Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 01:51:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o72_12743/10_2023/7o72_12743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o72_12743/10_2023/7o72_12743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o72_12743/10_2023/7o72_12743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o72_12743/10_2023/7o72_12743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o72_12743/10_2023/7o72_12743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o72_12743/10_2023/7o72_12743_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 132 5.49 5 Mg 2 5.21 5 S 401 5.16 5 Be 1 3.05 5 C 46229 2.51 5 N 12729 2.21 5 O 14146 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 230": "OD1" <-> "OD2" Residue "W TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 73664 Number of models: 1 Model: "" Number of chains: 43 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2274 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2794 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 334} Chain breaks: 1 Chain: "7" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4954 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 2 Chain: "A" Number of atoms: 11230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11230 Classifications: {'peptide': 1427} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1360} Chain breaks: 3 Chain: "B" Number of atoms: 9404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9404 Classifications: {'peptide': 1180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "C" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1321 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2367 Classifications: {'peptide': 309} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 2 Chain: "N" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1332 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 172} Chain: "Q" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1878 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "R" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2173 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 2 Chain: "T" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1333 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 885 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 2 Chain: "V" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'TRANS': 103} Chain breaks: 1 Chain: "W" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2470 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 4 Chain: "X" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1653 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" 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: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 76.584 89.634 187.987 1.00126.42 S ATOM 1265 SG CYS 0 156 71.462 89.137 192.133 1.00142.84 S ATOM 1080 SG CYS 0 133 73.649 94.950 189.973 1.00132.67 S ATOM 1566 SG CYS 0 191 76.684 92.022 194.160 1.00128.61 S ATOM 13941 SG CYS 3 13 61.745 119.778 141.882 1.00163.05 S ATOM 13962 SG CYS 3 16 62.833 119.451 138.278 1.00164.11 S ATOM 14157 SG CYS 3 39 64.167 122.324 140.408 1.00156.98 S ATOM 14178 SG CYS 3 42 60.616 122.407 139.285 1.00154.76 S ATOM 14110 SG CYS 3 34 54.327 124.768 150.998 1.00151.96 S ATOM 14268 SG CYS 3 54 53.546 124.001 147.290 1.00157.81 S ATOM 14306 SG CYS 3 59 50.828 123.360 149.973 1.00157.50 S ATOM 16970 SG CYS 4 289 125.830 50.216 208.850 1.00154.81 S ATOM 16989 SG CYS 4 292 129.382 50.851 209.995 1.00150.33 S ATOM 17081 SG CYS 4 305 126.925 49.130 212.325 1.00168.09 S ATOM 17099 SG CYS 4 308 126.450 52.811 211.526 1.00162.43 S ATOM 19766 SG CYS 6 349 129.877 32.840 195.366 1.00163.37 S ATOM 19787 SG CYS 6 352 128.029 30.373 193.119 1.00165.67 S ATOM 19866 SG CYS 6 363 128.651 33.886 191.913 1.00161.51 S ATOM 19885 SG CYS 6 366 126.156 33.327 194.679 1.00168.42 S ATOM 20187 SG CYS 6 403 156.838 68.458 205.705 1.00169.70 S ATOM 20210 SG CYS 6 406 158.312 67.460 202.332 1.00166.17 S ATOM 20404 SG CYS 6 437 155.773 70.337 202.546 1.00172.12 S ATOM 20425 SG CYS 6 440 154.759 66.719 203.065 1.00166.80 S ATOM 20337 SG CYS 6 429 146.748 66.433 212.670 1.00170.77 S ATOM 20360 SG CYS 6 432 150.050 65.296 214.322 1.00167.90 S ATOM 20518 SG CYS 6 451 149.031 63.933 210.964 1.00162.22 S ATOM 20535 SG CYS 6 454 147.074 62.906 214.041 1.00167.71 S ATOM 19665 SG CYS 6 336 133.559 33.679 181.042 1.00177.77 S ATOM 19677 SG CYS 6 338 132.640 36.549 183.427 1.00170.08 S ATOM 19825 SG CYS 6 357 136.309 35.681 182.789 1.00168.77 S ATOM 26347 SG CYS A 107 100.735 115.326 114.492 1.00 98.44 S ATOM 26371 SG CYS A 110 99.405 116.867 117.685 1.00103.07 S ATOM 26676 SG CYS A 148 103.121 116.003 117.366 1.00119.33 S ATOM 26814 SG CYS A 167 100.536 113.238 117.671 1.00128.89 S ATOM 26042 SG CYS A 67 61.445 140.124 100.322 1.00 82.95 S ATOM 26064 SG CYS A 70 62.049 143.782 101.314 1.00 75.77 S ATOM 26117 SG CYS A 77 64.153 142.178 98.540 1.00 63.40 S ATOM 45667 SG CYS B1163 74.588 144.956 112.253 1.00 60.07 S ATOM 45685 SG CYS B1166 75.796 142.081 110.003 1.00 62.85 S ATOM 45810 SG CYS B1182 72.095 142.464 110.880 1.00 65.47 S ATOM 45829 SG CYS B1185 74.670 141.342 113.482 1.00 74.99 S ATOM 46814 SG CYS C 86 45.145 180.199 46.389 1.00 65.13 S ATOM 46831 SG CYS C 88 44.823 176.728 47.955 1.00 74.72 S ATOM 46864 SG CYS C 92 43.188 177.544 44.585 1.00 62.58 S ATOM 46887 SG CYS C 95 46.995 177.258 44.899 1.00 54.68 S ATOM 54535 SG CYS I 7 132.774 91.275 59.025 1.00116.65 S ATOM 54560 SG CYS I 10 129.362 90.484 60.504 1.00118.39 S ATOM 54726 SG CYS I 29 131.964 92.091 62.717 1.00133.41 S ATOM 54750 SG CYS I 32 132.524 88.507 61.425 1.00133.13 S ATOM 55077 SG CYS I 75 135.810 124.439 30.464 1.00111.94 S ATOM 55099 SG CYS I 78 135.354 123.475 26.770 1.00120.55 S ATOM 55315 SG CYS I 103 132.337 123.833 28.972 1.00 98.68 S ATOM 55335 SG CYS I 106 134.703 120.933 29.546 1.00103.21 S ATOM 55480 SG CYS J 7 74.736 166.924 33.300 1.00 33.92 S ATOM 55503 SG CYS J 10 74.397 170.584 32.282 1.00 32.47 S ATOM 55783 SG CYS J 45 77.831 168.886 32.150 1.00 32.61 S ATOM 55789 SG CYS J 46 75.105 168.096 29.654 1.00 34.18 S ATOM 56969 SG CYS L 31 50.023 131.076 42.774 1.00 77.76 S ATOM 56989 SG CYS L 34 47.896 130.782 39.634 1.00 84.86 S ATOM 57093 SG CYS L 48 46.718 129.185 42.844 1.00 85.83 S ATOM 57116 SG CYS L 51 49.743 127.724 41.063 1.00 93.89 S ATOM 57360 SG CYS M 24 47.783 160.070 89.644 1.00 86.19 S ATOM 57382 SG CYS M 27 45.148 161.711 87.516 1.00 92.31 S ATOM 57526 SG CYS M 45 47.528 159.222 85.865 1.00 77.36 S ATOM 57545 SG CYS M 48 48.908 162.533 87.210 1.00 77.82 S ATOM 70431 SG CYS W 124 47.462 137.186 109.325 1.00146.66 S ATOM 70452 SG CYS W 127 50.830 136.580 107.819 1.00142.11 S ATOM 70637 SG CYS W 149 49.791 140.113 108.948 1.00134.61 S ATOM 70657 SG CYS W 152 48.228 138.524 105.831 1.00134.18 S Time building chain proxies: 29.79, per 1000 atoms: 0.40 Number of scatterers: 73664 At special positions: 0 Unit cell: (215.25, 231, 241.