 through 202 Processing helix chain 'N' and resid 252 through 260 Processing helix chain 'N' and resid 263 through 272 Processing helix chain 'N' and resid 278 through 294 Processing helix chain 'N' and resid 299 through 312 removed outlier: 3.708A pdb=" N THR N 303 " --> pdb=" O SER N 299 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 334 removed outlier: 3.563A pdb=" N GLY N 327 " --> pdb=" O ASP N 323 " (cutoff:3.500A) Processing helix chain 'N' and resid 341 through 361 Processing helix chain 'N' and resid 371 through 373 No H-bonds generated for 'chain 'N' and resid 371 through 373' Processing helix chain 'N' and resid 379 through 409 removed outlier: 3.883A pdb=" N LEU N 383 " --> pdb=" O LEU N 379 " (cutoff:3.500A) Processing helix chain 'N' and resid 418 through 429 Processing helix chain 'N' and resid 433 through 444 Processing helix chain 'N' and resid 468 through 478 Processing helix chain 'N' and resid 482 through 487 removed outlier: 3.637A pdb=" N ALA N 486 " --> pdb=" O GLY N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 535 through 543 Processing helix chain 'N' and resid 573 through 596 removed outlier: 3.594A pdb=" N ASN N 596 " --> pdb=" O VAL N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 653 through 657 Processing helix chain 'N' and resid 677 through 682 Processing helix chain 'N' and resid 683 through 688 Processing helix chain 'N' and resid 696 through 708 removed outlier: 3.740A pdb=" N ASN N 700 " --> pdb=" O GLN N 696 " (cutoff:3.500A) Processing helix chain 'N' and resid 740 through 745 Processing helix chain 'N' and resid 746 through 750 Processing helix chain 'N' and resid 775 through 781 Processing helix chain 'N' and resid 821 through 826 Processing helix chain 'N' and resid 935 through 939 removed outlier: 3.681A pdb=" N PHE N 939 " --> pdb=" O PRO N 936 " (cutoff:3.500A) Processing helix chain 'N' and resid 944 through 961 removed outlier: 3.967A pdb=" N PHE N 948 " --> pdb=" O THR N 944 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS N 959 " --> pdb=" O LYS N 955 " (cutoff:3.500A) Processing helix chain 'N' and resid 976 through 989 Processing helix chain 'N' and resid 1059 through 1068 Processing helix chain 'N' and resid 1069 through 1078 Processing helix chain 'N' and resid 1152 through 1164 removed outlier: 3.631A pdb=" N ASN N1156 " --> pdb=" O PRO N1152 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 46 Processing helix chain 'O' and resid 66 through 79 removed outlier: 3.538A pdb=" N ALA O 70 " --> pdb=" O ASP O 66 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 110 removed outlier: 3.616A pdb=" N VAL O 110 " --> pdb=" O ARG O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 186 removed outlier: 4.100A pdb=" N GLU O 184 " --> pdb=" O GLY O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 227 Processing helix chain 'O' and resid 247 through 258 removed outlier: 3.513A pdb=" N PHE O 258 " --> pdb=" O PHE O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 292 Processing helix chain 'O' and resid 293 through 297 Processing helix chain 'O' and resid 319 through 345 removed outlier: 3.627A pdb=" N ILE O 345 " --> pdb=" O SER O 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 33 Processing helix chain 'P' and resid 45 through 58 Processing helix chain 'Q' and resid 6 through 14 Processing helix chain 'Q' and resid 37 through 45 Processing helix chain 'Q' and resid 83 through 88 Processing helix chain 'Q' and resid 88 through 97 removed outlier: 4.083A pdb=" N HIS Q 92 " --> pdb=" O ARG Q 88 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR Q 93 " --> pdb=" O THR Q 89 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU Q 94 " --> pdb=" O PHE Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 122 removed outlier: 3.775A pdb=" N LYS Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 163 Processing helix chain 'Q' and resid 177 through 184 Processing helix chain 'R' and resid 76 through 93 removed outlier: 4.102A pdb=" N ALA R 81 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 117 removed outlier: 3.706A pdb=" N GLN R 117 " --> pdb=" O LYS R 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 23 removed outlier: 4.531A pdb=" N ARG S 23 " --> pdb=" O GLY S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 37 removed outlier: 4.070A pdb=" N ALA S 28 " --> pdb=" O ASP S 24 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 71 Processing helix chain 'U' and resid 57 through 62 Processing helix chain 'V' and resid 14 through 17 Processing helix chain 'V' and resid 18 through 26 removed outlier: 4.422A pdb=" N LEU V 24 " --> pdb=" O THR V 20 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU V 25 " --> pdb=" O TYR V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 39 removed outlier: 3.888A pdb=" N LYS V 37 " --> pdb=" O GLU V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 52 removed outlier: 4.757A pdb=" N ILE V 49 " --> pdb=" O CYS V 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU V 50 " --> pdb=" O ARG V 46 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR V 51 " --> pdb=" O ARG V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Processing helix chain 'W' and resid 43 through 55 removed outlier: 4.596A pdb=" N SER W 49 " --> pdb=" O THR W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 113 removed outlier: 3.594A pdb=" N VAL W 90 " --> pdb=" O THR W 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU W 113 " --> pdb=" O PHE W 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 4.564A pdb=" N SER A 13 " --> pdb=" O GLU B1172 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B1172 " --> pdb=" O SER A 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.249A pdb=" N LYS A 30 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 81 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN A 363 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N ILE A 84 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N PHE A 361 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.992A pdb=" N ASN A 650 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.612A pdb=" N HIS A 543 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A 596 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA A 541 " --> pdb=" O HIS A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 734 through 736 removed outlier: 6.557A pdb=" N ILE H 75 " --> pdb=" O GLN A 735 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 767 removed outlier: 6.918A pdb=" N ASP A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 961 through 962 Processing sheet with id=AB1, first strand: chain 'A' and resid 1524 through 1529 removed outlier: 4.978A pdb=" N ARG A1526 " --> pdb=" O GLU A1545 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A1250 " --> pdb=" O ASN A1562 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN A1562 " --> pdb=" O ARG A1250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1270 through 1271 removed outlier: 7.216A pdb=" N LEU A1270 " --> pdb=" O ILE A1518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1479 through 1482 removed outlier: 3.567A pdb=" N VAL A1281 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR I 46 " --> pdb=" O VAL A1281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1678 through 1679 Processing sheet with id=AB5, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.660A pdb=" N LYS B 120 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 82 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 118 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE B 84 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG B 116 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 138 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 119 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU B 136 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE B 121 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N MET B 134 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.892A pdb=" N LEU B 185 