Starting phenix.real_space_refine (version: dev) on Mon Dec 19 03:29:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adl_15364/12_2022/8adl_15364.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adl_15364/12_2022/8adl_15364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adl_15364/12_2022/8adl_15364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adl_15364/12_2022/8adl_15364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adl_15364/12_2022/8adl_15364.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adl_15364/12_2022/8adl_15364.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 98972 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 6344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6344 Classifications: {'peptide': 782} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 739} Chain breaks: 8 Chain: "E" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2438 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 1 Chain: "G" Number of atoms: 6332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6332 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 26, 'TRANS': 759} Chain breaks: 9 Chain: "H" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2252 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "A" Number of atoms: 5039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5039 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 24, 'TRANS': 608} Chain breaks: 9 Chain: "B" Number of atoms: 6450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6450 Classifications: {'peptide': 801} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 773} Chain breaks: 9 Chain: "D" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2457 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 1 Chain: "F" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2469 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 11, 'TRANS': 299} Chain breaks: 1 Chain: "Q" Number of atoms: 6344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6344 Classifications: {'peptide': 782} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 739} Chain breaks: 8 Chain: "M" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2438 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 1 Chain: "O" Number of atoms: 6332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6332 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 26, 'TRANS': 759} Chain breaks: 9 Chain: "P" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2252 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "I" Number of atoms: 5039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5039 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 24, 'TRANS': 608} Chain breaks: 9 Chain: "J" Number of atoms: 6450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6450 Classifications: {'peptide': 801} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 773} Chain breaks: 9 Chain: "L" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2457 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 1 Chain: "N" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2469 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 11, 'TRANS': 299} Chain breaks: 1 Chain: "U" Number of atoms: 4641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4641 Classifications: {'peptide': 563} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 535} Chain breaks: 6 Chain: "W" Number of atoms: 7762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7762 Classifications: {'peptide': 938} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 898} Chain breaks: 11 Chain: "S" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3288 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain breaks: 3 Chain: "V" Number of atoms: 4641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4641 Classifications: {'peptide': 563} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 535} Chain breaks: 6 Chain: "X" Number of atoms: 7762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7762 Classifications: {'peptide': 938} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 898} Chain breaks: 11 Chain: "T" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3288 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5963 SG CYS C1098 148.231 70.026 204.182 1.00 62.26 S ATOM 5989 SG CYS C1101 147.595 73.759 204.762 1.00103.47 S ATOM 6158 SG CYS C1123 147.997 72.510 201.242 1.00 83.31 S ATOM 6078 SG CYS C1112 151.999 57.105 201.963 1.00108.64 S ATOM 6096 SG CYS C1115 153.459 59.151 205.003 1.00 96.84 S ATOM 6287 SG CYS C1140 155.708 56.891 202.962 1.00116.64 S ATOM 6301 SG CYS C1142 154.068 60.075 201.533 1.00104.13 S ATOM 6096 SG CYS C1115 153.459 59.151 205.003 1.00 96.84 S ATOM 6254 SG CYS C1134 154.555 62.861 204.839 1.00 77.58 S ATOM 6277 SG CYS C1138 156.652 60.314 206.767 1.00130.73 S ATOM 14704 SG CYS G 953 136.618 58.838 189.357 1.00 95.99 S ATOM 14723 SG CYS G 956 137.979 56.763 186.319 1.00105.02 S ATOM 14518 SG CYS G 881 136.461 46.763 205.004 1.00125.66 S ATOM 14541 SG CYS G 884 137.962 43.994 206.870 1.00124.99 S ATOM 14630 SG CYS G 943 139.135 44.702 203.219 1.00109.29 S ATOM 14653 SG CYS G 946 135.889 43.073 203.770 1.00125.07 S ATOM 14870 SG CYS G1005 134.773 65.665 201.913 1.00 96.27 S ATOM 14890 SG CYS G1008 131.918 63.887 200.331 1.00 85.41 S ATOM 15091 SG CYS G1034 131.385 67.443 201.697 1.00104.75 S ATOM 15106 SG CYS G1036 133.465 66.855 198.561 1.00 82.40 S ATOM 14890 SG CYS G1008 131.918 63.887 200.331 1.00 85.41 S ATOM 15047 SG CYS G1027 130.482 63.632 196.769 1.00 60.92 S ATOM 15078 SG CYS G1032 128.130 64.077 199.808 1.00115.02 S ATOM 22029 SG CYS A1293 78.056 129.551 163.678 1.00 77.68 S ATOM 22050 SG CYS A1296 80.687 131.776 162.190 1.00 94.36 S ATOM 22225 SG CYS A1318 81.272 130.412 165.656 1.00 80.69 S ATOM 21652 SG CYS A1246 67.333 122.401 150.898 1.00 92.76 S ATOM 21678 SG CYS A1249 64.754 121.365 148.337 1.00 76.43 S ATOM 21955 SG CYS A1283 68.337 120.408 147.799 1.00 88.74 S ATOM 21975 SG CYS A1286 67.352 124.093 147.541 1.00101.18 S ATOM 22162 SG CYS A1310 67.139 126.823 167.941 1.00 91.26 S ATOM 22342 SG CYS A1331 69.090 130.024 167.851 1.00 89.56 S ATOM 22363 SG CYS A1335 65.186 130.155 167.732 1.00106.58 S ATOM 28100 SG CYS B 881 61.866 108.108 163.106 1.00119.17 S ATOM 28123 SG CYS B 884 58.858 108.016 160.867 1.00 99.02 S ATOM 28233 SG CYS B 943 58.888 110.446 163.757 1.00103.11 S ATOM 28256 SG CYS B 946 58.574 106.704 164.424 1.00102.37 S ATOM 28601 SG CYS B1005 81.239 115.536 158.576 1.00 96.33 S ATOM 28621 SG CYS B1008 81.010 111.814 158.692 1.00 74.84 S ATOM 28822 SG CYS B1034 84.008 113.473 156.933 1.00 98.80 S ATOM 28837 SG CYS B1036 83.799 113.636 160.649 1.00 64.22 S ATOM 28307 SG CYS B 953 77.946 109.443 170.621 1.00 79.25 S ATOM 28326 SG CYS B 956 77.084 107.724 174.010 1.00107.38 S ATOM 28621 SG CYS B1008 81.010 111.814 158.692 1.00 74.84 S ATOM 28778 SG CYS B1027 82.396 109.370 161.329 1.00 91.31 S ATOM 28809 SG CYS B1032 82.799 108.543 157.558 1.00107.42 S ATOM 39744 SG CYS Q1098 131.987 216.027 204.177 1.00 72.07 S ATOM 39770 SG CYS Q1101 132.628 212.291 204.759 1.00100.14 S ATOM 39939 SG CYS Q1123 132.221 213.536 201.237 1.00 86.38 S ATOM 39859 SG CYS Q1112 128.248 228.926 201.960 1.00109.41 S ATOM 39877 SG CYS Q1115 126.790 226.883 204.991 1.00 97.40 S ATOM 40068 SG CYS Q1140 124.528 229.143 202.935 1.00120.80 S ATOM 40082 SG CYS Q1142 126.167 225.968 201.513 1.00104.96 S ATOM 39877 SG CYS Q1115 126.790 226.883 204.991 1.00 97.40 S ATOM 40035 SG CYS Q1134 125.679 223.179 204.834 1.00 81.49 S ATOM 40058 SG CYS Q1138 123.576 225.736 206.738 1.00131.17 S ATOM 48485 SG CYS O 953 143.630 227.209 189.374 1.00 97.58 S ATOM 48504 SG CYS O 956 142.273 229.284 186.328 1.00103.55 S ATOM 48299 SG CYS O 881 143.780 239.303 205.009 1.00125.36 S ATOM 48322 SG CYS O 884 142.279 242.078 206.867 1.00129.80 S ATOM 48411 SG CYS O 943 141.119 241.371 203.223 1.00112.40 S ATOM 48434 SG CYS O 946 144.358 243.017 203.781 1.00127.32 S ATOM 48651 SG CYS O1005 145.469 220.392 201.874 1.00100.23 S ATOM 48671 SG CYS O1008 148.326 222.162 200.301 1.00 87.42 S ATOM 48872 SG CYS O1034 148.853 218.606 201.664 1.00107.20 S ATOM 48887 SG CYS O1036 146.765 219.177 198.529 1.00 82.62 S ATOM 48671 SG CYS O1008 148.326 222.162 200.301 1.00 87.42 S ATOM 48828 SG CYS O1027 149.763 222.414 196.742 1.00 61.72 S ATOM 48859 SG CYS O1032 152.116 221.963 199.777 1.00114.04 S ATOM 55810 SG CYS I1293 202.164 156.538 163.676 1.00 74.85 S ATOM 55831 SG CYS I1296 199.552 154.292 162.189 1.00 94.53 S ATOM 56006 SG CYS I1318 198.944 155.645 165.643 1.00 78.35 S ATOM 55433 SG CYS I1246 212.870 163.638 150.888 1.00 93.31 S ATOM 55459 SG CYS I1249 215.449 164.669 148.336 1.00 82.61 S ATOM 55736 SG CYS I1283 211.874 165.668 147.789 1.00 87.98 S ATOM 55756 SG CYS I1286 212.853 161.984 147.503 1.00 99.78 S ATOM 55943 SG CYS I1310 213.093 159.236 167.931 1.00 94.29 S ATOM 56123 SG CYS I1331 211.146 156.041 167.875 1.00 86.86 S ATOM 56144 SG CYS I1335 215.045 155.911 167.746 1.00106.36 S ATOM 61881 SG CYS J 881 218.374 177.959 163.112 1.00120.44 S ATOM 61904 SG CYS J 884 221.374 178.045 160.874 1.00103.50 S ATOM 62014 SG CYS J 943 221.344 175.607 163.768 1.00105.91 S ATOM 62037 SG CYS J 946 221.669 179.343 164.440 1.00105.78 S ATOM 62382 SG CYS J1005 198.995 170.525 158.551 1.00 97.26 S ATOM 62402 SG CYS J1008 199.229 174.230 158.675 1.00 77.21 S ATOM 62603 SG CYS J1034 196.209 172.572 156.932 1.00100.99 S ATOM 62618 SG CYS J1036 196.440 172.420 160.650 1.00 66.27 S ATOM 62088 SG CYS J 953 202.297 176.619 170.634 1.00 76.53 S ATOM 62107 SG CYS J 956 203.163 178.324 174.026 1.00106.98 S ATOM 62402 SG CYS J1008 199.229 174.230 158.675 1.00 77.21 S ATOM 62559 SG CYS J1027 197.793 176.632 161.308 1.00 90.13 S ATOM 62590 SG CYS J1032 197.426 177.475 157.539 1.00109.02 S Time building chain proxies: 40.21, per 1000 atoms: 0.41 Number of scatterers: 98972 At special positions: 0 Unit cell: (280.962, 288.222, 260.634, 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 28 29.99 S 536 16.00 O 18444 8.00 N 16788 7.00 C 63176 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 - 3.50 Amino acid : False - 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: 29.95 Conformation dependent library (CDL) restraints added in 11.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" ND1 HIS A1315 " pdb="ZN ZN A1401 " - pdb=" SG CYS A1296 " pdb="ZN ZN A1401 " - pdb=" SG CYS A1293 " pdb="ZN ZN A1401 " - pdb=" SG CYS A1318 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A1283 " pdb="ZN ZN A1402 " - pdb=" SG CYS A1246 " pdb="ZN ZN A1402 " - pdb=" SG CYS A1249 " pdb="ZN ZN A1402 " - pdb=" SG CYS A1286 " pdb=" ZN A1403 " pdb="ZN ZN A1403 " - pdb=" ND1 HIS A1312 " pdb="ZN ZN A1403 " - pdb=" SG CYS A1310 " pdb="ZN ZN A1403 " - pdb=" SG CYS A1331 " pdb="ZN ZN A1403 " - pdb=" SG CYS A1335 " pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 884 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 881 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 946 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 943 " pdb=" ZN B1102 " pdb="ZN ZN B1102 " - pdb=" SG CYS B1005 " pdb="ZN ZN B1102 " - pdb=" SG CYS B1036 " pdb="ZN ZN B1102 " - pdb=" SG CYS B1008 " pdb="ZN ZN B1102 " - pdb=" SG CYS B1034 " pdb=" ZN B1103 " pdb="ZN ZN B1103 " - pdb=" ND1 HIS B1016 " pdb="ZN ZN B1103 " - pdb=" ND1 HIS B1013 " pdb="ZN ZN B1103 " - pdb=" SG CYS B 953 " pdb="ZN ZN B1103 " - pdb=" SG CYS B 956 " pdb=" ZN B1104 " pdb="ZN ZN B1104 " - pdb=" ND1 HIS B1010 " pdb="ZN ZN B1104 " - pdb=" SG CYS B1027 " pdb="ZN ZN B1104 " - pdb=" SG CYS B1008 " pdb="ZN ZN B1104 " - pdb=" SG CYS B1032 " pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" ND1 HIS C1120 " pdb="ZN ZN C1201 " - pdb=" SG CYS C1101 " pdb="ZN ZN C1201 " - pdb=" SG CYS C1123 " pdb="ZN ZN C1201 " - pdb=" SG CYS C1098 " pdb=" ZN C1202 " pdb="ZN ZN C1202 " - pdb=" SG CYS C1142 " pdb="ZN ZN C1202 " - pdb=" SG CYS C1115 " pdb="ZN ZN C1202 " - pdb=" SG CYS C1112 " pdb="ZN ZN C1202 " - pdb=" SG CYS C1140 " pdb=" ZN C1203 " pdb="ZN ZN C1203 " - pdb=" ND1 HIS C1117 " pdb="ZN ZN C1203 " - pdb=" SG CYS C1138 " pdb="ZN ZN C1203 " - pdb=" SG CYS C1134 " pdb="ZN ZN C1203 " - pdb=" SG CYS C1115 " pdb=" ZN G1101 " pdb="ZN ZN G1101 " - pdb=" ND1 HIS G1016 " pdb="ZN ZN G1101 " - pdb=" ND1 HIS G1013 " pdb="ZN ZN G1101 " - pdb=" SG CYS G 956 " pdb="ZN ZN G1101 " - pdb=" SG CYS G 953 " pdb=" ZN G1102 " pdb="ZN ZN G1102 " - pdb=" SG CYS G 881 " pdb="ZN ZN G1102 " - pdb=" SG CYS G 943 " pdb="ZN ZN G1102 " - pdb=" SG CYS G 884 " pdb="ZN ZN G1102 " - pdb=" SG CYS G 946 " pdb=" ZN G1103 " pdb="ZN ZN G1103 " - pdb=" SG CYS G1008 " pdb="ZN ZN G1103 " - pdb=" SG CYS G1036 " pdb="ZN ZN G1103 " - pdb=" SG CYS G1005 " pdb="ZN ZN G1103 " - pdb=" SG CYS G1034 " pdb=" ZN G1104 " pdb="ZN ZN G1104 " - pdb=" ND1 HIS G1010 " pdb="ZN ZN G1104 " - pdb=" SG CYS G1008 " pdb="ZN ZN G1104 " - pdb=" SG CYS G1032 " pdb="ZN ZN G1104 " - pdb=" SG CYS G1027 " pdb=" ZN I1401 " pdb="ZN ZN I1401 " - pdb=" ND1 HIS I1315 " pdb="ZN ZN I1401 " - pdb=" SG CYS I1296 " pdb="ZN ZN I1401 " - pdb=" SG CYS I1293 " pdb="ZN ZN I1401 " - pdb=" SG CYS I1318 " pdb=" ZN I1402 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1249 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1246 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1283 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1286 " pdb=" ZN I1403 " pdb="ZN ZN I1403 " - pdb=" ND1 HIS I1312 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1310 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1331 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1335 " pdb=" ZN J1101 " pdb="ZN ZN J1101 " - pdb=" SG CYS J 884 " pdb="ZN ZN J1101 " - pdb=" SG CYS J 943 " pdb="ZN ZN J1101 " - pdb=" SG CYS J 881 " pdb="ZN ZN J1101 " - pdb=" SG CYS J 946 " pdb=" ZN J1102 " pdb="ZN ZN J1102 " - pdb=" SG CYS J1005 " pdb="ZN ZN J1102 " - pdb=" SG CYS J1036 " pdb="ZN ZN J1102 " - pdb=" SG CYS J1008 " pdb="ZN ZN J1102 " - pdb=" SG CYS J1034 " pdb=" ZN J1103 " pdb="ZN ZN J1103 " - pdb=" ND1 HIS J1016 " pdb="ZN ZN J1103 " - pdb=" ND1 HIS J1013 " pdb="ZN ZN J1103 " - pdb=" SG CYS J 953 " pdb="ZN ZN J1103 " - pdb=" SG CYS J 956 " pdb=" ZN J1104 " pdb="ZN ZN J1104 " - pdb=" ND1 HIS J1010 " pdb="ZN ZN J1104 " - pdb=" SG CYS J1027 " pdb="ZN ZN J1104 " - pdb=" SG CYS J1008 " pdb="ZN ZN J1104 " - pdb=" SG CYS J1032 " pdb=" ZN O1101 " pdb="ZN ZN O1101 " - pdb=" ND1 HIS O1016 " pdb="ZN ZN O1101 " - pdb=" ND1 HIS O1013 " pdb="ZN ZN O1101 " - pdb=" SG CYS O 953 " pdb="ZN ZN O1101 " - pdb=" SG CYS O 956 " pdb=" ZN O1102 " pdb="ZN ZN O1102 " - pdb=" SG CYS O 943 " pdb="ZN ZN O1102 " - pdb=" SG CYS O 884 " pdb="ZN ZN O1102 " - pdb=" SG CYS O 881 " pdb="ZN ZN O1102 " - pdb=" SG CYS O 946 " pdb=" ZN O1103 " pdb="ZN ZN O1103 " - pdb=" SG CYS O1008 " pdb="ZN ZN O1103 " - pdb=" SG CYS O1005 " pdb="ZN ZN O1103 " - pdb=" SG CYS O1036 " pdb="ZN ZN O1103 " - pdb=" SG CYS O1034 " pdb=" ZN O1104 " pdb="ZN ZN O1104 " - pdb=" ND1 HIS O1010 " pdb="ZN ZN O1104 " - pdb=" SG CYS O1008 " pdb="ZN ZN O1104 " - pdb=" SG CYS O1032 " pdb="ZN ZN O1104 " - pdb=" SG CYS O1027 " pdb=" ZN Q1201 " pdb="ZN ZN Q1201 " - pdb=" ND1 HIS Q1120 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1101 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1123 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1098 " pdb=" ZN Q1202 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1142 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1115 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1112 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1140 " pdb=" ZN Q1203 " pdb="ZN ZN Q1203 " - pdb=" ND1 HIS Q1117 " pdb="ZN ZN Q1203 " - pdb=" SG CYS Q1138 " pdb="ZN ZN Q1203 " - pdb=" SG CYS Q1134 " pdb="ZN ZN Q1203 " - pdb=" SG CYS Q1115 " Number of angles added : 116 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23276 Finding SS restraints... Secondary structure from input PDB file: 343 helices and 172 sheets defined 29.