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 401 16.00 P 132 15.00 Mg 2 11.99 F 3 9.00 O 14146 8.00 N 12729 7.00 C 46229 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.88 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " Number of angles added : 93 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16854 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 348 helices and 71 sheets defined 39.7% alpha, 12.3% beta 64 base pairs and 111 stacking pairs defined. Time for finding SS restraints: 24.26 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 49 through 62 Processing helix chain '0' and resid 76 through 96 Processing helix chain '0' and resid 111 through 113 No H-bonds generated for 'chain '0' and resid 111 through 113' Processing helix chain '0' and resid 126 through 137 Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 164 removed outlier: 3.635A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 167 through 169 No H-bonds generated for 'chain '0' and resid 167 through 169' Processing helix chain '0' and resid 178 through 188 removed outlier: 3.543A pdb=" N LYS 0 183 " --> pdb=" O GLU 0 179 " (cutoff:3.500A) Processing helix chain '0' and resid 192 through 197 Processing helix chain '0' and resid 200 through 202 No H-bonds generated for 'chain '0' and resid 200 through 202' Processing helix chain '0' and resid 210 through 214 removed outlier: 4.146A pdb=" N LEU 0 214 " --> pdb=" O HIS 0 211 " (cutoff:3.500A) Processing helix chain '0' and resid 216 through 223 removed outlier: 3.856A pdb=" N GLU 0 220 " --> pdb=" O PRO 0 216 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG 0 221 " --> pdb=" O LYS 0 217 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) Processing helix chain '0' and resid 240 through 248 removed outlier: 4.075A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 removed outlier: 3.768A pdb=" N ARG 0 262 " --> pdb=" O ARG 0 258 " (cutoff:3.500A) Processing helix chain '0' and resid 280 through 291 Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 313 through 315 No H-bonds generated for 'chain '0' and resid 313 through 315' Processing helix chain '0' and resid 328 through 344 Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 388 removed outlier: 3.619A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS 0 377 " --> pdb=" O PRO 0 373 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 395 through 409 removed outlier: 4.098A pdb=" N ALA 0 398 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE 0 409 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) Processing helix chain '0' and resid 444 through 452 Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 466 through 472 Proline residue: 0 470 - end of helix No H-bonds generated for 'chain '0' and resid 466 through 472' Processing helix chain '0' and resid 510 through 512 No H-bonds generated for 'chain '0' and resid 510 through 512' Processing helix chain '0' and resid 516 through 532 removed outlier: 3.755A pdb=" N ILE 0 532 " --> pdb=" O GLU 0 528 " (cutoff:3.500A) Processing helix chain '0' and resid 544 through 557 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.626A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 591 Processing helix chain '0' and resid 606 through 608 No H-bonds generated for 'chain '0' and resid 606 through 608' Processing helix chain '0' and resid 614 through 616 No H-bonds generated for 'chain '0' and resid 614 through 616' Processing helix chain '0' and resid 633 through 645 Processing helix chain '0' and resid 650 through 668 removed outlier: 3.547A pdb=" N HIS 0 661 " --> pdb=" O ASP 0 657 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 688 removed outlier: 3.579A pdb=" N SER 0 687 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 684 through 688' Processing helix chain '0' and resid 690 through 692 No H-bonds generated for 'chain '0' and resid 690 through 692' Processing helix chain '0' and resid 695 through 698 No H-bonds generated for 'chain '0' and resid 695 through 698' Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 725 Processing helix chain '0' and resid 730 through 733 Processing helix chain '0' and resid 741 through 751 Processing helix chain '1' and resid 42 through 44 No H-bonds generated for 'chain '1' and resid 42 through 44' Processing helix chain '1' and resid 94 through 120 Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 removed outlier: 3.555A pdb=" N LEU 1 185 " --> pdb=" O GLN 1 181 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS 1 186 " --> pdb=" O GLN 1 182 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY 1 187 " --> pdb=" O SER 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 189 through 199 removed outlier: 3.542A pdb=" N GLU 1 197 " --> pdb=" O LYS 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 225 removed outlier: 4.189A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) Proline residue: 1 215 - end of helix removed outlier: 3.739A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 236 No H-bonds generated for 'chain '1' and resid 233 through 236' Processing helix chain '1' and resid 253 through 262 Processing helix chain '1' and resid 264 through 273 removed outlier: 3.628A pdb=" N ASP 1 272 " --> pdb=" O LYS 1 268 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 289 removed outlier: 3.591A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 291 through 296 Processing helix chain '1' and resid 309 through 329 removed outlier: 3.711A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 335 through 337 No H-bonds generated for 'chain '1' and resid 335 through 337' Processing helix chain '1' and resid 339 through 343 removed outlier: 3.662A pdb=" N ILE 1 343 " --> pdb=" O LEU 1 339 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 339 through 343' Processing helix chain '1' and resid 356 through 358 No H-bonds generated for 'chain '1' and resid 356 through 358' Processing helix chain '1' and resid 371 through 389 removed outlier: 3.529A pdb=" N LEU 1 375 " --> pdb=" O THR 1 371 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 419 Processing helix chain '1' and resid 422 through 424 No H-bonds generated for 'chain '1' and resid 422 through 424' Processing helix chain '1' and resid 466 through 482 Processing helix chain '1' and resid 487 through 489 No H-bonds generated for 'chain '1' and resid 487 through 489' Processing helix chain '1' and resid 494 through 516 removed outlier: 3.820A pdb=" N LYS 1 498 " --> pdb=" O GLU 1 494 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS 1 516 " --> pdb=" O LYS 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 544 through 568 Processing helix chain '1' and resid 573 through 604 removed outlier: 4.704A pdb=" N SER 1 577 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN 1 602 " --> pdb=" O ASP 1 599 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP 1 604 " --> pdb=" O LEU 1 601 " (cutoff:3.500A) Processing helix chain '1' and resid 609 through 615 Processing helix chain '1' and resid 617 through 638 Processing helix chain '2' and resid 6 through 16 Processing helix chain '2' and resid 19 through 26 removed outlier: 3.732A pdb=" N ARG 2 24 " --> pdb=" O GLN 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 37 removed outlier: 3.535A pdb=" N ALA 2 34 " --> pdb=" O ALA 2 30 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 52 removed outlier: 4.363A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 65 removed outlier: 3.513A pdb=" N TRP 2 65 " --> pdb=" O ASP 2 61 " (cutoff:3.500A) Processing helix chain '2' and resid 68 through 83 removed outlier: 4.475A pdb=" N LEU 2 72 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA 2 77 " --> pdb=" O PHE 2 74 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE 2 78 " --> pdb=" O GLN 2 75 " (cutoff:3.500A) Processing helix chain '2' and resid 102 through 112 Processing helix chain '2' and resid 135 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 193 Processing helix chain '2' and resid 196 through 210 removed outlier: 4.088A pdb=" N LEU 2 203 " --> pdb=" O GLN 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 removed outlier: 3.530A pdb=" N GLY 2 229 " --> pdb=" O ILE 2 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA 2 230 " --> pdb=" O PHE 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 244 through 256 removed outlier: 3.799A pdb=" N ILE 2 248 " --> pdb=" O GLU 2 244 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 2 256 " --> pdb=" O ASP 2 252 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 278 Processing helix chain '2' and resid 354 through 362 removed outlier: 3.874A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 389 Processing helix chain '2' and resid 393 through 402 Processing helix chain '2' and resid 406 through 422 Processing helix chain '2' and resid 435 through 448 Processing helix chain '2' and resid 465 through 478 Processing helix chain '2' and resid 498 through 506 Processing helix chain '3' and resid 40 through 47 removed outlier: 3.547A pdb=" N ARG 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 65 through 67 No H-bonds generated for 'chain '3' and resid 65 through 67' Processing helix chain '3' and resid 76 through 89 Processing helix chain '3' and resid 96 through 99 Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 126 through 138 removed outlier: 3.742A pdb=" N GLU 3 138 " --> pdb=" O ARG 3 134 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 43 Processing helix chain '4' and resid 49 through 67 Processing helix chain '4' and resid 116 through 138 removed outlier: 4.230A pdb=" N THR 4 124 " --> pdb=" O ASN 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 191 through 206 Proline residue: 4 195 - end of helix removed outlier: 3.668A pdb=" N PHE 4 201 " --> pdb=" O MET 4 197 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 231 removed outlier: 3.648A pdb=" N GLN 4 226 " --> pdb=" O THR 4 222 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 250 Processing helix chain '4' and resid 256 through 258 No H-bonds generated for 'chain '4' and resid 256 through 258' Processing helix chain '4' and resid 301 through 303 No H-bonds generated for 'chain '4' and resid 301 through 303' Processing helix chain '4' and resid 314 through 321 removed outlier: 3.820A pdb=" N LEU 4 320 " --> pdb=" O VAL 4 316 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 28 through 30 No H-bonds generated for 'chain '5' and resid 28 through 30' Processing helix chain '5' and resid 44 through 61 removed outlier: 4.454A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS 5 52 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG 5 56 " --> pdb=" O HIS 5 52 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 113 removed outlier: 4.009A pdb=" N ALA 6 111 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 199 Processing helix chain '6' and resid 210 through 220 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 281 removed outlier: 3.667A pdb=" N ASN 6 281 " --> pdb=" O CYS 6 277 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 305 removed outlier: 3.526A pdb=" N GLU 6 299 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL 6 305 " --> pdb=" O PHE 6 301 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 382 removed outlier: 4.126A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 446 removed outlier: 3.523A pdb=" N VAL 6 442 " --> pdb=" O VAL 6 438 " (cutoff:3.500A) Processing helix chain '6' and resid 452 through 456 Processing helix chain '7' and resid 110 through 112 No H-bonds generated for 'chain '7' and resid 110 through 112' Processing helix chain '7' and resid 150 through 160 removed outlier: 3.811A pdb=" N ASP 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL 7 158 " --> pdb=" O GLN 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 185 removed outlier: 3.818A pdb=" N SER 7 185 " --> pdb=" O TYR 7 181 " (cutoff:3.500A) Processing helix chain '7' and resid 190 through 200 Processing helix chain '7' and resid 207 through 216 removed outlier: 3.637A pdb=" N ALA 7 216 " --> pdb=" O PHE 7 212 " (cutoff:3.500A) Processing helix chain '7' and resid 239 through 245 removed outlier: 3.676A pdb=" N LEU 7 245 " --> pdb=" O LEU 7 242 " (cutoff:3.500A) Processing helix chain '7' and resid 321 through 332 removed outlier: 3.805A pdb=" N GLU 7 324 " --> pdb=" O GLU 7 321 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS 7 327 " --> pdb=" O GLU 7 324 " (cutoff:3.500A) Processing helix chain '7' and resid 364 through 374 Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 414 through 427 removed outlier: 3.516A pdb=" N GLN 7 422 " --> pdb=" O MET 7 418 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 434 No H-bonds generated for 'chain '7' and resid 432 through 434' Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 468 through 479 removed outlier: 3.522A pdb=" N LYS 7 472 " --> pdb=" O HIS 7 468 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL 7 473 " --> pdb=" O ASP 7 469 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 498 through 504 Processing helix chain '7' and resid 522 through 530 removed outlier: 3.536A pdb=" N GLY 7 525 " --> pdb=" O ASP 7 522 " (cutoff:3.500A) Processing helix chain '7' and resid 541 through 545 Processing helix chain '7' and resid 563 through 571 removed outlier: 3.984A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 582 removed outlier: 3.515A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 645 Processing helix chain '7' and resid 656 through 659 Processing helix chain '7' and resid 680 through 691 removed outlier: 3.941A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE 7 690 " --> pdb=" O ARG 7 686 " (cutoff:3.500A) Processing helix chain '7' and resid 714 through 722 Processing helix chain '7' and resid 724 through 729 removed outlier: 3.617A pdb=" N ASP 7 728 " --> pdb=" O ALA 7 724 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 766 removed outlier: 3.701A pdb=" N LYS 7 766 " --> pdb=" O GLU 7 762 " (cutoff:3.500A) Processing helix chain '7' and resid 832 through 835 removed outlier: 3.536A pdb=" N LYS 7 835 " --> pdb=" O LEU 7 832 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 832 through 835' Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 93 through 105 removed outlier: 3.837A pdb=" N ILE A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.315A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.671A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.734A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 removed outlier: 3.536A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 699 removed outlier: 3.563A pdb=" N GLN A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 810 through 844 Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.545A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.822A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1078 Proline residue: A1075 - end of helix removed outlier: 4.032A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1105 Processing helix chain 'A' and resid 1128 through 1138 removed outlier: 3.616A pdb=" N LEU A1133 " --> pdb=" O GLU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1146 Processing helix chain 'A' and resid 1165 through 1176 removed outlier: 3.630A pdb=" N GLU A1168 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A1170 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A1173 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A1174 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1256 through 1269 removed outlier: 3.583A pdb=" N ASN A1265 " --> pdb=" O LYS A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.892A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1339 Processing helix chain 'A' and resid 1341 through 1359 removed outlier: 4.265A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1401 removed outlier: 3.823A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.895A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 320 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.734A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 371 through 389 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 438 Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 488 through 496 removed outlier: 3.560A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 776 removed outlier: 