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.356A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 231 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 215 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 226 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS B 242 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.655A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 645 " --> pdb=" O HIS B 640 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.655A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 567 through 572 removed outlier: 5.621A pdb=" N ILE B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 563 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY B 569 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU B 625 " --> pdb=" O TRP B 558 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N CYS B 560 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 627 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLN B 562 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 725 through 729 removed outlier: 4.292A pdb=" N GLN B 885 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 870 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL B 871 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS L 51 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET L 49 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 737 through 738 Processing sheet with id=AC5, first strand: chain 'B' and resid 773 through 774 removed outlier: 3.566A pdb=" N ILE B 933 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE B 932 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 757 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 934 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 759 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 773 through 774 removed outlier: 3.566A pdb=" N ILE B 933 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE B 932 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 757 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 934 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 759 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 809 through 810 Processing sheet with id=AC8, first strand: chain 'B' and resid 843 through 845 removed outlier: 6.658A pdb=" N GLU B 858 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1085 through 1089 Processing sheet with id=AD1, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 53 removed outlier: 5.547A pdb=" N ILE C 50 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU C 61 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 237 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ASP C 306 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ARG C 235 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N TYR C 308 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N SER C 233 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N PHE C 310 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N THR C 231 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL C 312 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N VAL C 229 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.325A pdb=" N VAL C 140 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU C 208 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN C 94 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP C 210 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 216 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE C 86 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY C 218 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU C 84 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 89 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE L 60 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 91 " --> pdb=" O VAL L 58 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL L 58 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.507A pdb=" N GLU C 148 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 170 removed outlier: 6.694A pdb=" N VAL C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 263 through 267 removed outlier: 3.508A pdb=" N GLN C 274 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.611A pdb=" N LYS E 62 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR E 71 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR E 101 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 126 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 102 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.520A pdb=" N LYS E 147 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 9 through 17 removed outlier: 5.256A pdb=" N ASP G 77 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN G 53 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 9 through 17 Processing sheet with id=AE2, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AE3, first strand: chain 'G' and resid 109 through 114 removed outlier: 7.515A pdb=" N HIS G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL G 96 " --> pdb=" O HIS G 100 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY G 102 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL G 153 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 15 through 17 Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 26 removed outlier: 4.264A pdb=" N THR I 25 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR I 34 " --> pdb=" O THR I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 22 through 24 Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 35 removed outlier: 3.568A pdb=" N VAL K 35 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 11 through 13 removed outlier: 4.450A pdb=" N SER M 13 " --> pdb=" O GLU N1172 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU N1172 " --> pdb=" O SER M 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'M' and resid 16 through 18 Processing sheet with id=AF1, first strand: chain 'M' and resid 30 through 31 removed outlier: 6.249A pdb=" N LYS M 30 " --> pdb=" O HIS M 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL M 81 " --> pdb=" O LYS M 30 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN M 363 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N ILE M 84 " --> pdb=" O PHE M 361 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N PHE M 361 " --> pdb=" O ILE M 84 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 487 through 490 removed outlier: 3.992A pdb=" N ASN M 650 " --> pdb=" O ASN M 606 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 492 through 494 Processing sheet with id=AF4, first strand: chain 'M' and resid 514 through 515 removed outlier: 3.611A pdb=" N HIS M 543 " --> pdb=" O TYR M 594 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS M 596 " --> pdb=" O ALA M 541 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA M 541 " --> pdb=" O HIS M 596 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 734 through 736 removed outlier: 6.462A pdb=" N ILE T 75 " --> pdb=" O GLN M 735 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 764 through 767 removed outlier: 6.918A pdb=" N ASP M 787 " --> pdb=" O LEU M 791 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU M 791 " --> pdb=" O ASP M 787 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 961 through 962 Processing sheet with id=AF8, first strand: chain 'M' and resid 1524 through 1529 removed outlier: 4.978A pdb=" N ARG M1526 " --> pdb=" O GLU M1545 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG M1250 " --> pdb=" O ASN M1562 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN M1562 " --> pdb=" O ARG M1250 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 1270 through 1271 removed outlier: 7.216A pdb=" N LEU M1270 " --> pdb=" O ILE M1518 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 1479 through 1482 removed outlier: 3.500A pdb=" N THR U 46 " --> pdb=" O VAL M1281 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 1678 through 1679 Processing sheet with id=AG3, first strand: chain 'N' and resid 55 through 57 removed outlier: 6.659A pdb=" N LYS N 120 " --> pdb=" O