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'C' and resid 267 through 271 removed outlier: 3.601A pdb=" N ALA C 271 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'C' and resid 401 through 407 Processing helix chain 'C' and resid 429 through 441 Processing helix chain 'C' and resid 503 through 524 removed outlier: 3.936A pdb=" N SER C 524 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 537 Processing helix chain 'C' and resid 781 through 784 Processing helix chain 'C' and resid 787 through 792 removed outlier: 3.772A pdb=" N ALA C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 815 removed outlier: 3.846A pdb=" N ALA C 805 " --> pdb=" O PRO C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 831 Processing helix chain 'C' and resid 838 through 846 removed outlier: 4.089A pdb=" N THR C 842 " --> pdb=" O ASP C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 865 Processing helix chain 'C' and resid 867 through 881 Processing helix chain 'C' and resid 1004 through 1011 Processing helix chain 'C' and resid 1025 through 1040 Processing helix chain 'C' and resid 1042 through 1061 removed outlier: 4.088A pdb=" N ARG C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C1047 " --> pdb=" O PRO C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1090 through 1096 removed outlier: 4.495A pdb=" N ARG C1096 " --> pdb=" O LYS C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1128 Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'E' and resid 65 through 69 Processing helix chain 'G' and resid 39 through 43 Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 268 through 273 removed outlier: 3.605A pdb=" N ASP G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 380 No H-bonds generated for 'chain 'G' and resid 378 through 380' Processing helix chain 'G' and resid 498 through 506 Processing helix chain 'G' and resid 506 through 518 Processing helix chain 'G' and resid 522 through 532 Processing helix chain 'G' and resid 540 through 558 Processing helix chain 'G' and resid 572 through 579 Processing helix chain 'G' and resid 596 through 609 Processing helix chain 'G' and resid 629 through 640 removed outlier: 3.729A pdb=" N ARG G 634 " --> pdb=" O TYR G 630 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU G 635 " --> pdb=" O VAL G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 645 through 660 Processing helix chain 'G' and resid 661 through 673 Processing helix chain 'G' and resid 674 through 683 Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.610A pdb=" N ARG G 691 " --> pdb=" O LYS G 687 " (cutoff:3.500A) Processing helix chain 'G' and resid 710 through 723 Processing helix chain 'G' and resid 725 through 737 Processing helix chain 'G' and resid 740 through 745 removed outlier: 3.836A pdb=" N TYR G 745 " --> pdb=" O TRP G 741 " (cutoff:3.500A) Processing helix chain 'G' and resid 750 through 761 removed outlier: 3.564A pdb=" N PHE G 761 " --> pdb=" O VAL G 757 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 782 removed outlier: 4.028A pdb=" N THR G 769 " --> pdb=" O THR G 765 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU G 780 " --> pdb=" O SER G 776 " (cutoff:3.500A) Processing helix chain 'G' and resid 783 through 785 No H-bonds generated for 'chain 'G' and resid 783 through 785' Processing helix chain 'G' and resid 786 through 791 Processing helix chain 'G' and resid 793 through 808 Processing helix chain 'G' and resid 809 through 818 removed outlier: 3.742A pdb=" N ALA G 813 " --> pdb=" O ASP G 809 " (cutoff:3.500A) Processing helix chain 'G' and resid 820 through 825 Processing helix chain 'G' and resid 827 through 844 removed outlier: 3.713A pdb=" N ASP G 831 " --> pdb=" O ASP G 827 " (cutoff:3.500A) Processing helix chain 'G' and resid 846 through 861 Processing helix chain 'G' and resid 1013 through 1022 Processing helix chain 'H' and resid 109 through 113 removed outlier: 3.614A pdb=" N GLY H 113 " --> pdb=" O HIS H 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.698A pdb=" N ASN A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 678 Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 837 through 864 removed outlier: 3.747A pdb=" N ILE A 864 " --> pdb=" O VAL A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 890 removed outlier: 3.586A pdb=" N PHE A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1176 Processing helix chain 'A' and resid 1177 through 1188 Processing helix chain 'A' and resid 1196 through 1214 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.854A pdb=" N TYR A1226 " --> pdb=" O ASP A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1269 Processing helix chain 'A' and resid 1274 through 1278 Processing helix chain 'A' and resid 1315 through 1325 Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 506 through 518 removed outlier: 3.777A pdb=" N ARG B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 540 through 558 Processing helix chain 'B' and resid 572 through 578 Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.659A pdb=" N ILE B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 608 " --> pdb=" O MET B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 640 Processing helix chain 'B' and resid 645 through 659 removed outlier: 3.615A pdb=" N ASN B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 672 Processing helix chain 'B' and resid 674 through 683 Processing helix chain 'B' and resid 687 through 699 Processing helix chain 'B' and resid 710 through 723 Processing helix chain 'B' and resid 725 through 736 removed outlier: 3.692A pdb=" N ALA B 736 " --> pdb=" O PHE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 removed outlier: 3.955A pdb=" N ASP B 742 " --> pdb=" O ASP B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.628A pdb=" N VAL B 757 " --> pdb=" O GLU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 782 removed outlier: 3.952A pdb=" N THR B 768 " --> pdb=" O ASP B 764 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 769 " --> pdb=" O THR B 765 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 780 " --> pdb=" O SER B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 786 through 791 Processing helix chain 'B' and resid 793 through 808 Processing helix chain 'B' and resid 809 through 818 Processing helix chain 'B' and resid 820 through 825 removed outlier: 3.505A pdb=" N PHE B 825 " --> pdb=" O SER B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 844 removed outlier: 3.737A pdb=" N ASP B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 860 Processing helix chain 'B' and resid 989 through 999 Processing helix chain 'B' and resid 1013 through 1021 Processing helix chain 'D' and resid 118 through 122 Processing helix chain 'F' and resid 65 through 69 removed outlier: 3.513A pdb=" N GLY F 69 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'Q' and resid 267 through 271 removed outlier: 3.596A pdb=" N ALA Q 271 " --> pdb=" O GLY Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 348 Processing helix chain 'Q' and resid 401 through 407 Processing helix chain 'Q' and resid 429 through 441 Processing helix chain 'Q' and resid 503 through 524 removed outlier: 3.941A pdb=" N SER Q 524 " --> pdb=" O LYS Q 520 " (cutoff:3.500A) Processing helix chain 'Q' and resid 529 through 537 Processing helix chain 'Q' and resid 781 through 784 Processing helix chain 'Q' and resid 787 through 792 removed outlier: 3.770A pdb=" N ALA Q 791 " --> pdb=" O ARG Q 787 " (cutoff:3.500A) Processing helix chain 'Q' and resid 800 through 815 removed outlier: 3.851A pdb=" N ALA Q 805 " --> pdb=" O PRO Q 801 " (cutoff:3.500A) Processing helix chain 'Q' and resid 817 through 831 Processing helix chain 'Q' and resid 838 through 846 removed outlier: 4.084A pdb=" N THR Q 842 " --> pdb=" O ASP Q 838 " (cutoff:3.500A) Processing helix chain 'Q' and resid 851 through 865 Processing helix chain 'Q' and resid 867 through 881 Processing helix chain 'Q' and resid 1004 through 1011 Processing helix chain 'Q' and resid 1025 through 1040 Processing helix chain 'Q' and resid 1042 through 1061 removed outlier: 4.089A pdb=" N ARG Q1046 " --> pdb=" O LEU Q1042 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL Q1047 " --> pdb=" O PRO Q1043 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1090 through 1096 removed outlier: 4.497A pdb=" N ARG Q1096 " --> pdb=" O LYS Q1092 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1121 through 1128 Processing helix chain 'Q' and resid 1141 through 1146 Processing helix chain 'M' and resid 65 through 69 Processing helix chain 'O' and resid 39 through 43 Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 268 through 273 removed outlier: 3.605A pdb=" N ASP O 273 " --> pdb=" O ARG O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 378 through 380 No H-bonds generated for 'chain 'O' and resid 378 through 380' Processing helix chain 'O' and resid 498 through 506 Processing helix chain 'O' and resid 506 through 518 Processing helix chain 'O' and resid 522 through 532 Processing helix chain 'O' and resid 540 through 558 Processing helix chain 'O' and resid 572 through 579 Processing helix chain 'O' and resid 596 through 609 Processing helix chain 'O' and resid 629 through 640 removed outlier: 3.735A pdb=" N ARG O 634 " --> pdb=" O TYR O 630 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU O 635 " --> pdb=" O VAL O 631 " (cutoff:3.500A) Processing helix chain 'O' and resid 645 through 660 Processing helix chain 'O' and resid 661 through 673 Processing helix chain 'O' and resid 674 through 683 Processing helix chain 'O' and resid 687 through 699 removed outlier: 3.602A pdb=" N ARG O 691 " --> pdb=" O LYS O 687 " (cutoff:3.500A) Processing helix chain 'O' and resid 710 through 723 Processing helix chain 'O' and resid 725 through 737 Processing helix chain 'O' and resid 740 through 745 removed outlier: 3.828A pdb=" N TYR O 745 " --> pdb=" O TRP O 741 " (cutoff:3.500A) Processing helix chain 'O' and resid 750 through 761 removed outlier: 3.565A pdb=" N PHE O 761 " --> pdb=" O VAL O 757 " (cutoff:3.500A) Processing helix chain 'O' and resid 763 through 782 removed outlier: 4.022A pdb=" N THR O 769 " --> pdb=" O THR O 765 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU O 780 " --> pdb=" O SER O 776 " (cutoff:3.500A) Processing helix chain 'O' and resid 783 through 785 No H-bonds generated for 'chain 'O' and resid 783 through 785' Processing helix chain 'O' and resid 786 through 791 Processing helix chain 'O' and resid 793 through 808 Processing helix chain 'O' and resid 809 through 818 removed outlier: 3.733A pdb=" N ALA O 813 " --> pdb=" O ASP O 809 " (cutoff:3.500A) Processing helix chain 'O' and resid 820 through 825 Processing helix chain 'O' and resid 827 through 844 removed outlier: 3.713A pdb=" N ASP O 831 " --> pdb=" O ASP O 827 " (cutoff:3.500A) Processing helix chain 'O' and resid 846 through 861 Processing helix chain 'O' and resid 1013 through 1022 Processing helix chain 'P' and resid 109 through 113 removed outlier: 3.614A pdb=" N GLY P 113 " --> pdb=" O HIS P 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 522 No H-bonds generated for 'chain 'I' and resid 520 through 522' Processing helix chain 'I' and resid 524 through 529 removed outlier: 3.701A pdb=" N ASN I 528 " --> pdb=" O THR I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 678 Processing helix chain 'I' and resid 695 through 706 Processing helix chain 'I' and resid 837 through 864 removed outlier: 3.747A pdb=" N ILE I 864 " --> pdb=" O VAL I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 890 removed outlier: 3.587A pdb=" N PHE I 870 " --> pdb=" O ASP I 866 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE I 872 " --> pdb=" O THR I 868 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1176 Processing helix chain 'I' and resid 1177 through 1188 Processing helix chain 'I' and resid 1196 through 1214 Processing helix chain 'I' and resid 1217 through 1226 removed outlier: 3.858A pdb=" N TYR I1226 " --> pdb=" O ASP I1222 " (cutoff:3.500A) Processing helix chain 'I' and resid 1255 through 1269 Processing helix chain 'I' and resid 1274 through 1278 Processing helix chain 'I' and resid 1315 through 1325 Processing helix chain 'J' and resid 39 through 41 No H-bonds generated for 'chain 'J' and resid 39 through 41' Processing helix chain 'J' and resid 182 through 184 No H-bonds generated for 'chain 'J' and resid 182 through 184' Processing helix chain 'J' and resid 268 through 273 Processing helix chain 'J' and resid 498 through 505 Processing helix chain 'J' and resid 506 through 518 removed outlier: 3.765A pdb=" N ARG J 512 " --> pdb=" O SER J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 522 through 532 Processing helix chain 'J' and resid 540 through 558 Processing helix chain 'J' and resid 572 through 578 Processing helix chain 'J' and resid 596 through 609 removed outlier: 3.647A pdb=" N ILE J 607 " --> pdb=" O GLU J 603 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE J 608 " --> pdb=" O MET J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 630 through 640 Processing helix chain 'J' and resid 645 through 659 removed outlier: 3.619A pdb=" N ASN J 659 " --> pdb=" O ILE J 655 " (cutoff:3.500A) Processing helix chain 'J' and resid 661 through 672 Processing helix chain 'J' and resid 674 through 683 Processing helix chain 'J' and resid 687 through 699 Processing helix chain 'J' and resid 710 through 723 Processing helix chain 'J' and resid 725 through 736 removed outlier: 3.690A pdb=" N ALA J 736 " --> pdb=" O PHE J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 743 removed outlier: 3.950A pdb=" N ASP J 742 " --> pdb=" O