3.774A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 810 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.803A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 267 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 157 through 170 removed outlier: 4.600A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 204 through 216 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'E' and resid 118 through 123 removed outlier: 4.628A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'H' and resid 89 through 92 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.711A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.595A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.771A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.595A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 119 through 139 removed outlier: 4.425A pdb=" N ASP M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 168 through 182 Processing helix chain 'M' and resid 189 through 195 removed outlier: 4.019A pdb=" N LEU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 220 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 235 through 246 removed outlier: 3.585A pdb=" N ILE M 239 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Proline residue: M 240 - end of helix removed outlier: 3.820A pdb=" N CYS M 243 " --> pdb=" O PRO M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 265 removed outlier: 3.814A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 270 No H-bonds generated for 'chain 'M' and resid 267 through 270' Processing helix chain 'M' and resid 274 through 288 Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 306 through 317 removed outlier: 3.752A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 322 No H-bonds generated for 'chain 'M' and resid 320 through 322' Processing helix chain 'M' and resid 326 through 331 Processing helix chain 'M' and resid 336 through 338 No H-bonds generated for 'chain 'M' and resid 336 through 338' Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 237 removed outlier: 3.528A pdb=" N TYR O 224 " --> pdb=" O ARG O 220 " (cutoff:3.500A) Proline residue: O 232 - end of helix removed outlier: 4.141A pdb=" N PHE O 237 " --> pdb=" O VAL O 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 34 Processing helix chain 'Q' and resid 153 through 167 Processing helix chain 'Q' and resid 337 through 345 Processing helix chain 'Q' and resid 406 through 413 Processing helix chain 'Q' and resid 424 through 431 Processing helix chain 'Q' and resid 437 through 449 removed outlier: 3.531A pdb=" N LYS Q 444 " --> pdb=" O ARG Q 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 52 No H-bonds generated for 'chain 'R' and resid 49 through 52' Processing helix chain 'R' and resid 75 through 81 removed outlier: 4.132A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing helix chain 'R' and resid 236 through 245 removed outlier: 3.916A pdb=" N VAL R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 265 removed outlier: 3.759A pdb=" N SER R 264 " --> pdb=" O GLY R 260 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 285 removed outlier: 3.517A pdb=" N LYS R 284 " --> pdb=" O VAL R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 309 removed outlier: 4.166A pdb=" N ASP R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE R 304 " --> pdb=" O LEU R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 Processing helix chain 'R' and resid 353 through 356 No H-bonds generated for 'chain 'R' and resid 353 through 356' Processing helix chain 'U' and resid 4 through 28 removed outlier: 3.547A pdb=" N ARG U 22 " --> pdb=" O VAL U 18 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 49 removed outlier: 3.619A pdb=" N ILE U 41 " --> pdb=" O LEU U 38 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP U 42 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR U 47 " --> pdb=" O LYS U 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 12 Processing helix chain 'V' and resid 14 through 29 Processing helix chain 'V' and resid 34 through 54 removed outlier: 3.683A pdb=" N LYS V 46 " --> pdb=" O GLU V 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 20 Processing helix chain 'W' and resid 23 through 34 removed outlier: 3.536A pdb=" N ILE W 32 " --> pdb=" O VAL W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 91 through 116 Processing helix chain 'W' and resid 133 through 138 removed outlier: 3.775A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 178 removed outlier: 3.586A pdb=" N LYS W 166 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS W 168 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET W 176 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 191 Processing helix chain 'W' and resid 199 through 205 removed outlier: 3.590A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 269 through 288 Processing helix chain 'W' and resid 292 through 295 No H-bonds generated for 'chain 'W' and resid 292 through 295' Processing helix chain 'W' and resid 350 through 368 Processing helix chain 'X' and resid 107 through 115 Processing helix chain 'X' and resid 124 through 136 Processing helix chain 'X' and resid 144 through 150 Processing helix chain 'X' and resid 158 through 165 Processing helix chain 'X' and resid 189 through 197 Processing helix chain 'X' and resid 208 through 211 No H-bonds generated for 'chain 'X' and resid 208 through 211' Processing helix chain 'X' and resid 218 through 226 Processing helix chain 'X' and resid 257 through 265 removed outlier: 3.810A pdb=" N MET X 262 " --> pdb=" O GLU X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 271 through 281 Proline residue: X 275 - end of helix Processing sheet with id= A, first strand: chain '0' and resid 2 through 4 Processing sheet with id= B, first strand: chain '0' and resid 174 through 176 removed outlier: 4.424A pdb=" N GLY 0 107 " --> pdb=" O PHE 0 176 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE 0 205 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE 0 231 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS 0 72 " --> pdb=" O ILE 0 231 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE 0 233 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER 0 460 " --> pdb=" O LEU 0 40 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 478 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN 0 480 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU 0 41 " --> pdb=" O GLN 0 480 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER 0 482 " --> pdb=" O GLU 0 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 250 through 253 Processing sheet with id= D, first strand: chain '0' and resid 492 through 497 removed outlier: 7.294A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE 0 497 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU 0 681 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY 0 536 " --> pdb=" O THR 0 619 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LEU 0 621 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL 0 538 " --> pdb=" O LEU 0 621 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE 0 623 " --> pdb=" O VAL 0 538 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE 0 540 " --> pdb=" O ILE 0 623 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 4 through 9 Processing sheet with id= F, first strand: chain '1' and resid 86 through 90 removed outlier: 3.648A pdb=" N HIS 1 87 " --> pdb=" O LEU 1 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS 1 47 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '2' and resid 87 through 92 Processing sheet with id= H, first strand: chain '2' and resid 259 through 261 Processing sheet with id= I, first strand: chain '2' and resid 339 through 341 removed outlier: 5.833A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '2' and