ASP N 80 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL N 82 " --> pdb=" O VAL N 118 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL N 118 " --> pdb=" O VAL N 82 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE N 84 " --> pdb=" O ARG N 116 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG N 116 " --> pdb=" O ILE N 84 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY N 138 " --> pdb=" O LEU N 117 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU N 119 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU N 136 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE N 121 " --> pdb=" O MET N 134 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N MET N 134 " --> pdb=" O PHE N 121 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 173 through 175 Processing sheet with id=AG5, first strand: chain 'N' and resid 375 through 378 removed outlier: 3.892A pdb=" N LEU N 185 " --> pdb=" O LEU N 378 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 194 through 197 removed outlier: 5.355A pdb=" N TYR N 211 " --> pdb=" O TYR N 231 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR N 231 " --> pdb=" O TYR N 211 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE N 215 " --> pdb=" O ASN N 227 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR N 226 " --> pdb=" O HIS N 242 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS N 242 " --> pdb=" O THR N 226 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 526 through 528 removed outlier: 3.655A pdb=" N ARG N 633 " --> pdb=" O VAL N 528 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU N 645 " --> pdb=" O HIS N 640 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 526 through 528 removed outlier: 3.655A pdb=" N ARG N 633 " --> pdb=" O VAL N 528 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 567 through 572 removed outlier: 5.621A pdb=" N ILE N 567 " --> pdb=" O LEU N 563 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU N 563 " --> pdb=" O ILE N 567 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY N 569 " --> pdb=" O VAL N 561 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU N 625 " --> pdb=" O TRP N 558 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N CYS N 560 " --> pdb=" O LEU N 625 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU N 627 " --> pdb=" O CYS N 560 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN N 562 " --> pdb=" O LEU N 627 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 725 through 729 removed outlier: 4.293A pdb=" N GLN N 885 " --> pdb=" O LEU N 874 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU N 870 " --> pdb=" O LYS N 889 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL N 871 " --> pdb=" O LYS X 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET X 49 " --> pdb=" O LEU N 873 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 737 through 738 Processing sheet with id=AH3, first strand: chain 'N' and resid 773 through 774 removed outlier: 3.565A pdb=" N ILE N 933 " --> pdb=" O ILE N 773 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE N 932 " --> pdb=" O ASN N 755 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL N 757 " --> pdb=" O ILE N 932 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE N 934 " --> pdb=" O VAL N 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA N 759 " --> pdb=" O ILE N 934 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR N1012 " --> pdb=" O VAL N 760 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 773 through 774 removed outlier: 3.565A pdb=" N ILE N 933 " --> pdb=" O ILE N 773 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE N 932 " --> pdb=" O ASN N 755 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL N 757 " --> pdb=" O ILE N 932 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE N 934 " --> pdb=" O VAL N 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA N 759 " --> pdb=" O ILE N 934 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR N1012 " --> pdb=" O VAL N 760 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 809 through 810 Processing sheet with id=AH6, first strand: chain 'N' and resid 843 through 845 removed outlier: 6.658A pdb=" N GLU N 858 " --> pdb=" O ILE N 844 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 1085 through 1089 Processing sheet with id=AH8, first strand: chain 'N' and resid 1098 through 1099 Processing sheet with id=AH9, first strand: chain 'O' and resid 48 through 53 removed outlier: 5.547A pdb=" N ILE O 50 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU O 61 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU O 237 " --> pdb=" O VAL O 304 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ASP O 306 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ARG O 235 " --> pdb=" O ASP O 306 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N TYR O 308 " --> pdb=" O SER O 233 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N SER O 233 " --> pdb=" O TYR O 308 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N PHE O 310 " --> pdb=" O THR O 231 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N THR O 231 " --> pdb=" O PHE O 310 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL O 312 " --> pdb=" O VAL O 229 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N VAL O 229 " --> pdb=" O VAL O 312 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 175 through 177 removed outlier: 4.325A pdb=" N VAL O 140 " --> pdb=" O LYS O 177 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU O 208 " --> pdb=" O ASN O 94 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN O 94 " --> pdb=" O GLU O 208 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP O 210 " --> pdb=" O ILE O 92 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE O 216 " --> pdb=" O PHE O 86 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE O 86 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY O 218 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU O 84 " --> pdb=" O GLY O 218 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL O 89 " --> pdb=" O PHE X 60 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE X 60 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE O 91 " --> pdb=" O VAL X 58 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL X 58 " --> pdb=" O ILE O 91 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 148 through 149 removed outlier: 3.507A pdb=" N GLU O 148 " --> pdb=" O VAL O 165 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 168 through 170 removed outlier: 6.694A pdb=" N VAL O 169 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 263 through 267 removed outlier: 3.509A pdb=" N GLN O 274 " --> pdb=" O GLU O 266 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 27 through 28 removed outlier: 4.611A pdb=" N LYS Q 62 " --> pdb=" O GLY Q 28 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR Q 71 " --> pdb=" O HIS Q 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Q 101 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR Q 126 " --> pdb=" O LYS Q 100 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY Q 102 " --> pdb=" O THR Q 126 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 147 through 149 removed outlier: 3.519A pdb=" N LYS Q 147 " --> pdb=" O VAL Q 194 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'S' and resid 9 through 17 removed outlier: 5.256A pdb=" N ASP S 77 " --> pdb=" O ASN S 53 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN S 53 " --> pdb=" O ASP S 77 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'S' and resid 9 through 17 Processing sheet with id=AI9, first strand: chain 'S' and resid 40 through 41 Processing sheet with id=AJ1, first strand: chain 'S' and resid 109 through 114 removed outlier: 7.514A pdb=" N HIS S 100 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL S 96 " --> pdb=" O HIS S 100 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY S 102 " --> pdb=" O ASN S 94 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL S 153 " --> pdb=" O THR S 169 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'T' and resid 15 through 17 Processing sheet with id=AJ3, first strand: chain 'U' and resid 25 through 26 removed outlier: 4.264A pdb=" N THR U 25 " --> pdb=" O TYR U 34 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR U 34 " --> pdb=" O THR U 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'W' and resid 22 through 24 Processing sheet with id=AJ5, first strand: chain 'W' and resid 34 through 35 removed outlier: 3.568A pdb=" N VAL W 35 " --> pdb=" O ILE W 79 " (cutoff:3.500A) 2306 hydrogen bonds defined for protein. 