Starting phenix.real_space_refine (version: dev) on Mon Apr 25 05:02:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvk_11459/04_2022/6zvk_11459.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvk_11459/04_2022/6zvk_11459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvk_11459/04_2022/6zvk_11459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvk_11459/04_2022/6zvk_11459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvk_11459/04_2022/6zvk_11459.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvk_11459/04_2022/6zvk_11459.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "x2 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U2 PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a7 PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H5 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 228291 Number of models: 1 Model: "" Number of chains: 91 Chain: "Z2" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "e2" Number of atoms: 83971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3920, 83971 Inner-chain residues flagged as termini: ['pdbres=" Ue2 634 "', 'pdbres=" Ce2 889 "', 'pdbres=" Ge21041 "', 'pdbres=" Ge21158 "', 'pdbres=" Ae21825 "', 'pdbres=" Ge21841 "', 'pdbres=" Ce22243 "', 'pdbres=" Ue23583 "', 'pdbres=" Ce24843 "'] Classifications: {'RNA': 3920} Modifications used: {'5*END': 10, 'rna2p_pur': 349, 'rna3p_pur': 1770, 'rna2p_pyr': 226, 'rna3p_pyr': 1575} Link IDs: {'rna3p': 3344, 'rna2p': 575} Chain: "d2" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 7, 'rna3p_pyr': 52} Link IDs: {'rna3p': 106, 'rna2p': 13} Chain: "h2" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'rna3p_pyr': 69, 'rna2p_pur': 14, 'rna3p_pur': 62, 'rna2p_pyr': 11, '5*END': 1} Link IDs: {'rna3p': 130, 'rna2p': 25} Chain: "p2" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 568 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'CIS': 1, 'TRANS': 65} Chain: "w2" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1630 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "H2" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1243 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "S2" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "32" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1509 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "52" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3173 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "62" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1453 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "72" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "82" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "k2" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "l2" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 529 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "m2" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "o2" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1116 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "q2" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "r2" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "13" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "t2" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2884 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "u2" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 889 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "v2" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1054 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "x2" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "y2" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 907 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "92" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1869 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "A2" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "B2" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 831 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "C2" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 706 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "D2" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "E2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "F2" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 852 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "G2" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2387 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "I2" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "J2" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "K2" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1524 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "L2" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "M2" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1183 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'CIS': 3, 'TRANS': 141} Chain breaks: 2 Chain: "R2" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 285 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "T2" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1614 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 187} Chain: "U2" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1875 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "V2" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1872 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 14, 'TRANS': 218} Chain: "W2" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1517 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "X2" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 822 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "Y2" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1354 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "a7" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1702 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "12" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "22" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "42" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1744 