resid 456 through 459 removed outlier: 6.239A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '4' and resid 82 through 87 removed outlier: 6.365A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU 4 179 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '5' and resid 8 through 11 removed outlier: 3.771A pdb=" N GLU 5 33 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '6' and resid 178 through 183 removed outlier: 6.470A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '7' and resid 132 through 134 removed outlier: 6.663A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '7' and resid 226 through 228 removed outlier: 3.919A pdb=" N PHE 7 316 " --> pdb=" O VAL 7 234 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '7' and resid 435 through 437 removed outlier: 5.622A pdb=" N LEU 7 452 " --> pdb=" O ALA 7 436 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR 7 514 " --> pdb=" O GLY 7 382 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE 7 384 " --> pdb=" O THR 7 514 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL 7 385 " --> pdb=" O PRO 7 533 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU 7 535 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '7' and resid 551 through 554 removed outlier: 3.801A pdb=" N PHE 7 705 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 734 through 736 Processing sheet with id= S, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= T, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= U, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= V, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.715A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.303A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.533A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.715A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= AA, first strand: chain 'A' and resid 1115 through 1119 removed outlier: 4.057A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.120A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 69 through 73 Processing sheet with id= AD, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= AE, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= AF, first strand: chain 'B' and resid 125 through 127 Processing sheet with id= AG, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= AH, first strand: chain 'B' and resid 404 through 407 Processing sheet with id= AI, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.914A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= AK, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.297A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.695A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 4.173A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N MET B 839 " --> pdb=" O LYS B 987 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR B 989 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N MET B 841 " --> pdb=" O THR B 989 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLY B 991 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= AO, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= AP, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= AQ, first strand: chain 'C' and resid 176 through 179 removed outlier: 6.469A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 97 through 104 removed outlier: 6.167A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 111 through 113 Processing sheet with id= AT, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AU, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.727A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AW, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AX, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.179A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'G' and resid 142 through 146 removed outlier: 6.891A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE G 157 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N PHE G 109 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA G 159 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR G 111 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY G 161 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= BA, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.534A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 14 through 19 removed outlier: 3.790A pdb=" N ASP I 19 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 83 through 87 Processing sheet with id= BD, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.734A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'L' and resid 37 through 39 Processing sheet with id= BF, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.441A pdb=" N CYS M 45 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL M 51 " --> pdb=" O CYS M 45 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'O' and resid 120 through 124 removed outlier: 6.617A pdb=" N VAL O 161 " --> pdb=" O GLN O 68 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE O 70 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN O 159 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA O 217 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLY O 162 " --> pdb=" O THR O 215 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR O 215 " --> pdb=" O GLY O 162 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N CYS O 164 " --> pdb=" O VAL O 213 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL O 213 " --> pdb=" O CYS O 164 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE O 202 " --> pdb=" O MET O 197 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 102 through 106 Processing sheet with id= BI, first strand: chain 'Q' and resid 103 through 105 removed outlier: 6.149A pdb=" N PHE Q 384 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Q' and resid 117 through 121 removed outlier: 6.669A pdb=" N LYS Q 391 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LYS Q 120 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR Q 393 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'R' and resid 93 through 97 removed outlier: 4.096A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET R 225 " --> pdb=" O ASP R 121 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU R 70 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU R 221 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG R 72 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN R 223 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'R' and resid 135 through 138 removed outlier: 3.709A pdb=" N ALA R 213 " --> pdb=" O THR R 136 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'U' and resid 243 through 245 Processing sheet with id= BN, first strand: chain 'U' and resid 278 through 284 removed outlier: 3.699A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'V' and resid 60 through 63 removed outlier: 3.748A pdb=" N VAL V 87 " --> pdb=" O SER V 104 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER V 104 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'V' and resid 110 through 115 removed outlier: 3.579A pdb=" N ALA V 115 " --> pdb=" O TRP V 76 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'W' and resid 68 through 72 Processing sheet with id= BR, first strand: chain 'X' and resid 169 through 172 removed outlier: 3.613A pdb=" N THR X 177 " --> pdb=" O ASP X 172 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'X' and resid 230 through 234 removed outlier: 4.317A pdb=" N TYR X 243 " --> pdb=" O LEU X 233 " (cutoff:3.500A) 2603 hydrogen bonds defined for protein. 7245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 155 hydrogen bonds 310 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 111 stacking parallelities Total time for adding SS restraints: 35.36 Time building geometry restraints manager: 26.