6420 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: 25.59 Time building geometry restraints manager: 14.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 19660 1.36 - 1.49: 15236 1.49 - 1.63: 25012 1.63 - 1.76: 0 1.76 - 1.90: 528 Bond restraints: 60436 Sorted by residual: bond pdb=" SD MET F 112 " pdb=" CE MET F 112 " ideal model delta sigma weight residual 1.791 1.899 -0.108 2.50e-02 1.60e+03 1.86e+01 bond pdb=" SD MET R 112 " pdb=" CE MET R 112 " ideal model delta sigma weight residual 1.791 1.898 -0.107 2.50e-02 1.60e+03 1.85e+01 bond pdb=" CB GLN R 109 " pdb=" CG GLN R 109 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.85e+00 bond pdb=" CB GLN F 109 " pdb=" CG GLN F 109 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.80e+00 bond pdb=" C HIS B 192 " pdb=" N PRO B 193 " ideal model delta sigma weight residual 1.332 1.304 0.028 1.12e-02 7.97e+03 6.27e+00 ... (remaining 60431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 80207 2.70 - 5.39: 1300 5.39 - 8.09: 119 8.09 - 10.78: 22 10.78 - 13.48: 6 Bond angle restraints: 81654 Sorted by residual: angle pdb=" C GLY Q 49 " pdb=" N ARG Q 50 " pdb=" CA ARG Q 50 " ideal model delta sigma weight residual 121.70 131.83 -10.13 1.80e+00 3.09e-01 3.17e+01 angle pdb=" C GLY E 49 " pdb=" N ARG E 50 " pdb=" CA ARG E 50 " ideal model delta sigma weight residual 121.70 131.82 -10.12 1.80e+00 3.09e-01 3.16e+01 angle pdb=" N VAL E 91 " pdb=" CA VAL E 91 " pdb=" C VAL E 91 " ideal model delta sigma weight residual 111.62 107.54 4.08 7.90e-01 1.60e+00 2.67e+01 angle pdb=" N VAL Q 91 " pdb=" CA VAL Q 91 " pdb=" C VAL Q 91 " ideal model delta sigma weight residual 111.62 107.55 4.07 7.90e-01 1.60e+00 2.66e+01 angle pdb=" C ASP T 17 " pdb=" N LYS T 18 " pdb=" CA LYS T 18 " ideal model delta sigma weight residual 121.70 130.61 -8.91 1.80e+00 3.09e-01 2.45e+01 ... (remaining 81649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 32610 17.43 - 34.86: 3335 34.86 - 52.29: 590 52.29 - 69.73: 175 69.73 - 87.16: 50 Dihedral angle restraints: 36760 sinusoidal: 15056 harmonic: 21704 Sorted by residual: dihedral pdb=" CA ILE A 84 " pdb=" C ILE A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta harmonic sigma weight residual 180.00 -118.10 -61.90 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ILE M 84 " pdb=" C ILE M 84 " pdb=" N PRO M 85 " pdb=" CA PRO M 85 " ideal model delta harmonic sigma weight residual -180.00 -118.14 -61.86 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ARG E 50 " pdb=" C ARG E 50 " pdb=" N ASN E 51 " pdb=" CA ASN E 51 " ideal model delta harmonic sigma weight residual 180.00 138.02 41.98 0 5.00e+00 4.00e-02 7.05e+01 ... (remaining 36757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 5605 0.037 - 0.074: 2499 0.074 - 0.110: 841 0.110 - 0.147: 157 0.147 - 0.184: 24 Chirality restraints: 9126 Sorted by residual: chirality pdb=" CB ILE R 120 " pdb=" CA ILE R 120 " pdb=" CG1 ILE R 120 " pdb=" CG2 ILE R 120 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CB ILE F 120 " pdb=" CA ILE F 120 " pdb=" CG1 ILE F 120 " pdb=" CG2 ILE F 120 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CB VAL N 605 " pdb=" CA VAL N 605 " pdb=" CG1 VAL N 605 " pdb=" CG2 VAL N 605 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 9123 not shown) Planarity restraints: 10498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 84 " -0.058 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO M 85 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO M 85 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO M 85 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " 0.058 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO A 85 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 817 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO N 818 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO N 818 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO N 818 " -0.034 5.00e-02 4.00e+02 ... (remaining 10495 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 629 2.47 - 3.07: 46264 3.07 - 3.68: 94437 3.68 - 4.29: 135700 4.29 - 4.90: 214645 Nonbonded interactions: 491675 Sorted by model distance: nonbonded pdb=" O VAL A1279 " pdb=" OG SER I 48 " model vdw 1.858 3.040 nonbonded pdb=" N CYS M 106 " pdb="ZN ZN M1702 " model vdw 1.888 2.310 nonbonded pdb=" N CYS A 106 " pdb="ZN ZN A1702 " model vdw 1.889 2.310 nonbonded pdb=" OG1 THR V 23 " pdb=" OE2 GLU V 27 " model vdw 1.945 3.040 nonbonded pdb=" OG1 THR J 23 " pdb=" OE2 GLU J 27 " model vdw 1.945 3.040 ... (remaining 491670 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'B' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'F' selection = chain 'R' } ncs_group { reference = chain 'D' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'Q' } Set up NCS constraints Number of NCS constrained groups: 12 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'V' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'W' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'R' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'U' } pdb_interpretation.ncs_group { reference = chain 'L' selection = chain 'X' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'S' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'T' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'Q' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.060 Extract box with map and model: 1.840 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 115.380 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.007 0.108 60436 Z= 0.424 Angle : 0.892 13.479 81654 Z= 0.508 Chirality : 0.046 0.184 9126 Planarity : 0.005 0.089 10498 Dihedral : 14.842 87.157 22756 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.73 % Favored : 88.95 % Rotamer: Outliers : 1.95 % Allowed : 9.57 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.26 % 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: -4.20 (0.08), residues: 7346 helix: -2.26 (0.08), residues: 2412 sheet: -2.58 (0.14), residues: 1060 loop : -3.27 (0.08), residues: 3874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP Q 15 HIS 0.012 0.002 HIS M 543 PHE 0.024 0.002 PHE B 939 TYR 0.022 0.002 TYR A1031 ARG 0.017 0.001 ARG N 820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14692 Ramachandran restraints generated. 7346 Oldfield, 0 Emsley, 7346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14692 Ramachandran restraints generated. 