ASP J 739 " (cutoff:3.500A) Processing helix chain 'J' and resid 750 through 759 removed outlier: 3.630A pdb=" N VAL J 757 " --> pdb=" O GLU J 753 " (cutoff:3.500A) Processing helix chain 'J' and resid 763 through 782 removed outlier: 3.964A pdb=" N THR J 768 " --> pdb=" O ASP J 764 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR J 769 " --> pdb=" O THR J 765 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU J 780 " --> pdb=" O SER J 776 " (cutoff:3.500A) Processing helix chain 'J' and resid 783 through 785 No H-bonds generated for 'chain 'J' and resid 783 through 785' Processing helix chain 'J' and resid 786 through 791 Processing helix chain 'J' and resid 793 through 808 Processing helix chain 'J' and resid 809 through 818 Processing helix chain 'J' and resid 820 through 825 removed outlier: 3.518A pdb=" N PHE J 825 " --> pdb=" O SER J 821 " (cutoff:3.500A) Processing helix chain 'J' and resid 827 through 844 removed outlier: 3.742A pdb=" N ASP J 831 " --> pdb=" O ASP J 827 " (cutoff:3.500A) Processing helix chain 'J' and resid 846 through 860 Processing helix chain 'J' and resid 989 through 999 Processing helix chain 'J' and resid 1013 through 1021 Processing helix chain 'L' and resid 118 through 122 Processing helix chain 'N' and resid 65 through 69 removed outlier: 3.504A pdb=" N GLY N 69 " --> pdb=" O PRO N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 122 Processing helix chain 'U' and resid 33 through 39 Processing helix chain 'U' and resid 365 through 376 Processing helix chain 'U' and resid 382 through 387 removed outlier: 3.665A pdb=" N GLU U 387 " --> pdb=" O ILE U 384 " (cutoff:3.500A) Processing helix chain 'U' and resid 401 through 409 Processing helix chain 'U' and resid 526 through 530 removed outlier: 3.556A pdb=" N MET U 530 " --> pdb=" O LEU U 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 526 through 530' Processing helix chain 'U' and resid 545 through 557 Processing helix chain 'U' and resid 557 through 573 Processing helix chain 'U' and resid 573 through 591 removed outlier: 3.914A pdb=" N SER U 577 " --> pdb=" O SER U 573 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 598 removed outlier: 3.985A pdb=" N GLN U 597 " --> pdb=" O SER U 593 " (cutoff:3.500A) Processing helix chain 'U' and resid 601 through 617 Processing helix chain 'U' and resid 618 through 632 Processing helix chain 'U' and resid 678 through 683 Processing helix chain 'U' and resid 743 through 747 removed outlier: 3.615A pdb=" N ASN U 746 " --> pdb=" O ASP U 743 " (cutoff:3.500A) Processing helix chain 'U' and resid 754 through 763 Processing helix chain 'U' and resid 764 through 766 No H-bonds generated for 'chain 'U' and resid 764 through 766' Processing helix chain 'U' and resid 770 through 782 Processing helix chain 'U' and resid 788 through 792 Processing helix chain 'U' and resid 793 through 798 removed outlier: 3.583A pdb=" N ASP U 798 " --> pdb=" O TYR U 794 " (cutoff:3.500A) Processing helix chain 'U' and resid 815 through 831 removed outlier: 3.552A pdb=" N TRP U 831 " --> pdb=" O HIS U 827 " (cutoff:3.500A) Processing helix chain 'U' and resid 889 through 902 Processing helix chain 'U' and resid 907 through 915 Processing helix chain 'U' and resid 922 through 926 Processing helix chain 'U' and resid 929 through 931 No H-bonds generated for 'chain 'U' and resid 929 through 931' Processing helix chain 'U' and resid 932 through 946 Processing helix chain 'U' and resid 961 through 975 removed outlier: 3.529A pdb=" N LYS U 965 " --> pdb=" O ASP U 961 " (cutoff:3.500A) Processing helix chain 'U' and resid 1080 through 1091 removed outlier: 3.769A pdb=" N ILE U1091 " --> pdb=" O LEU U1087 " (cutoff:3.500A) Processing helix chain 'U' and resid 1095 through 1105 Processing helix chain 'U' and resid 1115 through 1123 Processing helix chain 'U' and resid 1125 through 1136 Processing helix chain 'W' and resid 160 through 167 Processing helix chain 'W' and resid 177 through 184 Processing helix chain 'W' and resid 199 through 203 removed outlier: 3.661A pdb=" N GLN W 203 " --> pdb=" O PHE W 200 " (cutoff:3.500A) Processing helix chain 'W' and resid 217 through 228 Processing helix chain 'W' and resid 286 through 290 removed outlier: 3.592A pdb=" N MET W 289 " --> pdb=" O THR W 286 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TRP W 290 " --> pdb=" O ASP W 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 286 through 290' Processing helix chain 'W' and resid 298 through 306 Processing helix chain 'W' and resid 307 through 319 Processing helix chain 'W' and resid 338 through 342 Processing helix chain 'W' and resid 366 through 386 removed outlier: 4.528A pdb=" N ARG W 382 " --> pdb=" O PHE W 378 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS W 383 " --> pdb=" O MET W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 408 through 418 Processing helix chain 'W' and resid 419 through 421 No H-bonds generated for 'chain 'W' and resid 419 through 421' Processing helix chain 'W' and resid 449 through 461 Processing helix chain 'W' and resid 522 through 527 Processing helix chain 'W' and resid 552 through 563 Processing helix chain 'W' and resid 859 through 866 Processing helix chain 'W' and resid 887 through 891 Processing helix chain 'W' and resid 904 through 909 removed outlier: 3.526A pdb=" N ASP W 909 " --> pdb=" O LYS W 905 " (cutoff:3.500A) Processing helix chain 'W' and resid 931 through 947 removed outlier: 3.807A pdb=" N LEU W 935 " --> pdb=" O THR W 931 " (cutoff:3.500A) Processing helix chain 'W' and resid 954 through 961 Processing helix chain 'W' and resid 1053 through 1063 Processing helix chain 'W' and resid 1090 through 1094 Processing helix chain 'W' and resid 1105 through 1122 Processing helix chain 'W' and resid 1151 through 1159 removed outlier: 3.630A pdb=" N PHE W1155 " --> pdb=" O PRO W1151 " (cutoff:3.500A) Processing helix chain 'W' and resid 1387 through 1405 removed outlier: 3.604A pdb=" N TYR W1405 " --> pdb=" O LEU W1401 " (cutoff:3.500A) Processing helix chain 'W' and resid 1416 through 1420 removed outlier: 3.519A pdb=" N ILE W1420 " --> pdb=" O LEU W1417 " (cutoff:3.500A) Processing helix chain 'W' and resid 1446 through 1453 Processing helix chain 'W' and resid 1455 through 1465 Processing helix chain 'W' and resid 1551 through 1560 Processing helix chain 'W' and resid 1561 through 1578 Processing helix chain 'S' and resid 34 through 39 Processing helix chain 'S' and resid 46 through 51 Processing helix chain 'S' and resid 82 through 86 removed outlier: 3.550A pdb=" N PHE S 86 " --> pdb=" O ALA S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 123 Processing helix chain 'S' and resid 123 through 128 Processing helix chain 'S' and resid 196 through 211 Processing helix chain 'S' and resid 260 through 267 Processing helix chain 'S' and resid 268 through 270 No H-bonds generated for 'chain 'S' and resid 268 through 270' Processing helix chain 'S' and resid 275 through 283 Processing helix chain 'S' and resid 286 through 300 Processing helix chain 'S' and resid 320 through 325 Processing helix chain 'S' and resid 329 through 339 removed outlier: 3.541A pdb=" N ASP S 333 " --> pdb=" O LEU S 329 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR S 339 " --> pdb=" O GLN S 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 345 through 349 Processing helix chain 'S' and resid 434 through 444 Processing helix chain 'S' and resid 450 through 458 Processing helix chain 'S' and resid 459 through 466 Processing helix chain 'S' and resid 468 through 479 Processing helix chain 'S' and resid 569 through 582 Processing helix chain 'S' and resid 585 through 594 Processing helix chain 'S' and resid 596 through 608 removed outlier: 3.521A pdb=" N VAL S 600 " --> pdb=" O PRO S 596 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 39 Processing helix chain 'V' and resid 365 through 376 Processing helix chain 'V' and resid 382 through 387 removed outlier: 3.681A pdb=" N GLU V 387 " --> pdb=" O ILE V 384 " (cutoff:3.500A) Processing helix chain 'V' and resid 401 through 409 Processing helix chain 'V' and resid 412 through 416 removed outlier: 3.576A pdb=" N CYS V 416 " --> pdb=" O ARG V 413 " (cutoff:3.500A) Processing helix chain 'V' and resid 526 through 530 removed outlier: 3.542A pdb=" N MET V 530 " --> pdb=" O LEU V 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 526 through 530' Processing helix chain 'V' and resid 545 through 557 Processing helix chain 'V' and resid 557 through 573 Processing helix chain 'V' and resid 573 through 591 removed outlier: 3.796A pdb=" N SER V 577 " --> pdb=" O SER V 573 " (cutoff:3.500A) Processing helix chain 'V' and resid 593 through 598 removed outlier: 3.991A pdb=" N GLN V 597 " --> pdb=" O SER V 593 " (cutoff:3.500A) Processing helix chain 'V' and resid 601 through 617 Processing helix chain 'V' and resid 618 through 632 Processing helix chain 'V' and resid 678 through 683 Processing helix chain 'V' and resid 743 through 747 removed outlier: 3.592A pdb=" N ASN V 746 " --> pdb=" O ASP V 743 " (cutoff:3.500A) Processing helix chain 'V' and resid 754 through 763 Processing helix chain 'V' and resid 764 through 766 No H-bonds generated for 'chain 'V' and resid 764 through 766' Processing helix chain 'V' and resid 770 through 782 Processing helix chain 'V' and resid 788 through 792 Processing helix chain 'V' and resid 793 through 798 removed outlier: 3.569A pdb=" N ASP V 798 " --> pdb=" O TYR V 794 " (cutoff:3.500A) Processing helix chain 'V' and resid 815 through 831 removed outlier: 3.521A pdb=" N TRP V 831 " --> pdb=" O HIS V 827 " (cutoff:3.500A) Processing helix chain 'V' and resid 889 through 902 Processing helix chain 'V' and resid 907 through 915 Processing helix chain 'V' and resid 922 through 926 Processing helix chain 'V' and resid 932 through 946 Processing helix chain 'V' and resid 961 through 975 removed outlier: 3.516A pdb=" N LYS V 965 " --> pdb=" O ASP V 961 " (cutoff:3.500A) Processing helix chain 'V' and resid 1080 through 1091 removed outlier: 3.741A pdb=" N ILE V1091 " --> pdb=" O LEU V1087 " (cutoff:3.500A) Processing helix chain 'V' and resid 1095 through 1105 Processing helix chain 'V' and resid 1115 through 1123 Processing helix chain 'V' and resid 1125 through 1136 Processing helix chain 'X' and resid 160 through 167 Processing helix chain 'X' and resid 177 through 184 Processing helix chain 'X' and resid 199 through 203 removed outlier: 3.671A pdb=" N GLN X 203 " --> pdb=" O PHE X 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 286 through 290 removed outlier: 3.558A pdb=" N MET X 289 " --> pdb=" O THR X 286 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP X 290 " --> pdb=" O ASP X 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 286 through 290' Processing helix chain 'X' and resid 298 through 306 Processing helix chain 'X' and resid 307 through 319 Processing helix chain 'X' and resid 338 through 342 Processing helix chain 'X' and resid 366 through 386 removed outlier: 4.566A pdb=" N ARG X 382 " --> pdb=" O PHE X 378 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS X 383 " --> pdb=" O MET X 379 " (cutoff:3.500A) Processing helix chain 'X' and resid 408 through 418 Processing helix chain 'X' and resid 419 through 421 No H-bonds generated for 'chain 'X' and resid 419 through 421' Processing helix chain 'X' and resid 449 through 461 Processing helix chain 'X' and resid 522 through 527 Processing helix chain 'X' and resid 552 through 563 Processing helix chain 'X' and resid 859 through 866 Processing helix chain 'X' and resid 887 through 891 Processing helix chain 'X' and resid 904 through 909 removed outlier: 3.526A pdb=" N ASP X 909 " --> pdb=" O LYS X 905 " (cutoff:3.500A) Processing helix chain 'X' and resid 931 through 947 removed outlier: 3.801A pdb=" N LEU X 935 " --> pdb=" O THR X 931 " (cutoff:3.500A) Processing helix chain 'X' and resid 954 through 961 Processing helix chain 'X' and resid 1053 through 1063 Processing helix chain 'X' and resid 1090 through 1094 Processing helix chain 'X' and resid 1105 through 1122 Processing helix chain 'X' and resid 1151 through 1159 removed outlier: 3.610A pdb=" N PHE X1155 " --> pdb=" O PRO X1151 " (cutoff:3.500A) Processing helix chain 'X' and resid 1387 through 1405 removed outlier: 3.605A pdb=" N TYR X1405 " --> pdb=" O LEU X1401 " (cutoff:3.500A) Processing helix chain 'X' and resid 1416 through 1420 removed outlier: 3.511A pdb=" N ILE X1420 " --> pdb=" O LEU X1417 " (cutoff:3.500A) Processing helix chain 'X' and resid 1446 through 1453 Processing helix chain 'X' and resid 1455 through 1465 Processing helix chain 'X' and resid 1551 through 1560 Processing helix chain 'X' and resid 1561 through 1578 Processing helix chain 'T' and resid 34 through 39 Processing helix chain 'T' and resid 42 through 45 Processing helix chain 'T' and resid 46 through 51 Processing helix chain 'T' and resid 82 through 86 removed outlier: 3.543A pdb=" N PHE T 86 " --> pdb=" O ALA T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 123 Processing helix chain 'T' and resid 123 through 128 Processing helix chain 'T' and resid 196 through 211 Processing helix chain 'T' and resid 260 through 267 Processing helix chain 'T' and resid 268 through 270 No H-bonds generated for 'chain 'T' and resid 268 through 270' Processing helix chain 'T' and resid 275 through 283 Processing helix chain 'T' and resid 286 through 300 Processing helix chain 'T' and resid 320 through 325 Processing helix chain 'T' and resid 329 through 339 removed outlier: 3.571A pdb=" N ASP T 333 " --> pdb=" O LEU T 329 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR T 339 " --> pdb=" O GLN T 335 " (cutoff:3.500A) Processing helix chain 'T' and resid 345 through 349 Processing helix chain 'T' and resid 434 through 444 Processing helix chain 'T' and resid 450 through 458 Processing helix chain 'T' and resid 459 through 466 Processing helix chain 'T' and resid 468 through 479 Processing helix chain 'T' and resid 569 through 582 Processing helix chain 'T' and resid 585 through 594 Processing helix chain 'T' and resid 596 through 608 Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 22 removed outlier: 3.568A pdb=" N LEU C 19 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 75 removed outlier: 6.391A pdb=" N ALA C 93 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL C 109 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE C 95 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 117 through 122 removed outlier: 6.737A pdb=" N CYS C 133 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE C 120 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA C 131 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE C 122 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL C 