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 30909 1.43 - 1.64: 43688 1.64 - 1.85: 628 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 75237 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" BE BEF 7 901 " pdb=" F2 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" BE BEF 7 901 " pdb=" F3 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.547 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CA ILE A 973 " pdb=" C ILE A 973 " ideal model delta sigma weight residual 1.521 1.560 -0.039 1.21e-02 6.83e+03 1.02e+01 ... (remaining 75232 not shown) Histogram of bond angle deviations from ideal: 73.68 - 85.74: 12 85.74 - 97.81: 1 97.81 - 109.87: 10193 109.87 - 121.93: 76210 121.93 - 134.00: 15693 Bond angle restraints: 102109 Sorted by residual: angle pdb=" N ILE A 973 " pdb=" CA ILE A 973 " pdb=" CB ILE A 973 " ideal model delta sigma weight residual 110.13 117.16 -7.03 1.34e+00 5.57e-01 2.75e+01 angle pdb=" N GLN 0 615 " pdb=" CA GLN 0 615 " pdb=" C GLN 0 615 " ideal model delta sigma weight residual 111.28 116.83 -5.55 1.09e+00 8.42e-01 2.59e+01 angle pdb=" CA ILE A 973 " pdb=" CB ILE A 973 " pdb=" CG2 ILE A 973 " ideal model delta sigma weight residual 110.50 103.38 7.12 1.70e+00 3.46e-01 1.75e+01 angle pdb=" C1' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C3' ADP 7 903 " ideal model delta sigma weight residual 111.00 98.81 12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" N ILE M 269 " pdb=" CA ILE M 269 " pdb=" C ILE M 269 " ideal model delta sigma weight residual 113.53 109.56 3.97 9.80e-01 1.04e+00 1.64e+01 ... (remaining 102104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.50: 43362 25.50 - 51.00: 2004 51.00 - 76.51: 321 76.51 - 102.01: 47 102.01 - 127.51: 2 Dihedral angle restraints: 45736 sinusoidal: 19792 harmonic: 25944 Sorted by residual: dihedral pdb=" O2A ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 67.51 -127.51 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" C5' ADP 7 903 " pdb=" O5' ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" O2A ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 -173.48 113.48 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" N TYR A 465 " pdb=" C TYR A 465 " pdb=" CA TYR A 465 " pdb=" CB TYR A 465 " ideal model delta harmonic sigma weight residual 122.80 135.32 -12.52 0 2.50e+00 1.60e-01 2.51e+01 ... (remaining 45733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 11121 0.100 - 0.201: 424 0.201 - 0.301: 1 0.301 - 0.402: 0 0.402 - 0.502: 2 Chirality restraints: 11548 Sorted by residual: chirality pdb=" CB ILE A 973 " pdb=" CA ILE A 973 " pdb=" CG1 ILE A 973 " pdb=" CG2 ILE A 973 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" CA TYR A 465 " pdb=" N TYR A 465 " pdb=" C TYR A 465 " pdb=" CB TYR A 465 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C3' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C4' ADP 7 903 " pdb=" O3' ADP 7 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 11545 not shown) Planarity restraints: 12650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 464 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.70e+00 pdb=" C PRO A 464 " -0.051 2.00e-02 2.50e+03 pdb=" O PRO A 464 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 465 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS 7 676 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C HIS 7 676 " 0.039 2.00e-02 2.50e+03 pdb=" O HIS 7 676 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR 7 677 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 83 " 0.032 2.00e-02 2.50e+03 1.31e-02 4.72e+00 pdb=" N9 DA T 83 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA T 83 " -0.015 2.00e-02 2.50e+03 pdb=" N7 DA T 83 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 83 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA T 83 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA T 83 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DA T 83 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA T 83 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DA T 83 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA T 83 " -0.006 2.00e-02 2.50e+03 ... (remaining 12647 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 469 2.56 - 3.14: 59247 3.14 - 3.73: 111923 3.73 - 4.31: 158437 4.31 - 4.90: 262916 Nonbonded interactions: 592992 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1803 " model vdw 1.971 2.170 nonbonded pdb=" OE1 GLU A 500 " pdb=" OG SER B1145 " model vdw 1.994 2.440 nonbonded pdb=" OH TYR U 248 " pdb=" OD1 ASN V 117 " model vdw 1.998 2.440 nonbonded pdb=" F1 BEF 7 901 " pdb="MG MG 7 902 " model vdw 2.001 2.120 nonbonded pdb="MG MG 7 902 " pdb=" O1B ADP 7 903 " model vdw 2.002 2.170 ... (remaining 592987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.040 Extract box with map and model: 13.700 Check model and map are aligned: 0.850 Set scattering table: 0.520 Process input model: 193.930 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.002 0.109 75237 Z= 0.144 Angle : 0.466 12.194 102109 Z= 0.279 Chirality : 0.039 0.502 11548 Planarity : 0.002 0.049 12650 Dihedral : 14.351 127.509 28882 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.89 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.54 % 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: 1.40 (0.09), residues: 8733 helix: 2.05 (0.09), residues: 3469 sheet: 0.39 (0.15), residues: 1300 loop : 0.19 (0.10), residues: 3964 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1751 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1749 time to evaluate : 7.672 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 2 outliers final: 1 residues processed: 1751 average time/residue: 0.7540 time to fit residues: 2193.7110 Evaluate side-chains 946 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 945 time to evaluate : 6.731 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5514 time to fit residues: 9.9363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 749 optimal weight: 20.0000 chunk 672 optimal weight: 2.9990 chunk 373 optimal weight: 0.2980 chunk 229 optimal weight: 6.9990 chunk 453 optimal weight: 7.9990 chunk 359 optimal weight: 4.9990 chunk 695 optimal weight: 0.9980 chunk 269 optimal weight: 7.9990 chunk 422 optimal weight: 0.1980 chunk 517 optimal weight: 4.9990 chunk 805 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 651 ASN ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 445 GLN ** 3 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 90 ASN 4 198 ASN ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 641 GLN 7 830 HIS A 124 GLN A 171 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN A 975 HIS A1130 GLN B 887 HIS B 986 GLN D 41 GLN ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 126 ASN H 33 GLN H 139 ASN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN L 53 HIS M 114 GLN M 208 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN Q 134 HIS Q 331 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 239 GLN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 75237 Z= 0.260 Angle : 0.618 12.644 102109 Z= 0.319 Chirality : 0.043 0.261 11548 Planarity : 0.004 0.105 12650 Dihedral : 11.885 116.609 10907 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.55 % Allowed : 9.39 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.09), residues: 8733 helix: 1.39 (0.09), residues: 3527 sheet: 0.33 (0.15), residues: 1279 loop : 0.06 (0.10), residues: 3927 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1022 time to evaluate : 6.762 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 123 outliers final: 79 residues processed: 1103 average time/residue: 0.7568 time to fit residues: 1423.6629 Evaluate side-chains 952 