7346 Oldfield, 0 Emsley, 7346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8864 (t) REVERT: A 568 GLN cc_start: 0.8688 (pt0) cc_final: 0.8286 (tt0) REVERT: A 624 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7793 (tp) REVERT: A 630 ILE cc_start: 0.8523 (pt) cc_final: 0.8044 (pt) REVERT: A 832 PHE cc_start: 0.8990 (m-10) cc_final: 0.8685 (m-10) REVERT: A 845 MET cc_start: 0.7904 (tpt) cc_final: 0.6364 (pmm) REVERT: A 947 LYS cc_start: 0.8341 (tptt) cc_final: 0.7710 (tmtt) REVERT: A 1036 LEU cc_start: 0.8469 (tp) cc_final: 0.8202 (tt) REVERT: A 1038 LYS cc_start: 0.8551 (tmtt) cc_final: 0.7832 (ttmt) outliers start: 11 outliers final: 3 residues processed: 171 average time/residue: 0.2119 time to fit residues: 50.4857 Evaluate side-chains 108 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 1.012 Evaluate side-chains 48 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.234 Fit side-chains REVERT: C 92 ILE cc_start: 0.7998 (mm) cc_final: 0.7150 (mm) REVERT: C 141 PHE cc_start: 0.8206 (m-80) cc_final: 0.7711 (m-80) REVERT: C 210 ASP cc_start: 0.8476 (t0) cc_final: 0.8192 (t0) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.1466 time to fit residues: 7.7205 Evaluate side-chains 21 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.233 Evaluate side-chains 16 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.053 Fit side-chains REVERT: J 58 LYS cc_start: 0.7999 (tttt) cc_final: 0.7177 (mptt) outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.0827 time to fit residues: 1.4694 Evaluate side-chains 9 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.053 Evaluate side-chains 154 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.5553 (tmm) cc_final: 0.4621 (tmm) REVERT: B 109 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.6902 (mmt-90) REVERT: B 267 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8786 (mm) REVERT: B 288 MET cc_start: 0.8191 (tmm) cc_final: 0.7962 (tpp) REVERT: B 634 MET cc_start: 0.7493 (mtm) cc_final: 0.7030 (mpp) REVERT: B 708 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7691 (ttpt) REVERT: B 721 ARG cc_start: 0.7819 (mtp85) cc_final: 0.6710 (mmm160) REVERT: B 745 TYR cc_start: 0.8198 (m-80) cc_final: 0.7984 (m-80) REVERT: B 772 MET cc_start: 0.8592 (ptm) cc_final: 0.7828 (ptm) REVERT: B 837 LYS cc_start: 0.8808 (tttt) cc_final: 0.8318 (mptt) REVERT: B 1161 GLU cc_start: 0.8769 (mm-30) cc_final: 0.7631 (tm-30) REVERT: B 1169 MET cc_start: 0.8425 (pmm) cc_final: 0.7526 (tpt) REVERT: B 1170 MET cc_start: 0.8061 (ptp) cc_final: 0.7853 (mpp) outliers start: 12 outliers final: 3 residues processed: 152 average time/residue: 0.1907 time to fit residues: 39.7293 Evaluate side-chains 99 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.803 Evaluate side-chains 27 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.067 Fit side-chains REVERT: K 41 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8341 (mmtp) REVERT: K 42 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7364 (mm-30) REVERT: K 75 MET cc_start: 0.7267 (ttm) cc_final: 0.6528 (ttm) outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.1175 time to fit residues: 3.4180 Evaluate side-chains 13 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.068 Evaluate side-chains 22 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: F 70 THR cc_start: 0.8470 (m) cc_final: 0.8108 (t) outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 0.0731 time to fit residues: 1.7245 Evaluate side-chains 13 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.060 Evaluate side-chains 15 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.032 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.2152 time to fit residues: 3.3175 Evaluate side-chains 6 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.032 Evaluate side-chains 16 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.040 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 16 average time/residue: 0.0714 time to fit residues: 1.2549 Evaluate side-chains 2 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.039 Evaluate side-chains 16 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.2743 time to fit residues: 4.4900 Evaluate side-chains 13 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.036 Evaluate side-chains 23 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.114 Fit side-chains REVERT: G 56 PHE cc_start: 0.8159 (p90) cc_final: 0.7894 (p90) outliers start: 5 outliers final: 0 residues processed: 23 average time/residue: 0.1314 time to fit residues: 3.3973 Evaluate side-chains 7 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.115 Evaluate side-chains 21 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: H 7 LEU cc_start: 0.7845 (mt) cc_final: 0.7624 (mt) REVERT: H 94 TYR cc_start: 0.8282 (m-80) cc_final: 0.7971 (m-80) outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1864 time to fit residues: 4.1952 Evaluate side-chains 12 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.091 Evaluate side-chains 35 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: E 11 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.8828 (p) outliers start: 8 outliers final: 2 residues processed: 34 average time/residue: 0.2186 time to fit residues: 8.0802 Evaluate side-chains 16 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 619 optimal weight: 2.9990 chunk 556 optimal weight: 0.5980 chunk 308 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 375 optimal weight: 0.0870 chunk 297 optimal weight: 0.0970 chunk 575 optimal weight: 9.9990 chunk 222 optimal weight: 0.0570 chunk 349 optimal weight: 4.9990 chunk 428 optimal weight: 7.9990 chunk 666 optimal weight: 8.9990 overall best weight: 0.7676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 GLN M 60 ASN M 117 HIS M 501 ASN M 533 ASN M 536 HIS ** M 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 546 ASN M 568 GLN M 599 ASN M 655 GLN M 856 ASN M 860 GLN M 889 ASN M 937 HIS ** M 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1073 GLN ** M1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1519 HIS ** M1548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1604 HIS ** M1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 182 GLN O 207 GLN O 214 HIS ** O 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 98 ASN B 126 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 300 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN B 733 GLN ** B 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 HIS ** B 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN ** B1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 29 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.073637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.064448 restraints weight = 75325.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.065694 restraints weight = 47678.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066603 restraints weight = 33483.812| |-----------------------------------------------------------------------------| r_work (final): 0.3508 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.062713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.055392 restraints weight = 19024.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056483 restraints weight = 12214.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.057208 restraints weight = 8571.206| |-----------------------------------------------------------------------------| r_work (final): 0.3401 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.053117 restraints weight = 4055.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.054426 restraints weight = 2631.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.055292 restraints weight = 1815.554| |-----------------------------------------------------------------------------| r_work (final): 0.3262 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.066143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.058263 restraints weight = 56857.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.059615 restraints weight = 35174.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060580 restraints weight = 24429.207| |-----------------------------------------------------------------------------| r_work (final): 0.3438 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.059679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.054548 restraints weight = 5211.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.055653 restraints weight = 3339.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056411 restraints weight = 2284.397| |-----------------------------------------------------------------------------| r_work (final): 0.3288 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.060408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054084 restraints weight = 4136.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.055275 restraints weight = 2560.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.056075 restraints weight = 1741.050| |-----------------------------------------------------------------------------| r_work (final): 0.3239 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.082833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.078920 restraints weight = 2297.