129 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 152 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 166 removed outlier: 6.830A pdb=" N SER C 177 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL C 164 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP C 166 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL C 173 " --> pdb=" O TRP C 166 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE C 182 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER C 196 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 184 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 209 removed outlier: 4.582A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C 241 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 248 through 253 removed outlier: 3.978A pdb=" N ARG C 250 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 272 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 295 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 445 through 450 removed outlier: 6.621A pdb=" N CYS C 457 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE C 449 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU C 455 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 624 through 626 Processing sheet with id=AB1, first strand: chain 'C' and resid 998 through 1001 removed outlier: 6.577A pdb=" N LEU F 330 " --> pdb=" O MET F 342 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL F 344 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL F 328 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS F 327 " --> pdb=" O GLY F 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1080 through 1082 Processing sheet with id=AB3, first strand: chain 'C' and resid 1109 through 1111 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 removed outlier: 6.037A pdb=" N LEU G 414 " --> pdb=" O ALA G 405 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA G 405 " --> pdb=" O LEU G 414 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER G 416 " --> pdb=" O SER G 403 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 12 through 17 removed outlier: 4.005A pdb=" N ASP E 14 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE E 33 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER E 50 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL E 35 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 63 removed outlier: 6.566A pdb=" N LEU E 83 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 111 through 116 removed outlier: 6.967A pdb=" N LEU E 128 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL E 114 " --> pdb=" O ALA E 126 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA E 126 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY E 129 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER E 152 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP E 138 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU E 150 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 173 removed outlier: 3.645A pdb=" N CYS E 170 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA E 191 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN E 195 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL E 204 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 215 through 220 removed outlier: 6.482A pdb=" N GLY E 234 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE E 218 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA E 232 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TRP E 220 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU E 230 " --> pdb=" O TRP E 220 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE E 240 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU E 299 " --> pdb=" O ILE E 240 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 242 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 307 through 311 removed outlier: 3.507A pdb=" N SER E 309 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER E 343 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS E 332 " --> pdb=" O CYS E 341 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N CYS E 341 " --> pdb=" O LYS E 332 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.577A pdb=" N LEU G 3 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP G 17 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS G 47 " --> pdb=" O HIS G 30 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS G 32 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS G 45 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 58 through 60 removed outlier: 3.773A pdb=" N PHE G 80 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL G 144 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 154 through 157 removed outlier: 3.823A pdb=" N GLY G 156 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN G 177 " --> pdb=" O MET G 165 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER G 174 " --> pdb=" O THR G 199 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR G 199 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 205 through 207 Processing sheet with id=AC6, first strand: chain 'G' and resid 242 through 246 removed outlier: 4.256A pdb=" N ILE G 244 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER G 255 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU G 246 " --> pdb=" O GLN G 253 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLN G 253 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 307 through 309 removed outlier: 3.524A pdb=" N THR G 325 " --> pdb=" O HIS G 321 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE G 326 " --> pdb=" O ASP G 361 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP G 361 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG G 328 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL G 359 " --> pdb=" O ARG G 328 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG G 330 " --> pdb=" O SER G 357 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR G 334 " --> pdb=" O ASN G 353 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 369 through 376 removed outlier: 3.701A pdb=" N SER G 383 " --> pdb=" O ILE G 375 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 14 through 17 removed outlier: 5.577A pdb=" N ILE H 33 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR H 48 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE H 35 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 56 through 61 removed outlier: 3.665A pdb=" N ARG H 58 " --> pdb=" O CYS H 73 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL H 79 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL H 94 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE H 81 " --> pdb=" O ILE H 92 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 102 through 107 removed outlier: 4.127A pdb=" N LYS H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 148 through 153 removed outlier: 6.854A pdb=" N VAL H 182 " --> pdb=" O THR H 199 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR H 199 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE H 184 " --> pdb=" O GLU H 197 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR H 193 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 207 through 212 removed outlier: 3.523A pdb=" N ASP H 209 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 257 through 262 removed outlier: 6.705A pdb=" N SER H 272 " --> pdb=" O TRP H 258 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA H 260 " --> pdb=" O ALA H 270 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA H 270 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP H 262 " --> pdb=" O VAL H 268 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL H 268 " --> pdb=" O TRP H 262 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY H 273 " --> pdb=" O LYS H 277 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS H 277 " --> pdb=" O GLY H 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY H 293 " --> pdb=" O LEU H 280 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS H 282 " --> pdb=" O PRO H 291 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.580A pdb=" N CYS A 157 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 164 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 177 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER A 169 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 175 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.502A pdb=" N LYS A 216 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 261 through 266 Processing sheet with id=AD9, first strand: chain 'A' and resid 282 through 285 Processing sheet with id=AE1, first strand: chain 'A' and resid 310 through 315 removed outlier: 4.115A pdb=" N ASP A 312 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 314 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS A 345 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 372 through 377 removed outlier: 3.513A pdb=" N GLY A 387 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 394 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY A 388 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 444 through 449 removed outlier: 7.043A pdb=" N SER A 465 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 447 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 463 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE A 449 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU A 461 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.915A pdb=" N GLY A 496 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 547 through 548 removed outlier: 3.560A pdb=" N CYS A 659 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.675A pdb=" N ASP B 17 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 47 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS B 32 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LYS B 45 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 55 through 60 removed outlier: 4.123A pdb=" N CYS B 57 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 72 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 152 through 157 removed outlier: 3.638A pdb=" N GLY B 156 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER B 175 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER B 174 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 199 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.974A pdb=" N TYR B 234 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 253 through 256 Processing sheet with id=AF2, first strand: chain 'B' and resid 307 through 309 removed outlier: 6.358A pdb=" N ILE B 326 " --> pdb=" O ASP B 361 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B 361 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG B 328 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 359 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG B 330 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 369 through 376 Processing sheet with id=AF4, first strand: chain 'B' and resid 402 through 406 removed outlier: 6.541A pdb=" N SER B 416 " --> pdb=" O SER B 403 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 405 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU B 414 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1003 through 1004 Processing sheet with id=AF6, first strand: chain 'D' and resid 12 through 17 removed outlier: 3.527A pdb=" N ASP D 14 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N HIS D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE D 33 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER D 50 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 35 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 58 through 63 removed outlier: 6.333A pdb=" N VAL D 81 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR D 103 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU D 83 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 111 through 116 removed outlier: 6.907A pdb=" N LEU D 128 " --> pdb=" O TYR D 112 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 114 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA D 126 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU D 134 " --> pdb=" O GLU D 153 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU D 153 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU D 136 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 170 through 173 removed outlier: 3.738A pdb=" N CYS D 170 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 183 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA D 191 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN D 195 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL D 204 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 215 through 220 removed outlier: 6.215A pdb=" N ILE D 240 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU D 299 " --> pdb=" O ILE D 240 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE D 242 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 309 through 311 removed outlier: 3.743A pdb=" N SER D 309 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 328 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL D 344 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU D 330 " --> pdb=" O MET D 342 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 12 through 17 removed outlier: 3.529A pdb=" N ASP F 14 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE F 33 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER F 50 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL F 35 " --> pdb=" O SER F 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 58 through 63 removed outlier: 6.099A pdb=" N VAL F 81 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR F 103 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU F 83 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 111 through 116 removed outlier: 6.791A pdb=" N LEU F 128 " --> pdb=" O TYR F 112 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL F 114 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA F 126 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE F 116 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS F 124 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY F 129 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER F 152 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP F 138 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU F 150 " --> pdb=" O ASP F 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 170 through 173 removed outlier: 6.613A pdb=" N ILE F 193 " --> pdb=" O ALA F 205 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 215 through 220 removed outlier: 6.191A pdb=" N LYS F 244 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU F 296 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR F 246 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL F 294 " --> pdb=" O THR F 246 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LYS F 248 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU F 292 " --> pdb=" O LYS F 248 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 19 through 22 removed outlier: 3.520A pdb=" N LEU Q 19 " --> pdb=" O LEU Q 337 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP Q 334 " --> pdb=" O SER Q 330 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP Q 306 " --> pdb=" O TRP Q 329 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 29 through 32 removed outlier: 3.509A pdb=" N ALA Q 29 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 73 through 75 removed outlier: 3.829A pdb=" N PHE Q 108 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASN Q 97 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE Q 106 " --> pdb=" O ASN Q 97 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 117 through 122 removed outlier: 6.812A pdb=" N CYS Q 133 " --> pdb=" O THR Q 118 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE Q 120 " --> pdb=" O ALA Q 131 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 120 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE Q 122 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL Q 129 " --> pdb=" O PHE Q 122 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR Q 152 " --> pdb=" O ALA Q 141 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 161 through 166 removed outlier: 6.826A pdb=" N SER Q 177 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL Q 164 " --> pdb=" O ALA Q 175 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA Q 175 " --> pdb=" O VAL Q 164 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TRP Q 166 " --> pdb=" O VAL Q 173 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL Q 173 " --> pdb=" O TRP Q 166 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE Q 182 " --> pdb=" O SER Q 196 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER Q 196 " --> pdb=" O ILE Q 182 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL Q 184 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 204 through 209 removed outlier: 3.512A pdb=" N SER Q 221 " --> pdb=" O THR Q 225 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR Q 225 " --> pdb=" O SER Q 221 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR Q 241 " --> pdb=" O THR Q 289 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 248 through 253 removed outlier: 3.989A pdb=" N ARG Q 250 " --> pdb=" O MET Q 263 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL Q 272 " --> pdb=" O PHE Q 297 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR Q 295 " --> pdb=" O LEU Q 274 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 445 through 450 removed outlier: 6.554A pdb=" N CYS Q 457 " --> pdb=" O GLU Q 447 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE Q 449 " --> pdb=" O GLU Q 455 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLU Q 455 " --> pdb=" O ILE Q 449 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 624 through 626 removed outlier: 3.510A pdb=" N PHE Q 636 " --> pdb=" O GLY Q 624 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 998 through 1001 removed outlier: 6.582A pdb=" N LEU N 330 " --> pdb=" O MET N 342 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL N 344 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL N 328 " --> pdb=" O VAL N 344 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS N 327 " --> pdb=" O GLY N 323 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 1080 through 1082 Processing sheet with id=AI1, first strand: chain 'Q' and resid 1109 through 1111 Processing sheet with id=AI2, first strand: chain 'M' and resid 3 through 4 removed outlier: 6.030A pdb=" N LEU O 414 " --> pdb=" O ALA O 405 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA O 405 " --> pdb=" O LEU O 414 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER O 416 " --> pdb=" O SER O 403 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 12 through 17 removed outlier: 3.999A pdb=" N ASP M 14 " --> pdb=" O CYS M 27 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS M 32 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE M 33 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER M 50 " --> pdb=" O ILE M 33 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL M 35 " --> pdb=" O SER M 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 58 through 63 removed outlier: 6.552A pdb=" N LEU M 83 " --> pdb=" O LEU M 101 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 111 through 116 removed outlier: 6.979A pdb=" N LEU M 128 " --> pdb=" O TYR M 112 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL M 114 " --> pdb=" O ALA M 126 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA M 126 " --> pdb=" O VAL M 114 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY M 129 " --> pdb=" O ILE M 133 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE M 133 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER M 152 " --> pdb=" O LEU M 136 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP M 138 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU M 150 " --> pdb=" O ASP M 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 169 through 173 removed outlier: 3.652A pdb=" N CYS M 170 " --> pdb=" O SER M 186 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA M 191 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN M 195 " --> pdb=" O VAL M 204 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL M 204 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 215 through 220 removed outlier: 6.472A pdb=" N GLY M 234 " --> pdb=" O ARG M 216 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE M 218 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA M 232 " --> pdb=" O ILE M 218 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TRP M 220 " --> pdb=" O LEU M 230 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU M 230 " --> pdb=" O TRP M 220 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE M 240 " --> pdb=" O GLU M 299 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU M 299 " --> pdb=" O ILE M 240 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE M 242 " --> pdb=" O LEU M 297 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'M' and resid 307 through 311 removed outlier: 3.567A pdb=" N SER M 309 " --> pdb=" O ALA M 322 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER M 343 " --> pdb=" O LEU M 330 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS M 332 " --> pdb=" O CYS M 341 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS M 341 " --> pdb=" O LYS M 332 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.557A pdb=" N LEU O 3 " --> pdb=" O VAL O 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP O 17 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS O 47 " --> pdb=" O HIS O 30 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LYS O 32 " --> pdb=" O LYS O 45 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS O 45 " --> pdb=" O LYS O 32 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 58 through 60 removed outlier: 3.762A pdb=" N PHE O 80 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL O 144 " --> pdb=" O LEU O 77 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 154 through 157 removed outlier: 3.822A pdb=" N GLY O 156 " --> pdb=" O ALA O 164 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN O 177 " --> pdb=" O MET O 165 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER O 174 " --> pdb=" O THR O 199 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR O 199 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 205 through 207 Processing sheet with id=AJ4, first strand: chain 'O' and resid 242 through 246 removed outlier: 4.288A pdb=" N ILE O 244 " --> pdb=" O SER O 255 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER O 255 " --> pdb=" O ILE O 244 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU O 246 " --> pdb=" O GLN O 253 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLN O 253 " --> pdb=" O LEU O 246 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 307 through 309 removed outlier: 3.515A pdb=" N THR O 325 " --> pdb=" O HIS O 321 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE O 326 " --> pdb=" O ASP O 361 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP O 361 " --> pdb=" O ILE O 326 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG O 328 " --> pdb=" O VAL O 359 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL O 359 " --> pdb=" O ARG O 328 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG O 330 " --> pdb=" O SER O 357 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR O 334 " --> pdb=" O ASN O 353 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 369 through 376 removed outlier: 3.701A pdb=" N SER O 383 " --> pdb=" O ILE O 375 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'P' and resid 14 through 17 removed outlier: 5.519A pdb=" N ILE P 33 " --> pdb=" O THR P 48 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR P 48 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE P 35 " --> pdb=" O ILE P 46 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'P' and resid 56 through 61 removed outlier: 3.678A pdb=" N ARG P 58 " --> pdb=" O CYS P 73 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL P 79 " --> pdb=" O VAL P 94 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL P 94 " --> pdb=" O VAL P 79 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE P 81 " --> pdb=" O ILE P 92 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'P' and resid 102 through 107 removed outlier: 4.134A pdb=" N LYS P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'P' and resid 148 through 153 removed outlier: 6.843A pdb=" N VAL P 182 " --> pdb=" O THR P 199 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR P 199 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE P 184 " --> pdb=" O GLU P 197 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR P 193 " --> pdb=" O ASN P 188 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'P' and resid 207 through 212 removed outlier: 3.523A pdb=" N ASP P 209 " --> pdb=" O VAL P 225 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'P' and resid 257 through 262 removed outlier: 6.691A pdb=" N SER P 272 " --> pdb=" O TRP P 258 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA P 260 " --> pdb=" O ALA P 270 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA P 270 " --> pdb=" O ALA P 260 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP P 262 " --> pdb=" O VAL P 268 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL P 268 " --> pdb=" O TRP P 262 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY P 273 " --> pdb=" O LYS P 277 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS P 277 " --> pdb=" O GLY P 273 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY P 293 " --> pdb=" O LEU P 280 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS P 282 " --> pdb=" O PRO P 291 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 143 through 146 removed outlier: 3.582A pdb=" N CYS I 157 " --> pdb=" O GLY I 164 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY I 164 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS I 177 " --> pdb=" O LYS I 167 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N SER I 169 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE I 175 " --> pdb=" O SER I 169 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'I' and resid 216 through 217 Processing sheet with id=AK6, first strand: chain 'I' and resid 261 through 266 Processing sheet with id=AK7, first strand: chain 'I' and resid 282 through 285 Processing sheet with id=AK8, first strand: chain 'I' and resid 310 through 315 removed outlier: 4.149A pdb=" N ASP I 312 " --> pdb=" O ILE I 344 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 314 " --> pdb=" O ALA I 342 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS I 345 " --> pdb=" O TYR I 349 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR I 349 " --> pdb=" O HIS I 345 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'I' and resid 372 through 377 removed outlier: 3.505A pdb=" N GLY I 387 " --> pdb=" O CYS I 374 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS I 394 " --> pdb=" O THR I 386 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY I 388 " --> pdb=" O LYS I 392 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS I 392 " --> pdb=" O GLY I 388 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'I' and resid 444 through 449 removed outlier: 7.019A pdb=" N SER I 465 " --> pdb=" O THR I 445 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU I 447 " --> pdb=" O GLY I 463 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY I 463 " --> pdb=" O LEU I 447 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE I 449 " --> pdb=" O LEU I 461 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU I 461 " --> pdb=" O PHE I 449 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'I' and resid 494 through 499 removed outlier: 3.908A pdb=" N GLY I 496 " --> pdb=" O ILE I 508 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'I' and resid 547 through 548 removed outlier: 3.546A pdb=" N CYS I 659 " --> pdb=" O ASP I 548 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.503A pdb=" N LEU J 3 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP J 17 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS J 47 " --> pdb=" O HIS J 30 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS J 32 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS J 45 " --> pdb=" O LYS J 32 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 55 through 60 removed outlier: 4.125A pdb=" N CYS J 57 " --> pdb=" O GLY J 71 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU J 72 " --> pdb=" O TYR J 76 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR J 76 " --> pdb=" O GLU J 72 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'J' and resid 152 through 157 removed outlier: 3.632A pdb=" N GLY J 156 " --> pdb=" O ALA J 164 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER J 175 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N SER J 174 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR J 199 " --> pdb=" O SER J 174 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'J' and resid 205 through 208 removed outlier: 3.960A pdb=" N TYR J 234 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'J' and resid 253 through 256 Processing sheet with id=AL9, first strand: chain 'J' and resid 307 through 309 removed outlier: 5.858A pdb=" N GLY J 332 " --> pdb=" O VAL J 356 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL J 356 " --> pdb=" O GLY J 332 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR J 334 " --> pdb=" O