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 873 time to evaluate : 6.757 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 79 outliers final: 1 residues processed: 79 average time/residue: 0.5760 time to fit residues: 94.2942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 447 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 chunk 670 optimal weight: 3.9990 chunk 548 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 806 optimal weight: 7.9990 chunk 871 optimal weight: 30.0000 chunk 718 optimal weight: 0.9980 chunk 800 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 647 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 GLN ** 2 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 31 ASN 3 53 GLN ** 4 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 633 GLN A 118 HIS A 171 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 ASN D 132 GLN D 200 ASN M 208 ASN ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN Q 113 ASN R 109 ASN ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 277 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 75237 Z= 0.309 Angle : 0.611 14.167 102109 Z= 0.314 Chirality : 0.043 0.183 11548 Planarity : 0.004 0.057 12650 Dihedral : 11.940 122.433 10907 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.25 % Allowed : 11.89 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % 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: 0.64 (0.09), residues: 8733 helix: 1.13 (0.09), residues: 3536 sheet: 0.22 (0.14), residues: 1285 loop : -0.03 (0.10), residues: 3912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 916 time to evaluate : 6.899 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 45 residues processed: 981 average time/residue: 0.7034 time to fit residues: 1178.2267 Evaluate side-chains 846 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 801 time to evaluate : 6.742 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.5725 time to fit residues: 56.4510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 797 optimal weight: 8.9990 chunk 606 optimal weight: 0.9990 chunk 418 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 385 optimal weight: 5.9990 chunk 541 optimal weight: 8.9990 chunk 809 optimal weight: 30.0000 chunk 857 optimal weight: 1.9990 chunk 423 optimal weight: 0.1980 chunk 767 optimal weight: 9.9990 chunk 231 optimal weight: 0.0970 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 92 ASN 1 352 ASN ** 2 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 GLN ** 4 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 303 ASN 4 311 GLN 7 169 HIS 7 633 GLN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A 706 HIS ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS D 132 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN I 87 GLN M 114 GLN M 208 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 212 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 75237 Z= 0.220 Angle : 0.575 12.328 102109 Z= 0.294 Chirality : 0.042 0.304 11548 Planarity : 0.004 0.060 12650 Dihedral : 11.932 125.550 10907 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.15 % Allowed : 13.25 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % 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: 0.63 (0.09), residues: 8733 helix: 1.12 (0.09), residues: 3555 sheet: 0.25 (0.14), residues: 1312 loop : -0.07 (0.10), residues: 3866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 884 time to evaluate : 6.964 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: 91 outliers final: 44 residues processed: 944 average time/residue: 0.7092 time to fit residues: 1146.3536 Evaluate side-chains 859 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 815 time to evaluate : 6.727 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5649 time to fit residues: 55.6085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 714 optimal weight: 0.7980 chunk 486 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 638 optimal weight: 0.9990 chunk 353 optimal weight: 2.9990 chunk 731 optimal weight: 9.9990 chunk 592 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 437 optimal weight: 30.0000 chunk 769 optimal weight: 10.0000 chunk 216 optimal weight: 50.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 610 ASN ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 206 GLN ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 39 HIS 5 61 ASN 6 184 GLN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 702 ASN A 171 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 79 GLN I 87 GLN K 89 ASN M 208 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 369 ASN ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 ASN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 75237 Z= 0.239 Angle : 0.577 11.862 102109 Z= 0.294 Chirality : 0.042 0.282 11548 Planarity : 0.004 0.071 12650 Dihedral : 11.919 126.132 10907 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.91 % Allowed : 14.49 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % 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: 0.63 (0.09), residues: 8733 helix: 1.14 (0.09), residues: 3545 sheet: 0.26 (0.14), residues: 1301 loop : -0.08 (0.10), residues: 3887 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 867 time to evaluate : 7.156 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 outliers start: 72 outliers final: 29 residues processed: 919 average time/residue: 0.7440 time to fit residues: 1173.6492 Evaluate side-chains 818 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 789 time to evaluate : 6.828 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5902 time to fit residues: 41.5954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 288 optimal weight: 9.9990 chunk 772 optimal weight: 0.0170 chunk 169 optimal weight: 3.9990 chunk 503 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 858 optimal weight: 9.9990 chunk 712 optimal weight: 3.9990 chunk 397 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 283 optimal weight: 10.0000 chunk 450 optimal weight: 4.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 194 GLN ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 61 ASN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 200 ASN G 126 ASN I 87 GLN K 89 ASN M 114 GLN M 208 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 75237 Z= 0.274 Angle : 0.596 15.458 102109 Z= 0.303 Chirality : 0.042 0.255 11548 Planarity : 0.004 0.048 12650 Dihedral : 11.935 126.557 10907 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.02 % Allowed : 15.80 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8733 helix: 1.11 (0.09), residues: 3556 sheet: 0.28 (0.14), residues: 1268 loop : -0.11 (0.10), residues: 3909 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 831 time to evaluate : 6.803 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 outliers start: 81 outliers final: 34 residues processed: 881 average time/residue: 0.7196 time to fit residues: 1082.9626 Evaluate side-chains 815 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 781 time to evaluate : 6.710 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.5674 time to fit residues: 44.