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.079149 restraints weight = 1995.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.079329 restraints weight = 1809.754| |-----------------------------------------------------------------------------| r_work (final): 0.3632 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.068666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.064126 restraints weight = 3697.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.064869 restraints weight = 2791.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.065501 restraints weight = 2182.012| |-----------------------------------------------------------------------------| r_work (final): 0.3538 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.086574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080866 restraints weight = 2170.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.082370 restraints weight = 1179.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.083217 restraints weight = 762.054| |-----------------------------------------------------------------------------| r_work (final): 0.3527 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.056623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.051252 restraints weight = 11881.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.052259 restraints weight = 7936.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.052966 restraints weight = 5735.603| |-----------------------------------------------------------------------------| r_work (final): 0.3423 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.044458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.037456 restraints weight = 9823.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.038536 restraints weight = 6384.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.039255 restraints weight = 4682.586| |-----------------------------------------------------------------------------| r_work (final): 0.3105 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.051442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.043319 restraints weight = 15731.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.044487 restraints weight = 10399.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.045334 restraints weight = 7547.339| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 60436 Z= 0.269 Angle : 0.792 14.544 81654 Z= 0.405 Chirality : 0.046 0.239 9126 Planarity : 0.006 0.179 10498 Dihedral : 6.209 63.427 8114 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.70 % Rotamer: Outliers : 0.21 % Allowed : 5.74 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.34 % 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: -2.77 (0.09), residues: 7346 helix: -0.69 (0.10), residues: 2460 sheet: -2.23 (0.15), residues: 1086 loop : -2.55 (0.09), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 37 HIS 0.012 0.001 HIS W 44 PHE 0.029 0.002 PHE A 247 TYR 0.040 0.002 TYR A1047 ARG 0.034 0.001 ARG X 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11928 Ramachandran restraints generated. 5964 Oldfield, 0 Emsley, 5964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11928 Ramachandran restraints generated. 5964 Oldfield, 0 Emsley, 5964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 70 GLU cc_start: 0.7942 (pm20) cc_final: 0.7550 (mt-10) REVERT: M 476 ARG cc_start: 0.6770 (ttm170) cc_final: 0.6485 (tpp80) REVERT: M 568 GLN cc_start: 0.8220 (pt0) cc_final: 0.7984 (tt0) REVERT: M 649 MET cc_start: 0.8436 (mtm) cc_final: 0.8106 (ptm) REVERT: M 686 ILE cc_start: 0.8709 (pt) cc_final: 0.8340 (pt) REVERT: M 792 LEU cc_start: 0.8682 (mt) cc_final: 0.8190 (tp) REVERT: M 832 PHE cc_start: 0.8847 (m-10) cc_final: 0.8544 (m-10) REVERT: M 845 MET cc_start: 0.7579 (tpt) cc_final: 0.6251 (pmm) REVERT: M 947 LYS cc_start: 0.8257 (tptt) cc_final: 0.7601 (tmtt) REVERT: M 1561 MET cc_start: 0.5095 (tpt) cc_final: 0.4844 (tpt) REVERT: M 1562 ASN cc_start: 0.8740 (t0) cc_final: 0.8454 (t0) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1874 time to fit residues: 43.1637 Evaluate side-chains 109 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.987 Evaluate side-chains 32 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: O 30 TYR cc_start: 0.7093 (m-80) cc_final: 0.6075 (p90) REVERT: O 100 ASP cc_start: 0.8595 (m-30) cc_final: 0.8205 (t70) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1290 time to fit residues: 5.0162 Evaluate side-chains 17 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.231 Evaluate side-chains 15 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.053 Fit side-chains REVERT: J 58 LYS cc_start: 0.8173 (tttt) cc_final: 0.7120 (mttt) outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.1455 time to fit residues: 2.3242 Evaluate side-chains 10 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.052 Evaluate side-chains 151 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.5500 (tmm) cc_final: 0.4323 (tmm) REVERT: B 109 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.6773 (mmt-90) REVERT: B 288 MET cc_start: 0.8307 (tmm) cc_final: 0.8050 (tpt) REVERT: B 634 MET cc_start: 0.7215 (mtm) cc_final: 0.6974 (mpp) REVERT: B 769 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8145 (mp0) REVERT: B 772 MET cc_start: 0.8627 (ptm) cc_final: 0.7835 (ptm) REVERT: B 902 PHE cc_start: 0.7471 (m-80) cc_final: 0.6993 (m-10) REVERT: B 1059 MET cc_start: 0.6151 (mmm) cc_final: 0.5830 (mmm) REVERT: B 1073 MET cc_start: 0.9337 (tmm) cc_final: 0.9091 (tmm) REVERT: B 1161 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7740 (tm-30) REVERT: B 1169 MET cc_start: 0.8357 (pmm) cc_final: 0.7517 (tpt) REVERT: B 1170 MET cc_start: 0.8173 (ptp) cc_final: 0.7819 (mpp) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.1729 time to fit residues: 36.4350 Evaluate side-chains 99 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.797 Evaluate side-chains 26 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: W 40 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8030 (tp40) REVERT: W 41 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8318 (mmtp) REVERT: W 42 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7922 (mm-30) REVERT: W 51 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8128 (ttm170) REVERT: W 72 GLU cc_start: 0.8559 (pm20) cc_final: 0.8153 (mp0) REVERT: W 93 LYS cc_start: 0.8585 (tptp) cc_final: 0.8361 (tppt) REVERT: W 103 ASP cc_start: 0.8904 (t0) cc_final: 0.8585 (t0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1088 time to fit residues: 3.0673 Evaluate side-chains 19 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.067 Evaluate side-chains 22 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 76 THR cc_start: 0.8878 (p) cc_final: 0.8627 (t) REVERT: R 78 TYR cc_start: 0.7929 (m-10) cc_final: 0.6954 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0905 time to fit residues: 2.1827 Evaluate side-chains 14 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.060 Evaluate side-chains 11 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.032 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.1679 time to fit residues: 1.9236 Evaluate side-chains 4 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.032 Evaluate side-chains 8 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1090 time to fit residues: 0.9595 Evaluate side-chains 0 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.040 Evaluate side-chains 14 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.035 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.1987 time to fit residues: 2.8762 Evaluate side-chains 8 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.035 Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 110 ASN cc_start: 0.7712 (m-40) cc_final: 0.7424 (p0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1220 time to fit residues: 