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 206} Chain: "E1" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3208 Classifications: {'RNA': 153} Modifications used: {'rna3p_pyr': 69, 'rna2p_pur': 18, 'rna3p_pur': 48, 'rna2p_pyr': 18} Link IDs: {'rna3p': 116, 'rna2p': 36} Chain: "I3" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "s3" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 350 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "G3" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1247 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 6, 'TRANS': 146} Chain: "f3" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K3" Number of atoms: 39862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1869, 39862 Classifications: {'RNA': 1869} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna3p_pur': 825, 'rna2p_pyr': 121, 'rna3p_pyr': 780} Link IDs: {'rna3p': 1604, 'rna2p': 264} Chain: "P3" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1522 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "a5" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "A3" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1061 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "B3" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "C3" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1048 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "D3" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 631 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G5" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1140 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 134} Chain: "H5" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1113 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "J5" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125, 'PCIS': 1} Chain: "I5" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L3" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "M3" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 599 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "O3" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 782 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "Q3" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain breaks: 1 Chain: "a3" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2437 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "T3" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "U3" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1645 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "V3" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1730 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "W3" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1691 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "X3" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 223 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Link IDs: {'TRANS': 22} Chain: "Y3" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "j3" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2075 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "N3" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "b3" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1924 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "c3" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1687 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d3" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1526 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "e3" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F3" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "E3" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "H3" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 445 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "C2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H3" 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 A0G09 SG CYSC2 19 178.461 72.184 123.045 1.00 33.91 S ATOM A0G11 SG CYSC2 22 178.389 71.397 126.760 1.00 34.72 S ATOM A0G3K SG CYSC2 34 178.907 74.990 125.505 1.00 38.01 S ATOM A0G43 SG CYSC2 37 181.628 72.664 125.417 1.00 36.93 S ATOM A0GWT SG CYSE2 96 139.377 145.893 204.218 1.00 42.60 S ATOM A0GXJ SG CYSE2 99 137.522 142.836 203.135 1.00 38.15 S ATOM A0H01 SG CYSE2 110 137.749 143.572 206.841 1.00 43.18 S ATOM A0H19 SG CYSE2 115 140.829 142.473 204.928 1.00 41.16 S ATOM A0H6R SG CYSF2 12 241.979 134.736 159.249 1.00 42.60 S ATOM A0H7F SG CYSF2 15 246.080 134.813 158.774 1.00 47.50 S ATOM A0HKG SG CYSF2 72 243.103 136.685 156.602 1.00 45.69 S ATOM A0HLH SG CYSF2 77 246.253 134.224 156.847 1.00 58.16 S ATOM A0JUJ SG CYSI2 39 154.035 113.795 77.032 1.00 30.15 S ATOM A0JV6 SG CYSI2 42 150.644 113.411 75.475 1.00 31.43 S ATOM A0JYK SG CYSI2 57 151.889 111.144 78.590 1.00 26.72 S ATOM A0JZ0 SG CYSI2 60 152.916 110.923 74.834 1.00 34.33 S ATOM A28K3 SG CYSO3 23 176.672 169.593 94.116 1.00 36.61 S ATOM A28KO SG CYSO3 26 175.433 169.705 97.541 1.00 41.16 S ATOM A28VB SG CYSO3 74 173.698 171.986 94.869 1.00 36.56 S ATOM A28VU SG CYSO3 77 176.934 172.594 96.320 1.00 37.58 S ATOM A2QRC SG CYSH3 21 167.342 236.773 133.310 1.00 75.74 S ATOM A2QS0 SG CYSH3 24 164.733 234.231 134.286 1.00 80.18 S ATOM A2QVD SG CYSH3 39 167.614 233.248 132.169 1.00 70.89 S ATOM A2QW3 SG CYSH3 42 164.899 235.047 130.562 1.00 71.66 S Time building chain proxies: 81.61, per 1000 atoms: 0.36 Number of scatterers: 228291 At special positions: 0 Unit cell: (304.7, 297, 300.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 437 16.00 P 6205 15.00 O 59696 8.00 N 42437 7.00 C 119510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 81.46 Conformation dependent library (CDL) restraints added in 11.