LEU J 354 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU J 354 " --> pdb=" O TYR J 334 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'J' and resid 369 through 376 Processing sheet with id=AM2, first strand: chain 'J' and resid 402 through 406 removed outlier: 6.539A pdb=" N SER J 416 " --> pdb=" O SER J 403 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA J 405 " --> pdb=" O LEU J 414 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU J 414 " --> pdb=" O ALA J 405 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'J' and resid 1003 through 1004 Processing sheet with id=AM4, first strand: chain 'L' and resid 12 through 17 removed outlier: 3.518A pdb=" N ASP L 14 " --> pdb=" O CYS L 27 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS L 32 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE L 33 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER L 50 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL L 35 " --> pdb=" O SER L 48 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'L' and resid 58 through 63 removed outlier: 6.315A pdb=" N VAL L 81 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR L 103 " --> pdb=" O VAL L 81 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU L 83 " --> pdb=" O LEU L 101 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'L' and resid 111 through 116 removed outlier: 6.904A pdb=" N LEU L 128 " --> pdb=" O TYR L 112 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL L 114 " --> pdb=" O ALA L 126 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA L 126 " --> pdb=" O VAL L 114 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU L 134 " --> pdb=" O GLU L 153 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU L 153 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU L 136 " --> pdb=" O THR L 151 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'L' and resid 170 through 173 removed outlier: 3.737A pdb=" N CYS L 170 " --> pdb=" O SER L 186 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU L 183 " --> pdb=" O TYR L 194 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA L 191 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN L 195 " --> pdb=" O VAL L 204 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL L 204 " --> pdb=" O GLN L 195 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'L' and resid 215 through 220 removed outlier: 6.216A pdb=" N ILE L 240 " --> pdb=" O GLU L 299 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU L 299 " --> pdb=" O ILE L 240 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE L 242 " --> pdb=" O LEU L 297 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'L' and resid 309 through 311 removed outlier: 3.750A pdb=" N SER L 309 " --> pdb=" O ALA L 322 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL L 328 " --> pdb=" O VAL L 344 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL L 344 " --> pdb=" O VAL L 328 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU L 330 " --> pdb=" O MET L 342 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'N' and resid 12 through 17 removed outlier: 3.534A pdb=" N ASP N 14 " --> pdb=" O CYS N 27 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS N 32 " --> pdb=" O SER N 28 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE N 33 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER N 50 " --> pdb=" O ILE N 33 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL N 35 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'N' and resid 58 through 63 removed outlier: 6.100A pdb=" N VAL N 81 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR N 103 " --> pdb=" O VAL N 81 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU N 83 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'N' and resid 111 through 116 removed outlier: 6.805A pdb=" N LEU N 128 " --> pdb=" O TYR N 112 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL N 114 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA N 126 " --> pdb=" O VAL N 114 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE N 116 " --> pdb=" O LYS N 124 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS N 124 " --> pdb=" O PHE N 116 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY N 129 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE N 133 " --> pdb=" O GLY N 129 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER N 152 " --> pdb=" O LEU N 136 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP N 138 " --> pdb=" O LEU N 150 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU N 150 " --> pdb=" O ASP N 138 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'N' and resid 170 through 173 removed outlier: 6.625A pdb=" N ILE N 193 " --> pdb=" O ALA N 205 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'N' and resid 215 through 220 removed outlier: 6.157A pdb=" N LYS N 244 " --> pdb=" O LEU N 296 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU N 296 " --> pdb=" O LYS N 244 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR N 246 " --> pdb=" O VAL N 294 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL N 294 " --> pdb=" O THR N 246 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LYS N 248 " --> pdb=" O LEU N 292 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU N 292 " --> pdb=" O LYS N 248 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.875A pdb=" N VAL U 538 " --> pdb=" O LEU U 11 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR S 62 " --> pdb=" O THR U 423 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR S 73 " --> pdb=" O PHE S 91 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE S 91 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER S 88 " --> pdb=" O PHE S 19 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE S 14 " --> pdb=" O GLU S 30 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU S 30 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR S 16 " --> pdb=" O LYS S 28 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'U' and resid 23 through 25 removed outlier: 3.740A pdb=" N MET U 532 " --> pdb=" O SER U 18 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'U' and resid 636 through 640 Processing sheet with id=AN9, first strand: chain 'U' and resid 655 through 656 Processing sheet with id=AO1, first strand: chain 'U' and resid 748 through 751 Processing sheet with id=AO2, first strand: chain 'U' and resid 846 through 848 Processing sheet with id=AO3, first strand: chain 'U' and resid 1071 through 1073 removed outlier: 4.319A pdb=" N ILE U 958 " --> pdb=" O ILE U1073 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR U 954 " --> pdb=" O VAL U1113 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL U1113 " --> pdb=" O THR U 954 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE U 956 " --> pdb=" O GLY U1111 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'U' and resid 1071 through 1073 removed outlier: 4.319A pdb=" N ILE U 958 " --> pdb=" O ILE U1073 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'W' and resid 102 through 104 removed outlier: 3.517A pdb=" N PHE W 154 " --> pdb=" O VAL W 134 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'W' and resid 107 through 109 removed outlier: 6.422A pdb=" N GLY W 107 " --> pdb=" O ILE W 174 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'W' and resid 257 through 259 removed outlier: 4.215A pdb=" N ILE W 252 " --> pdb=" O ILE W 259 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL W 207 " --> pdb=" O ILE W 271 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG W 273 " --> pdb=" O VAL W 207 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE W 209 " --> pdb=" O ARG W 273 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'W' and resid 231 through 234 removed outlier: 3.671A pdb=" N THR W 231 " --> pdb=" O ILE W 264 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'W' and resid 238 through 239 removed outlier: 3.668A pdb=" N GLY W 247 " --> pdb=" O LEU W 239 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'W' and resid 400 through 401 removed outlier: 3.542A pdb=" N ARG W 400 " --> pdb=" O ASP W 333 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER W 331 " --> pdb=" O ILE W 285 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG W 278 " --> pdb=" O HIS W 435 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N MET W 437 " --> pdb=" O ARG W 278 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE W 280 " --> pdb=" O MET W 437 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE W 439 " --> pdb=" O ILE W 280 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU W 282 " --> pdb=" O ILE W 439 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ASP W 468 " --> pdb=" O THR W 434 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL W 436 " --> pdb=" O ASP W 468 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE W 470 " --> pdb=" O VAL W 436 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE W 438 " --> pdb=" O ILE W 470 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'W' and resid 400 through 401 removed outlier: 3.542A pdb=" N ARG W 400 " --> pdb=" O ASP W 333 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE W 324 " --> pdb=" O ASP W 360 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP W 360 " --> pdb=" O ILE W 324 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE W 326 " --> pdb=" O VAL W 358 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N LEU W1028 " --> pdb=" O SER W 351 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP W 353 " --> pdb=" O LEU W1028 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LYS W1030 " --> pdb=" O ASP W 353 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE W 355 " --> pdb=" O LYS W1030 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG W1038 " --> pdb=" O VAL W1029 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'W' and resid 387 through 389 Processing sheet with id=AP4, first strand: chain 'W' and resid 445 through 447 removed outlier: 6.410A pdb=" N PHE W 446 " --> pdb=" O ARG W 484 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ARG W 486 " --> pdb=" O PHE W 446 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS W 494 " --> pdb=" O ILE W 851 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'W' and resid 898 through 899 removed outlier: 3.638A pdb=" N ILE W 899 " --> pdb=" O ILE W 950 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN W 949 " --> pdb=" O MET W 989 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR W 987 " --> pdb=" O CYS W 951 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL W1007 " --> pdb=" O HIS W 917 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'W' and resid 1344 through 1350 removed outlier: 3.516A pdb=" N ASN W1345 " --> pdb=" O TYR W1367 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR W1367 " --> pdb=" O ASN W1345 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS W1366 " --> pdb=" O ARG W1380 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP W1368 " --> pdb=" O HIS W1378 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS W1378 " --> pdb=" O ASP W1368 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE W1377 " --> pdb=" O VAL W1082 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS W1079 " --> pdb=" O ILE W1412 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'W' and resid 1340 through 1342 removed outlier: 5.686A pdb=" N LEU W1341 " --> pdb=" O MET W1487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP7 Processing sheet with id=AP8, first strand: chain 'W' and resid 1430 through 1432 removed outlier: 3.815A pdb=" N LEU W1519 " --> pdb=" O VAL W1430 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR W1507 " --> pdb=" O HIS W1502 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'S' and resid 213 through 217 Processing sheet with id=AQ1, first strand: chain 'S' and resid 244 through 247 Processing sheet with id=AQ2, first strand: chain 'S' and resid 315 through 317 Processing sheet with id=AQ3, first strand: chain 'S' and resid 486 through 490 removed outlier: 3.560A pdb=" N TYR S 486 " --> pdb=" O SER S 615 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.803A pdb=" N VAL V 538 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR T 73 " --> pdb=" O PHE T 91 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE T 91 " --> pdb=" O TYR T 73 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER T 88 " --> pdb=" O PHE T 19 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR T 13 " --> pdb=" O VAL T 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE T 14 " --> pdb=" O GLU T 30 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU T 30 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR T 16 " --> pdb=" O LYS T 28 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'V' and resid 23 through 25 removed outlier: 3.845A pdb=" N MET V 532 " --> pdb=" O SER V 18 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'V' and resid 636 through 640 Processing sheet with id=AQ7, first strand: chain 'V' and resid 655 through 656 Processing sheet with id=AQ8, first strand: chain 'V' and resid 748 through 751 Processing sheet with id=AQ9, first strand: chain 'V' and resid 846 through 848 Processing sheet with id=AR1, first strand: chain 'V' and resid 1071 through 1073 removed outlier: 4.329A pdb=" N ILE V 958 " --> pdb=" O ILE V1073 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR V 954 " --> pdb=" O VAL V1113 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL V1113 " --> pdb=" O THR V 954 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE V 956 " --> pdb=" O GLY V1111 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'V' and resid 1071 through 1073 removed outlier: 4.329A pdb=" N ILE V 958 " --> pdb=" O ILE V1073 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'X' and resid 102 through 104 removed outlier: 3.542A pdb=" N PHE X 154 " --> pdb=" O VAL X 134 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'X' and resid 107 through 109 removed outlier: 6.425A pdb=" N GLY X 107 " --> pdb=" O ILE X 174 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'X' and resid 257 through 259 removed outlier: 4.192A pdb=" N ILE X 252 " --> pdb=" O ILE X 259 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL X 207 " --> pdb=" O ILE X 271 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG X 273 " --> pdb=" O VAL X 207 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE X 209 " --> pdb=" O ARG X 273 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'X' and resid 231 through 234 removed outlier: 3.629A pdb=" N THR X 231 " --> pdb=" O ILE X 264 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'X' and resid 238 through 239 removed outlier: 3.662A pdb=" N GLY X 247 " --> pdb=" O LEU X 239 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'X' and