2.3965 Evaluate side-chains 9 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.115 Evaluate side-chains 17 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: H 76 MET cc_start: 0.8022 (ttm) cc_final: 0.7796 (ttm) REVERT: H 94 TYR cc_start: 0.8426 (m-80) cc_final: 0.7974 (m-80) REVERT: H 102 MET cc_start: 0.8716 (tpt) cc_final: 0.8459 (tpt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1158 time to fit residues: 2.2231 Evaluate side-chains 12 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.089 Evaluate side-chains 24 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: Q 130 PHE cc_start: 0.8055 (m-80) cc_final: 0.7836 (m-80) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1659 time to fit residues: 4.4925 Evaluate side-chains 11 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 618 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 255 optimal weight: 9.9990 chunk 697 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 601 optimal weight: 0.9980 chunk 378 optimal weight: 50.0000 chunk 423 optimal weight: 30.0000 chunk 194 optimal weight: 0.0770 chunk 583 optimal weight: 0.0770 chunk 563 optimal weight: 5.9990 overall best weight: 1.2298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 573 GLN M 689 HIS M 891 ASN ** M1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1604 HIS ** M1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 214 HIS ** O 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN B 733 GLN ** B 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B1038 HIS ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 7 ASN ** Q 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.073570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.064273 restraints weight = 78052.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.065483 restraints weight = 50016.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066405 restraints weight = 35417.955| |-----------------------------------------------------------------------------| r_work (final): 0.3510 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.062684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055371 restraints weight = 19185.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.056566 restraints weight = 11838.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.057369 restraints weight = 8093.941| |-----------------------------------------------------------------------------| r_work (final): 0.3396 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.059328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.053329 restraints weight = 3878.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.054533 restraints weight = 2547.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055294 restraints weight = 1819.793| |-----------------------------------------------------------------------------| r_work (final): 0.3301 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.066607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058781 restraints weight = 57225.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.060101 restraints weight = 34865.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.061093 restraints weight = 24066.224| |-----------------------------------------------------------------------------| r_work (final): 0.3453 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.060861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.054760 restraints weight = 5397.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.055981 restraints weight = 3447.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.056811 restraints weight = 2373.233| |-----------------------------------------------------------------------------| r_work (final): 0.3317 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.059541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052651 restraints weight = 4354.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053896 restraints weight = 2658.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054516 restraints weight = 1836.975| |-----------------------------------------------------------------------------| r_work (final): 0.3185 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.082565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.077939 restraints weight = 2536.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.078825 restraints weight = 1873.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.079461 restraints weight = 1435.769| |-----------------------------------------------------------------------------| r_work (final): 0.3618 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.068414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.065112 restraints weight = 3910.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.065762 restraints weight = 2832.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.066184 restraints weight = 2080.839| |-----------------------------------------------------------------------------| r_work (final): 0.3542 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.085558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.081119 restraints weight = 2310.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.082376 restraints weight = 1325.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.083185 restraints weight = 847.493| |-----------------------------------------------------------------------------| r_work (final): 0.3542 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.056741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.051697 restraints weight = 13764.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.052750 restraints weight = 8901.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.053478 restraints weight = 6190.880| |-----------------------------------------------------------------------------| r_work (final): 0.3446 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.044865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.037582 restraints weight = 10152.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.038622 restraints weight = 6672.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.039363 restraints weight = 4939.248| |-----------------------------------------------------------------------------| r_work (final): 0.3107 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.051970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.043346 restraints weight = 15486.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.044502 restraints weight = 10503.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.045421 restraints weight = 7863.387| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.945 60436 Z= 0.957 Angle : 1.074 26.936 81654 Z= 0.543 Chirality : 0.058 0.641 9126 Planarity : 0.011 0.323 10498 Dihedral : 6.578 54.789 8114 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.80 % Favored : 89.98 % Rotamer: Outliers : 0.55 % Allowed : 5.56 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 1.15 % Twisted General : 0.17 % 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: -3.19 (0.09), residues: 7346 helix: -1.44 (0.09), residues: 2480 sheet: -2.12 (0.15), residues: 1056 loop : -2.62 (0.09), residues: 3810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 570 HIS 0.059 0.004 HIS M 937 PHE 0.082 0.004 PHE M 234 TYR 0.146 0.006 TYR A 19 ARG 0.047 0.001 ARG A1052 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11530 Ramachandran restraints generated. 5765 Oldfield, 0 Emsley, 5765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11530 Ramachandran restraints generated. 