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 827 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 488 optimal weight: 2.9990 chunk 626 optimal weight: 6.9990 chunk 485 optimal weight: 0.7980 chunk 722 optimal weight: 0.9990 chunk 479 optimal weight: 0.8980 chunk 854 optimal weight: 0.7980 chunk 535 optimal weight: 0.7980 chunk 521 optimal weight: 1.9990 chunk 394 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 379 ASN ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 431 GLN ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 61 ASN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1074 ASN I 87 GLN M 208 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 75237 Z= 0.169 Angle : 0.581 15.237 102109 Z= 0.292 Chirality : 0.041 0.353 11548 Planarity : 0.003 0.052 12650 Dihedral : 11.901 125.548 10907 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.53 % Allowed : 16.45 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % 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: 0.67 (0.09), residues: 8733 helix: 1.18 (0.09), residues: 3543 sheet: 0.35 (0.15), residues: 1266 loop : -0.09 (0.10), residues: 3924 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 849 time to evaluate : 6.886 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 outliers start: 42 outliers final: 16 residues processed: 872 average time/residue: 0.7312 time to fit residues: 1095.5890 Evaluate side-chains 795 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 779 time to evaluate : 6.993 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6229 time to fit residues: 28.4310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 528 optimal weight: 0.8980 chunk 341 optimal weight: 6.9990 chunk 510 optimal weight: 0.0870 chunk 257 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 165 optimal weight: 20.0000 chunk 543 optimal weight: 9.9990 chunk 582 optimal weight: 3.9990 chunk 422 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 671 optimal weight: 7.9990 overall best weight: 2.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 164 ASN ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 61 ASN 7 551 ASN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN D 146 GLN G 126 ASN I 87 GLN K 89 ASN M 208 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 113 ASN R 232 ASN ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN U 272 ASN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 353 ASN ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 75237 Z= 0.292 Angle : 0.621 17.427 102109 Z= 0.313 Chirality : 0.043 0.391 11548 Planarity : 0.004 0.046 12650 Dihedral : 11.935 125.382 10907 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.71 % Allowed : 17.12 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % 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: 0.61 (0.09), residues: 8733 helix: 1.15 (0.09), residues: 3556 sheet: 0.27 (0.15), residues: 1252 loop : -0.13 (0.10), residues: 3925 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 799 time to evaluate : 6.968 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 outliers start: 56 outliers final: 27 residues processed: 830 average time/residue: 0.7210 time to fit residues: 1026.3006 Evaluate side-chains 795 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 768 time to evaluate : 6.799 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5681 time to fit residues: 37.5992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 777 optimal weight: 8.9990 chunk 819 optimal weight: 30.0000 chunk 747 optimal weight: 10.0000 chunk 796 optimal weight: 0.0670 chunk 818 optimal weight: 20.0000 chunk 479 optimal weight: 4.9990 chunk 347 optimal weight: 0.0270 chunk 625 optimal weight: 1.9990 chunk 244 optimal weight: 0.0570 chunk 719 optimal weight: 9.9990 chunk 753 optimal weight: 0.0970 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 168 GLN 7 423 GLN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 517 ASN B 60 GLN B 887 HIS I 87 GLN K 89 ASN M 208 ASN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 ASN R 239 GLN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN ** W 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 75237 Z= 0.160 Angle : 0.606 17.057 102109 Z= 0.302 Chirality : 0.042 0.538 11548 Planarity : 0.003 0.057 12650 Dihedral : 11.904 122.889 10907 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.25 % Allowed : 17.35 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % 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: 0.66 (0.09), residues: 8733 helix: 1.15 (0.09), residues: 3568 sheet: 0.35 (0.15), residues: 1247 loop : -0.09 (0.10), residues: 3918 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 843 time to evaluate : 6.810 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 outliers start: 20 outliers final: 6 residues processed: 858 average time/residue: 0.7309 time to fit residues: 1075.4150 Evaluate side-chains 784 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 778 time to evaluate : 6.884 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6199 time to fit residues: 16.3979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 793 optimal weight: 10.0000 chunk 523 optimal weight: 6.9990 chunk 842 optimal weight: 9.9990 chunk 514 optimal weight: 0.0980 chunk 399 optimal weight: 3.9990 chunk 585 optimal weight: 5.9990 chunk 883 optimal weight: 0.6980 chunk 813 optimal weight: 20.0000 chunk 703 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 543 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN K 89 ASN M 208 ASN ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 113 ASN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN ** W 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 75237 Z= 0.229 Angle : 0.627 16.066 102109 Z= 0.315 Chirality : 0.043 0.450 11548 Planarity : 0.004 0.065 12650 Dihedral : 11.910 121.541 10907 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.25 % Allowed : 17.99 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % 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: 0.65 (0.09), residues: 8733 helix: 1.14 (0.09), residues: 3576 sheet: 0.27 (0.14), residues: 1277 loop : -0.06 (0.10), residues: 3880 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17466 Ramachandran restraints generated. 8733 Oldfield, 0 Emsley, 8733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 797 time to evaluate : 7.055 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 outliers start: 20 outliers final: 11 residues processed: 804 average time/residue: 0.7412 time to fit residues: 1025.8813 Evaluate side-chains 785 residues out of total 7929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 774 time to evaluate : 6.821 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6019 time to fit residues: 21.5551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 431 optimal weight: 5.9990 chunk 558 optimal weight: 0.5980 chunk 749 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 648 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 704 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 723 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 119 GLN ** 6 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 419 GLN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS D 31 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 89 ASN M 208 ASN ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 HIS ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN ** W 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.118834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072146 restraints weight = 201208.582| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.98 r_work: 0.2856 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 75237 Z= 0.300 Angle : 0.645 15.276 102109 Z= 0.325 Chirality : 0.043 0.412 11548 Planarity : 0.004 0.050 12650 Dihedral : 11.990 122.818 10907 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.23 % Allowed : 17.97 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % 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: 0.59 (0.09), residues: 8733 helix: 1.10 (0.09), residues: 3570 sheet: 0.25 (0.15), residues: 1258 loop : -0.12 (0.10), residues: 3905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20028.56 seconds wall clock time: 351 minutes 31.49 seconds (21091.49 seconds total)