resid 400 through 401 removed outlier: 3.624A pdb=" N ARG X 400 " --> pdb=" O ASP X 333 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER X 331 " --> pdb=" O ILE X 285 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG X 278 " --> pdb=" O HIS X 435 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET X 437 " --> pdb=" O ARG X 278 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE X 280 " --> pdb=" O MET X 437 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE X 439 " --> pdb=" O ILE X 280 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU X 282 " --> pdb=" O ILE X 439 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ASP X 468 " --> pdb=" O THR X 434 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL X 436 " --> pdb=" O ASP X 468 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE X 470 " --> pdb=" O VAL X 436 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE X 438 " --> pdb=" O ILE X 470 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'X' and resid 400 through 401 removed outlier: 3.624A pdb=" N ARG X 400 " --> pdb=" O ASP X 333 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE X 324 " --> pdb=" O ASP X 360 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP X 360 " --> pdb=" O ILE X 324 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE X 326 " --> pdb=" O VAL X 358 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N LEU X1028 " --> pdb=" O SER X 351 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP X 353 " --> pdb=" O LEU X1028 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS X1030 " --> pdb=" O ASP X 353 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE X 355 " --> pdb=" O LYS X1030 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG X1038 " --> pdb=" O VAL X1029 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'X' and resid 387 through 389 Processing sheet with id=AS2, first strand: chain 'X' and resid 445 through 447 removed outlier: 6.311A pdb=" N PHE X 446 " --> pdb=" O ARG X 484 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ARG X 486 " --> pdb=" O PHE X 446 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS X 494 " --> pdb=" O ILE X 851 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'X' and resid 898 through 899 removed outlier: 3.651A pdb=" N ILE X 899 " --> pdb=" O ILE X 950 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN X 949 " --> pdb=" O MET X 989 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR X 987 " --> pdb=" O CYS X 951 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL X1007 " --> pdb=" O HIS X 917 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'X' and resid 1344 through 1350 removed outlier: 3.545A pdb=" N ASN X1345 " --> pdb=" O TYR X1367 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR X1367 " --> pdb=" O ASN X1345 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP X1368 " --> pdb=" O HIS X1378 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS X1378 " --> pdb=" O ASP X1368 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE X1377 " --> pdb=" O VAL X1082 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS X1079 " --> pdb=" O ILE X1412 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'X' and resid 1340 through 1342 removed outlier: 5.724A pdb=" N LEU X1341 " --> pdb=" O MET X1487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS5 Processing sheet with id=AS6, first strand: chain 'X' and resid 1430 through 1432 removed outlier: 3.810A pdb=" N LEU X1519 " --> pdb=" O VAL X1430 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR X1507 " --> pdb=" O HIS X1502 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'T' and resid 213 through 217 Processing sheet with id=AS8, first strand: chain 'T' and resid 244 through 247 Processing sheet with id=AS9, first strand: chain 'T' and resid 315 through 317 Processing sheet with id=AT1, first strand: chain 'T' and resid 486 through 491 3730 hydrogen bonds defined for protein. 10395 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: 62.86 Time building geometry restraints manager: 32.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 29039 1.34 - 1.45: 17210 1.45 - 1.57: 54233 1.57 - 1.69: 0 1.69 - 1.81: 764 Bond restraints: 101246 Sorted by residual: bond pdb=" CA LYS J 147 " pdb=" C LYS J 147 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.27e-02 6.20e+03 6.72e+00 bond pdb=" N LYS J 147 " pdb=" CA LYS J 147 " ideal model delta sigma weight residual 1.459 1.431 0.028 1.19e-02 7.06e+03 5.72e+00 bond pdb=" CA LYS B 147 " pdb=" C LYS B 147 " ideal model delta sigma weight residual 1.524 1.494 0.029 1.27e-02 6.20e+03 5.37e+00 bond pdb=" CA LYS J 147 " pdb=" CB LYS J 147 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.55e-02 4.16e+03 4.86e+00 bond pdb=" N LYS B 147 " pdb=" CA LYS B 147 " ideal model delta sigma weight residual 1.459 1.433 0.026 1.19e-02 7.06e+03 4.80e+00 ... (remaining 101241 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.58: 2801 106.58 - 113.51: 55199 113.51 - 120.44: 37770 120.44 - 127.38: 40078 127.38 - 134.31: 1228 Bond angle restraints: 137076 Sorted by residual: angle pdb=" N LYS J 147 " pdb=" CA LYS J 147 " pdb=" C LYS J 147 " ideal model delta sigma weight residual 111.07 106.41 4.66 1.07e+00 8.73e-01 1.90e+01 angle pdb=" N LYS B 147 " pdb=" CA LYS B 147 " pdb=" C LYS B 147 " ideal model delta sigma weight residual 111.07 106.68 4.39 1.07e+00 8.73e-01 1.69e+01 angle pdb=" C ASP N 41 " pdb=" N THR N 42 " pdb=" CA THR N 42 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C ASP F 41 " pdb=" N THR F 42 " pdb=" CA THR F 42 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C ASP M 30 " pdb=" N GLN M 31 " pdb=" CA GLN M 31 " ideal model delta sigma weight residual 122.07 126.80 -4.73 1.43e+00 4.89e-01 1.09e+01 ... (remaining 137071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 54490 17.66 - 35.32: 5189 35.32 - 52.98: 779 52.98 - 70.64: 80 70.64 - 88.30: 38 Dihedral angle restraints: 60576 sinusoidal: 24716 harmonic: 35860 Sorted by residual: dihedral pdb=" CA VAL U 837 " pdb=" C VAL U 837 " pdb=" N ILE U 838 " pdb=" CA ILE U 838 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA VAL V 837 " pdb=" C VAL V 837 " pdb=" N ILE V 838 " pdb=" CA ILE V 838 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" C ILE W1420 " pdb=" N ILE W1420 " pdb=" CA ILE W1420 " pdb=" CB ILE W1420 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 60573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 12187 0.057 - 0.114: 2490 0.114 - 0.171: 356 0.171 - 0.228: 20 0.228 - 0.285: 5 Chirality restraints: 15058 Sorted by residual: chirality pdb=" CB THR W 138 " pdb=" CA THR W 138 " pdb=" OG1 THR W 138 " pdb=" CG2 THR W 138 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB THR X 138 " pdb=" CA THR X 138 " pdb=" OG1 THR X 138 " pdb=" CG2 THR X 138 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU J 566 " pdb=" CB LEU J 566 " pdb=" CD1 LEU J 566 " pdb=" CD2 LEU J 566 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 15055 not shown) Planarity restraints: 17372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1001 " -0.037 2.00e-02 2.50e+03 2.89e-02 2.09e+01 pdb=" CG TRP B1001 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP B1001 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B1001 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B1001 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1001 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1001 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1001 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1001 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B1001 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J1001 " 0.037 2.00e-02 2.50e+03 2.86e-02 2.05e+01 pdb=" CG TRP J1001 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP J1001 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP J1001 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP J1001 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J1001 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J1001 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP J1001 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J1001 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J1001 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 793 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO B 794 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 794 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 794 " -0.041 5.00e-02 4.00e+02 ... (remaining 17369 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 14138 2.76 - 3.30: 86369 3.30 - 3.83: 166678 3.83 - 4.37: 197640 4.37 - 4.90: 342006 Nonbonded interactions: 806831 Sorted by model distance: nonbonded pdb=" O VAL U 667 " pdb=" OH TYR U 862 " model vdw 2.230 2.440 nonbonded pdb=" O VAL V 667 " pdb=" OH TYR V 862 " model vdw 2.234 2.440 nonbonded pdb=" OG SER M 76 " pdb=" OD1 ASP M 78 " model vdw 2.247 2.440 nonbonded pdb=" OG SER E 76 " pdb=" OD1 ASP E 78 " model vdw 2.247 2.440 nonbonded pdb=" OD2 ASP C 786 " pdb=" OG SER H 265 " model vdw 2.275 2.440 ... (remaining 806826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 2 through 611 or resid 626 through 937 or resid 940 throug \ h 963 or resid 995 through 1037 or resid 1101 through 1104)) selection = (chain 'G' and (resid 2 through 533 or resid 539 through 611 or resid 626 throug \ h 1037 or resid 1101 through 1104)) selection = (chain 'J' and (resid 2 through 611 or resid 626 through 937 or resid 940 throug \ h 963 or resid 995 through 1037 or resid 1101 through 1104)) selection = (chain 'O' and (resid 2 through 533 or resid 539 through 611 or resid 626 throug \ h 1037 or resid 1101 through 1104)) } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = (chain 'D' and (resid 1 through 248 or resid 288 through 346)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 248 or resid 288 through 346)) selection = (chain 'L' and (resid 1 through 248 or resid 288 through 346)) selection = chain 'M' selection = (chain 'N' and (resid 1 through 248 or resid 288 through 346)) } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 28 6.06 5 S 536 5.16 5 C 63176 2.51 5 N 16788 2.21 5 O 18444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 54.770 Check model and map are aligned: 1.440 Convert atoms to be neutral: 0.620 Process input model: 233.150 Find NCS groups from input model: 6.110 Set up NCS constraints: 0.700 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 315.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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 : 0.003 0.050 101246 Z= 0.170 Angle : 0.589 10.349 137076 Z= 0.309 Chirality : 0.047 0.285 15058 Planarity : 0.005 0.074 17372 Dihedral : 13.450 88.304 37300 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.07), residues: 11958 helix: -0.68 (0.08), residues: 3268 sheet: -0.53 (0.10), residues: 3086 loop : -1.16 (0.08), residues: 5604 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2632 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2632 time to evaluate : 8.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 6 residues processed: 2632 average time/residue: 1.5493 time to fit residues: 5758.4630 Evaluate side-chains 1856 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1850 time to evaluate : 8.670 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 3 average time/residue: 1.0918 time to fit residues: 17.5204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1026 optimal weight: 20.0000 chunk 921 optimal weight: 20.0000 chunk 511 optimal weight: 0.9980 chunk 314 optimal weight: 1.9990 chunk 621 optimal weight: 0.5980 chunk 492 optimal weight: 2.9990 chunk 953 optimal weight: 7.9990 chunk 368 optimal weight: 2.9990 chunk 579 optimal weight: 2.9990 chunk 709 optimal weight: 3.9990 chunk 1104 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 HIS E 195 GLN E 291 ASN E 337 ASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 HIS G 236 HIS G 350 ASN G 379 ASN G 715 GLN G 876 GLN H 95 HIS ** H 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 539 ASN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 HIS D 337 ASN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 ASN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 ASN Q 439 HIS ** Q 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 847 HIS Q1003 HIS Q1081 HIS ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 HIS ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 379 ASN ** O 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 886 GLN ** P 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 227 GLN ** I 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 542 ASN ** I 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 ASN J 389 GLN J 539 ASN J 811 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 HIS ** N 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 GLN N 211 HIS N 337 ASN U 7 ASN U 24 GLN ** U 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 555 GLN U 938 ASN U 945 GLN ** W 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 533 ASN S 12 HIS ** S 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 ASN T 348 ASN ** T 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 101246 Z= 0.343 Angle : 0.659 11.693 137076 Z= 0.342 Chirality : 0.047 0.191 15058 Planarity : 0.005 0.072 17372 Dihedral : 4.679 49.248 13198 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.08), residues: 11958 helix: 0.19 (0.09), residues: 3340 sheet: -0.44 (0.09), residues: 3020 loop : -1.01 (0.08), residues: 5598 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2383 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1995 time to evaluate : 8.