5765 Oldfield, 0 Emsley, 5765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 476 ARG cc_start: 0.6659 (ttm170) cc_final: 0.6346 (tpp80) REVERT: M 568 GLN cc_start: 0.8698 (pt0) cc_final: 0.8128 (tt0) REVERT: M 649 MET cc_start: 0.8365 (mtm) cc_final: 0.7675 (ptm) REVERT: M 651 MET cc_start: 0.7307 (ptp) cc_final: 0.7038 (ptp) REVERT: M 832 PHE cc_start: 0.8920 (m-10) cc_final: 0.8606 (m-10) REVERT: M 845 MET cc_start: 0.7827 (tpt) cc_final: 0.6210 (pmm) REVERT: M 947 LYS cc_start: 0.8168 (tptt) cc_final: 0.7588 (tmtt) REVERT: M 1089 LEU cc_start: 0.8303 (tp) cc_final: 0.7997 (tp) REVERT: M 1187 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7452 (mp) REVERT: M 1192 GLU cc_start: 0.8577 (tt0) cc_final: 0.7596 (mm-30) REVERT: M 1200 GLN cc_start: 0.8681 (mt0) cc_final: 0.8310 (mt0) outliers start: 15 outliers final: 1 residues processed: 150 average time/residue: 0.1766 time to fit residues: 38.8540 Evaluate side-chains 102 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.997 Evaluate side-chains 32 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: O 30 TYR cc_start: 0.7005 (m-80) cc_final: 0.6089 (p90) REVERT: O 37 TRP cc_start: 0.4739 (t60) cc_final: 0.2698 (m100) REVERT: O 42 PHE cc_start: 0.8149 (m-10) cc_final: 0.7890 (m-10) REVERT: O 100 ASP cc_start: 0.8515 (m-30) cc_final: 0.8116 (t70) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1273 time to fit residues: 4.9638 Evaluate side-chains 20 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.231 Evaluate side-chains 11 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.052 Fit side-chains REVERT: J 58 LYS cc_start: 0.8200 (tttt) cc_final: 0.7077 (mttt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0857 time to fit residues: 1.0679 Evaluate side-chains 9 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.053 Evaluate side-chains 130 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.5705 (tmm) cc_final: 0.5176 (tmm) REVERT: B 109 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.6735 (mmt-90) REVERT: B 288 MET cc_start: 0.8229 (tmm) cc_final: 0.8010 (tmm) REVERT: B 504 MET cc_start: 0.8005 (pmm) cc_final: 0.7460 (pmm) REVERT: B 634 MET cc_start: 0.7126 (mtm) cc_final: 0.6774 (mtp) REVERT: B 648 MET cc_start: 0.7301 (mmm) cc_final: 0.7099 (mmm) REVERT: B 708 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7501 (ttpp) REVERT: B 768 MET cc_start: 0.8147 (pmm) cc_final: 0.7852 (pmm) REVERT: B 772 MET cc_start: 0.8548 (ptm) cc_final: 0.7911 (ptm) REVERT: B 869 ASP cc_start: 0.7084 (m-30) cc_final: 0.6435 (m-30) REVERT: B 902 PHE cc_start: 0.7270 (m-80) cc_final: 0.6845 (m-80) REVERT: B 1073 MET cc_start: 0.9272 (tmm) cc_final: 0.8863 (tmm) REVERT: B 1077 LEU cc_start: 0.8341 (mt) cc_final: 0.7894 (mp) REVERT: B 1148 LEU cc_start: 0.7439 (mt) cc_final: 0.6954 (pp) REVERT: B 1161 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7692 (tm-30) REVERT: B 1169 MET cc_start: 0.8247 (pmm) cc_final: 0.7595 (tpt) REVERT: B 1170 MET cc_start: 0.8063 (ptp) cc_final: 0.7823 (mpp) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1889 time to fit residues: 33.7516 Evaluate side-chains 96 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.795 Evaluate side-chains 27 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.068 Fit side-chains REVERT: W 40 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8213 (tp40) REVERT: W 41 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8314 (mmtp) REVERT: W 51 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8165 (ttm170) REVERT: W 72 GLU cc_start: 0.8537 (pm20) cc_final: 0.8136 (mp0) REVERT: W 93 LYS cc_start: 0.8651 (tptp) cc_final: 0.8408 (tppt) REVERT: W 103 ASP cc_start: 0.8999 (t0) cc_final: 0.8759 (t0) REVERT: W 107 GLU cc_start: 0.9140 (pt0) cc_final: 0.8793 (pp20) outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.1084 time to fit residues: 2.9411 Evaluate side-chains 18 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.068 Evaluate side-chains 17 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 78 TYR cc_start: 0.7995 (m-10) cc_final: 0.6915 (t80) REVERT: R 125 ARG cc_start: 0.7764 (ttm170) cc_final: 0.6567 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1182 time to fit residues: 2.1794 Evaluate side-chains 14 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.059 Evaluate side-chains 9 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.031 Fit side-chains REVERT: D 29 TYR cc_start: 0.6889 (t80) cc_final: 0.6664 (t80) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0537 time to fit residues: 0.5545 Evaluate side-chains 5 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.036 Evaluate side-chains 4 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0713 time to fit residues: 0.3581 Evaluate side-chains 1 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.039 Evaluate side-chains 13 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.035 Fit side-chains REVERT: X 50 TYR cc_start: 0.7592 (m-80) cc_final: 0.7167 (m-80) REVERT: X 63 ARG cc_start: 0.3956 (mtt180) cc_final: 0.2278 (mmt180) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.2257 time to fit residues: 3.0252 Evaluate side-chains 11 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.035 Evaluate side-chains 11 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.114 Fit side-chains REVERT: G 36 MET cc_start: 0.7801 (tpp) cc_final: 0.7585 (tpt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0639 time to fit residues: 0.9751 Evaluate side-chains 6 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.114 Evaluate side-chains 15 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.128 Fit side-chains REVERT: H 94 TYR cc_start: 0.8302 (m-80) cc_final: 0.7935 (m-80) REVERT: H 102 MET cc_start: 0.8295 (tpt) cc_final: 0.7163 (tmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1317 time to fit residues: 2.2420 Evaluate side-chains 10 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.090 Evaluate side-chains 18 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 110 MET cc_start: 0.5378 (tpt) cc_final: 0.5016 (tpt) REVERT: Q 130 PHE cc_start: 0.8048 (m-80) cc_final: 0.7769 (m-80) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1325 time to fit residues: 2.8217 Evaluate side-chains 13 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1866 > 50: distance: 0 - 1: 4.844 distance: 1 - 4: 3.970 distance: 2 - 3: 5.156 distance: 2 - 8: 6.666 distance: 3 - 33: 13.060 distance: 4 - 5: 3.343 distance: 8 - 9: 17.494 distance: 9 - 10: 11.172 distance: 9 - 12: 20.438 distance: 10 - 11: 20.470 distance: 10 - 17: 23.973 distance: 12 - 13: 23.370 distance: 13 - 14: 7.275 distance: 14 - 15: 46.795 distance: 14 - 16: 11.616 distance: 17 - 18: 13.656 distance: 18 - 19: 23.758 distance: 18 - 21: 21.171 distance: 19 - 20: 6.024 distance: 19 - 26: 19.159 distance: 21 - 22: 40.466 distance: 22 - 23: 9.873 distance: 23 - 24: 8.406 distance: 23 - 25: 19.756 distance: 26 - 27: 21.370 distance: 27 - 28: 34.221 distance: 27 - 30: 13.672 distance: 28 - 29: 14.101 distance: 28 - 33: 24.045 distance: 30 - 31: 12.078 distance: 30 - 32: 36.515 distance: 33 - 34: 12.406 distance: 34 - 35: 14.264 distance: 34 - 37: 18.144 distance: 35 - 36: 5.646 distance: 35 - 45: 6.093 distance: 37 - 38: 4.911 distance: 38 - 39: 3.408 distance: 38 - 40: 8.386 distance: 39 - 41: 5.545 distance: 40 - 42: 8.065 distance: 41 - 43: 3.137 distance: 42 - 43: 3.231 distance: 45 - 46: 8.306 distance: 46 - 47: 5.865 distance: 46 - 49: 10.174 distance: 47 - 48: 13.258 distance: 47 - 56: 12.459 distance: 49 - 50: 13.151 distance: 51 - 52: 10.395 distance: 52 - 53: 9.230 distance: 53 - 54: 9.968 distance: 53 - 55: 8.535 distance: 56 - 57: 9.238 distance: 57 - 58: 13.699 distance: 57 - 60: 11.058 distance: 58 - 59: 8.993 distance: 58 - 64: 7.660 distance: 60 - 61: 16.389 distance: 61 - 62: 10.296 distance: 61 - 63: 15.349 distance: 64 - 65: 6.498 distance: 65 - 66: 7.152 distance: 65 - 68: 16.790 distance: 66 - 67: 19.630 distance: 66 - 72: 9.332 distance: 68 - 69: 8.659 distance: 69 - 70: 9.922 distance: 69 - 71: 8.843 distance: 72 - 73: 16.172 distance: 73 - 74: 15.716 distance: 73 - 76: 20.312 distance: 74 - 75: 12.232 distance: 74 - 81: 6.445 distance: 76 - 77: 25.184 distance: 77 - 78: 48.777 distance: 78 - 79: 18.040 distance: 78 - 80: 12.713 distance: 81 - 82: 10.463 distance: 82 - 83: 6.005 distance: 82 - 85: 9.347 distance: 83 - 84: 21.136 distance: 85 - 86: 4.969 distance: 86 - 87: 8.648 distance: 87 - 88: 5.980 distance: 88 - 89: 7.578