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 388 outliers final: 159 residues processed: 2164 average time/residue: 1.5706 time to fit residues: 4798.1963 Evaluate side-chains 1946 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1787 time to evaluate : 8.566 Switching outliers to nearest non-outliers outliers start: 159 outliers final: 84 residues processed: 81 average time/residue: 0.9048 time to fit residues: 137.5491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 613 optimal weight: 0.9990 chunk 342 optimal weight: 0.9980 chunk 919 optimal weight: 10.0000 chunk 751 optimal weight: 0.9980 chunk 304 optimal weight: 0.4980 chunk 1106 optimal weight: 6.9990 chunk 1195 optimal weight: 5.9990 chunk 985 optimal weight: 10.0000 chunk 1097 optimal weight: 20.0000 chunk 377 optimal weight: 2.9990 chunk 887 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 291 ASN G 172 HIS ** G 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 ASN G 632 GLN ** G 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 856 HIS ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN B 14 ASN B 417 ASN B 539 ASN B 659 ASN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS F 163 ASN ** F 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN ** O 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1037 ASN ** P 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 ASN ** P 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 ASN I 381 GLN I 671 ASN I 856 HIS ** I1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1327 ASN J 149 GLN J 539 ASN J 659 ASN J 781 ASN J 801 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 293 GLN U 631 GLN U 784 GLN W 305 ASN ** S 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 ASN V 631 GLN V 756 ASN ** V 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 323 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 101246 Z= 0.209 Angle : 0.588 15.657 137076 Z= 0.300 Chirality : 0.044 0.269 15058 Planarity : 0.004 0.067 17372 Dihedral : 4.424 50.852 13198 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.08), residues: 11958 helix: 0.55 (0.09), residues: 3368 sheet: -0.38 (0.09), residues: 3014 loop : -0.92 (0.08), residues: 5576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2222 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 1859 time to evaluate : 8.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 363 outliers final: 164 residues processed: 2045 average time/residue: 1.5865 time to fit residues: 4575.9799 Evaluate side-chains 1920 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1756 time to evaluate : 8.619 Switching outliers to nearest non-outliers outliers start: 164 outliers final: 91 residues processed: 77 average time/residue: 1.0356 time to fit residues: 143.5351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1092 optimal weight: 8.9990 chunk 831 optimal weight: 0.0270 chunk 574 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 527 optimal weight: 5.9990 chunk 742 optimal weight: 2.9990 chunk 1110 optimal weight: 9.9990 chunk 1175 optimal weight: 20.0000 chunk 580 optimal weight: 0.6980 chunk 1052 optimal weight: 0.4980 chunk 316 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS G 172 HIS G 379 ASN ** G 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 671 ASN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 GLN A1327 ASN B 14 ASN B 149 GLN B 417 ASN B 539 ASN B 659 ASN B 781 ASN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 236 HIS O 632 GLN ** O 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 715 GLN O 801 GLN O 805 ASN ** P 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 284 ASN ** I 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 671 ASN I 706 GLN I1183 ASN I1327 ASN J 539 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 163 ASN N 293 GLN U 7 ASN U 555 GLN W 217 ASN W 305 ASN S 323 ASN V 938 ASN V 951 GLN X1514 ASN T 258 ASN ** T 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 101246 Z= 0.192 Angle : 0.581 14.718 137076 Z= 0.295 Chirality : 0.044 0.241 15058 Planarity : 0.004 0.116 17372 Dihedral : 4.334 50.200 13198 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.08), residues: 11958 helix: 0.73 (0.09), residues: 3374 sheet: -0.24 (0.09), residues: 3004 loop : -0.91 (0.08), residues: 5580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2202 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 1835 time to evaluate : 8.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 367 outliers final: 183 residues processed: 2039 average time/residue: 1.5463 time to fit residues: 4479.4217 Evaluate side-chains 1926 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1743 time to evaluate : 8.660 Switching outliers to nearest non-outliers outliers start: 183 outliers final: 111 residues processed: 78 average time/residue: 0.9609 time to fit residues: 137.7185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 978 optimal weight: 10.0000 chunk 667 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 875 optimal weight: 5.9990 chunk 484 optimal weight: 0.4980 chunk 1003 optimal weight: 4.9990 chunk 812 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 600 optimal weight: 4.9990 chunk 1055 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN C 245 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 HIS ** G 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 ASN G 601 ASN G 738 ASN A 148 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN B 14 ASN B 235 GLN B 304 ASN B 417 ASN B 539 ASN F 120 HIS F 195 GLN F 337 ASN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 715 GLN O 738 ASN O 886 GLN ** P 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 515 ASN I 671 ASN I1327 ASN J 350 ASN J 539 ASN J 715 GLN ** J 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 293 GLN N 337 ASN W 284 GLN ** W 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 493 HIS W 533 ASN W1366 HIS ** W1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 746 ASN ** V 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 323 ASN ** T 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.103 101246 Z= 0.538 Angle : 0.778 14.899 137076 Z= 0.401 Chirality : 0.051 0.328 15058 Planarity : 0.006 0.095 17372 Dihedral : 5.192 44.086 13198 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.19 % Favored : 94.80 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.07), residues: 11958 helix: 0.28 (0.09), residues: 3322 sheet: -0.55 (0.09), residues: 3020 loop : -1.25 (0.08), residues: 5616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2402 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 529 poor density : 1873 time to evaluate : 8.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 529 outliers final: 255 residues processed: 2148 average time/residue: 1.5843 time to fit residues: 4858.3976 Evaluate side-chains 2019 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1764 time to evaluate : 8.747 Switching outliers to nearest non-outliers outliers start: 255 outliers final: 143 residues processed: 118 average time/residue: 1.0109 time to fit residues: 211.3298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 395 optimal weight: 0.6980 chunk 1058 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 690 optimal weight: 0.7980 chunk 290 optimal weight: 1.9990 chunk 1176 optimal weight: 7.9990 chunk 976 optimal weight: 20.0000 chunk 544 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 389 optimal weight: 0.6980 chunk 617 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 HIS ** G 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 539 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 GLN B 153 ASN B 417 ASN B 539 ASN B 889 ASN D 163 ASN D 195 GLN F 105 ASN F 120 HIS F 293 GLN F 337 ASN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1003 HIS Q1076 ASN ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 172 HIS ** O 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 715 GLN O 801 GLN ** P 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 671 ASN I1327 ASN J 350 ASN J 539 ASN L 163 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 163 ASN N 211 HIS N 293 GLN N 337 ASN U 24 GLN ** U 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 833 HIS ** V1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 995 HIS X1514 ASN ** T 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 449 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 101246 Z= 0.208 Angle : 0.635 15.594 137076 Z= 0.320 Chirality : 0.045 0.285 15058 Planarity : 0.004 0.121 17372 Dihedral : 4.664 42.144 13198 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.08), residues: 11958 helix: 0.59 (0.09), residues: 3362 sheet: -0.39 (0.09), residues: 3004 loop : -1.06 (0.08), residues: 5592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2202 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1814 time to evaluate : 8.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 388 outliers final: 220 residues processed: 2058 average time/residue: 1.6199 time to fit residues: 4794.8555 Evaluate side-chains 1947 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1727 time to evaluate : 8.641 Switching outliers to nearest non-outliers outliers start: 220 outliers final: 149 residues processed: 77 average time/residue: 0.9384 time to fit residues: 137.0715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1134 optimal weight: 0.0870 chunk 132 optimal weight: 0.5980 chunk 670 optimal weight: 0.7980 chunk 859 optimal weight: 6.9990 chunk 665 optimal weight: 0.6980 chunk 990 optimal weight: 7.9990 chunk 656 optimal weight: 3.9990 chunk 1172 optimal weight: 10.0000 chunk 733 optimal weight: 0.8980 chunk 714 optimal weight: 2.9990 chunk 541 optimal weight: 7.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1141 ASN E 13 HIS ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 HIS ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 886 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 GLN B 417 ASN B 539 ASN D 163 ASN F 120 HIS F 166 GLN F 293 GLN Q 33 ASN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1076 ASN M 2 GLN ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 661 HIS ** P 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 357 GLN I 671 ASN I 706 GLN I1327 ASN J 350 ASN J 539 ASN ** J 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 293 GLN ** U 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 217 ASN W 284 GLN ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 350 ASN ** T 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 101246 Z= 0.196 Angle : 0.632 15.776 137076 Z= 0.317 Chirality : 0.045 0.254 15058 Planarity : 0.004 0.125 17372 Dihedral : 4.512 43.074 13198 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.08), residues: 11958 helix: 0.68 (0.09), residues: 3366 sheet: -0.27 (0.09), residues: 3032 loop : -0.99 (0.08), residues: 5560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2134 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 1782 time to evaluate : 11.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 352 outliers final: 222 residues processed: 1992 average time/residue: 1.5705 time to fit residues: 4455.0459 Evaluate side-chains 1939 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1717 time to evaluate : 8.592 Switching outliers to nearest non-outliers outliers start: 222 outliers final: 152 residues processed: 77 average time/residue: 0.9704 time to fit residues: 137.5672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 725 optimal weight: 1.9990 chunk 468 optimal weight: 1.9990 chunk 699 optimal weight: 0.8980 chunk 353 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 745 optimal weight: 1.9990 chunk 798 optimal weight: 0.2980 chunk 579 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 921 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN ** G 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 632 GLN ** G 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 GLN A1327 ASN B 172 HIS B 417 ASN B 539 ASN D 163 ASN D 303 HIS F 120 HIS F 293 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 HIS Q 865 GLN Q1076 ASN O 886 GLN ** P 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 671 ASN I1327 ASN J 350 ASN J 539 ASN ** J 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS N 293 GLN N 337 ASN U 833 HIS U1067 GLN ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 222 ASN ** T 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 101246 Z= 0.230 Angle : 0.656 17.289 137076 Z= 0.330 Chirality : 0.045 0.316 15058 Planarity : 0.004 0.134 17372 Dihedral : 4.518 39.574 13198 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.08), residues: 11958 helix: 0.70 (0.09), residues: 3350 sheet: -0.25 (0.09), residues: 3038 loop : -0.99 (0.08), residues: 5570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23916 Ramachandran restraints generated. 11958 Oldfield, 0 Emsley, 11958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2087 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1746 time to evaluate : 8.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 341 outliers final: 225 residues processed: 1957 average time/residue: 1.5614 time to fit residues: 4379.2291 Evaluate side-chains 1924 residues out of total 11084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1699 time to evaluate : 8.668 Switching outliers to nearest non-outliers outliers start: 225 outliers final: 162 residues processed: 67 average time/residue: 0.9126 time to fit residues: 117.9894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.4023 > 50: distance: 100 - 117: 11.651 distance: 108 - 128: 30.513 distance: 111 - 117: 10.073 distance: 112 - 133: 16.195 distance: 117 - 118: 15.807 distance: 118 - 119: 13.537 distance: 119 - 120: 29.387 distance: 119 - 121: 19.469 distance: 121 - 122: 22.388 distance: 122 - 123: 28.491 distance: 122 - 125: 9.048 distance: 123 - 124: 35.145 distance: 123 - 128: 23.137 distance: 125 - 126: 40.728 distance: 125 - 127: 26.946 distance: 128 - 129: 23.481 distance: 129 - 130: 28.780 distance: 129 - 132: 14.801 distance: 130 - 131: 12.617 distance: 130 - 133: 12.553 distance: 133 - 134: 27.166 distance: 134 - 135: 17.116 distance: 134 - 137: 8.522 distance: 135 - 136: 3.026 distance: 135 - 141: 27.293 distance: 137 - 138: 37.781 distance: 138 - 139: 40.585 distance: 138 - 140: 40.011 distance: 141 - 142: 18.121 distance: 142 - 143: 24.289 distance: 142 - 145: 32.786 distance: 143 - 144: 25.393 distance: 143 - 152: 30.102 distance: 145 - 146: 35.516 distance: 146 - 147: 6.290 distance: 147 - 148: 16.317 distance: 148 - 149: 9.438 distance: 149 - 150: 9.598 distance: 149 - 151: 16.679 distance: 152 - 153: 11.236 distance: 153 - 154: 10.463 distance: 153 - 156: 5.147 distance: 154 - 155: 12.446 distance: 154 - 163: 16.053 distance: 156 - 157: 17.370 distance: 157 - 158: 12.947 distance: 157 - 159: 13.972 distance: 158 - 160: 23.945 distance: 159 - 161: 21.374 distance: 160 - 162: 28.107 distance: 161 - 162: 35.547 distance: 163 - 164: 17.804 distance: 164 - 165: 3.537 distance: 164 - 167: 16.874 distance: 165 - 166: 20.008 distance: 165 - 171: 14.033 distance: 167 - 168: 5.100 distance: 168 - 169: 24.347 distance: 168 - 170: 33.836 distance: 171 - 172: 22.216 distance: 172 - 173: 19.762 distance: 172 - 175: 16.954 distance: 173 - 174: 12.416 distance: 173 - 179: 28.332 distance: 174 - 202: 28.062 distance: 175 - 176: 23.123 distance: 176 - 177: 22.799 distance: 176 - 178: 12.028 distance: 179 - 180: 22.033 distance: 180 - 181: 17.240 distance: 180 - 183: 11.137 distance: 181 - 182: 25.060 distance: 181 - 187: 43.009 distance: 183 - 184: 18.024 distance: 184 - 185: 14.829 distance: 187 - 188: 23.635 distance: 188 - 189: 11.808 distance: 188 - 191: 5.559 distance: 189 - 190: 14.735 distance: 189 - 194: 26.151 distance: 191 - 192: 18.700 distance: 191 - 193: 24.256