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZNC2 101 " pdb="ZN ZNC2 101 " - pdb=" SG CYSC2 34 " pdb="ZN ZNC2 101 " - pdb=" SG CYSC2 37 " pdb="ZN ZNC2 101 " - pdb=" SG CYSC2 22 " pdb="ZN ZNC2 101 " - pdb=" SG CYSC2 19 " pdb=" ZNE2 201 " pdb="ZN ZNE2 201 " - pdb=" SG CYSE2 115 " pdb="ZN ZNE2 201 " - pdb=" SG CYSE2 99 " pdb="ZN ZNE2 201 " - pdb=" SG CYSE2 110 " pdb="ZN ZNE2 201 " - pdb=" SG CYSE2 96 " pdb=" ZNF2 301 " pdb="ZN ZNF2 301 " - pdb=" SG CYSF2 15 " pdb="ZN ZNF2 301 " - pdb=" SG CYSF2 72 " pdb="ZN ZNF2 301 " - pdb=" SG CYSF2 77 " pdb="ZN ZNF2 301 " - pdb=" SG CYSF2 12 " pdb=" ZNH3 401 " pdb="ZN ZNH3 401 " - pdb=" SG CYSH3 24 " pdb="ZN ZNH3 401 " - pdb=" SG CYSH3 39 " pdb="ZN ZNH3 401 " - pdb=" SG CYSH3 42 " pdb="ZN ZNH3 401 " - pdb=" SG CYSH3 21 " pdb=" ZNI2 601 " pdb="ZN ZNI2 601 " - pdb=" SG CYSI2 60 " pdb="ZN ZNI2 601 " - pdb=" SG CYSI2 39 " pdb="ZN ZNI2 601 " - pdb=" SG CYSI2 42 " pdb="ZN ZNI2 601 " - pdb=" SG CYSI2 57 " pdb=" ZNO3 501 " pdb="ZN ZNO3 501 " - pdb=" SG CYSO3 74 " pdb="ZN ZNO3 501 " - pdb=" SG CYSO3 77 " pdb="ZN ZNO3 501 " - pdb=" SG CYSO3 23 " pdb="ZN ZNO3 501 " - pdb=" SG CYSO3 26 " Number of angles added : 36 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22056 Finding SS restraints... Secondary structure from input PDB file: 383 helices and 135 sheets defined 33.9% alpha, 13.0% beta 1714 base pairs and 2706 stacking pairs defined. Time for finding SS restraints: 66.00 Creating SS restraints... Processing helix chain 'Z2' and resid 70 through 79 removed outlier: 3.664A pdb=" N LYSZ2 75 " --> pdb=" O LYSZ2 71 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALAZ2 76 " --> pdb=" O TYRZ2 72 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 81 through 86 Processing helix chain 'Z2' and resid 89 through 102 removed outlier: 3.841A pdb=" N LYSZ2 93 " --> pdb=" O THRZ2 89 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYSZ2 94 " --> pdb=" O ARGZ2 90 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 105 through 138 removed outlier: 3.521A pdb=" N ASNZ2 120 " --> pdb=" O LYSZ2 116 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILEZ2 123 " --> pdb=" O ARGZ2 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALAZ2 133 " --> pdb=" O LYSZ2 129 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALAZ2 134 " --> pdb=" O LEUZ2 130 " (cutoff:3.500A) Processing helix chain 'p2' and resid 8 through 14 removed outlier: 3.673A pdb=" N LEUp2 12 " --> pdb=" O ILEp2 8 " (cutoff:3.500A) Processing helix chain 'p2' and resid 49 through 59 removed outlier: 3.894A pdb=" N GLUp2 54 " --> pdb=" O LYSp2 50 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYSp2 55 " --> pdb=" O GLUp2 51 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLNp2 58 " --> pdb=" O GLUp2 54 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SERp2 59 " --> pdb=" O LYSp2 55 " (cutoff:3.500A) Processing helix chain 'w2' and resid 15 through 30 removed outlier: 3.716A pdb=" N ILEw2 22 " --> pdb=" O ARGw2 18 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYSw2 25 " --> pdb=" O ALAw2 21 " (cutoff:3.500A) Processing helix chain 'w2' and resid 37 through 41 removed outlier: 3.622A pdb=" N GLYw2 40 " --> pdb=" O ARGw2 37 " (cutoff:3.500A) Processing helix chain 'w2' and resid 47 through 53 Processing helix chain 'w2' and resid 75 through 86 Processing helix chain 'w2' and resid 95 through 100 removed outlier: 3.820A pdb=" N ASPw2 100 " --> pdb=" O GLNw2 96 " (cutoff:3.500A) Processing helix chain 'w2' and resid 109 through 113 Processing helix chain 'w2' and resid 124 through 129 Processing helix chain 'w2' and resid 137 through 145 Processing helix chain 'w2' and resid 149 through 186 removed outlier: 3.696A pdb=" N THRw2 153 " --> pdb=" O TYRw2 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALAw2 154 " --> pdb=" O GLNw2 150 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HISw2 167 " --> pdb=" O LYSw2 163 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEUw2 177 " --> pdb=" O GLNw2 173 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYSw2 183 " --> pdb=" O LYSw2 179 " (cutoff:3.500A) Processing helix chain 'w2' and resid 189 through 199 removed outlier: 3.988A pdb=" N VALw2 195 " --> pdb=" O LYSw2 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYSw2 197 " --> pdb=" O THRw2 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HISw2 199 " --> pdb=" O VALw2 195 " (cutoff:3.500A) Processing helix chain 'H2' and resid 10 through 14 removed outlier: 3.708A pdb=" N SERH2 14 " --> pdb=" O PROH2 11 " (cutoff:3.500A) Processing helix chain 'H2' and resid 25 through 37 removed outlier: 4.278A pdb=" N GLUH2 31 " --> pdb=" O LYSH2 27 " (cutoff:3.500A) Processing helix chain 'H2' and resid 40 through 53 removed outlier: 3.783A pdb=" N ASPH2 50 " --> pdb=" O LYSH2 46 " (cutoff:3.500A) Processing helix chain 'H2' and resid 70 through 76 removed outlier: 3.855A pdb=" N ALAH2 73 " --> pdb=" O CYSH2 70 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYSH2 74 " --> pdb=" O ALAH2 71 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLNH2 75 " --> pdb=" O GLNH2 72 " (cutoff:3.500A) Processing helix chain 'H2' and resid 84 through 91 removed outlier: 3.656A pdb=" N LEUH2 91 " --> pdb=" O SERH2 87 " (cutoff:3.500A) Processing helix chain 'H2' and resid 92 through 106 removed outlier: 3.564A pdb=" N GLUH2 103 " --> pdb=" O GLUH2 99 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEUH2 104 " --> pdb=" O SERH2 100 " (cutoff:3.500A) Processing helix chain 'H2' and resid 132 through 134 No H-bonds generated for 'chain 'H2' and resid 132 through 134' Processing helix chain 'S2' and resid 22 through 39 removed outlier: 3.884A pdb=" N PHES2 34 " --> pdb=" O LYSS2 30 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARGS2 38 " --> pdb=" O PHES2 34 " (cutoff:3.500A) Processing helix chain 'S2' and resid 42 through 52 removed outlier: 3.702A pdb=" N PHES2 52 " --> pdb=" O LEUS2 48 " (cutoff:3.500A) Processing helix chain 'S2' and resid 63 through 71 Processing helix chain 'S2' and resid 106 through 114 removed outlier: 3.515A pdb=" N LEUS2 114 " --> pdb=" O ARGS2 110 " (cutoff:3.500A) Processing helix chain 'S2' and resid 124 through 130 removed outlier: 3.965A pdb=" N LEUS2 128 " --> pdb=" O ASPS2 124 " (cutoff:3.500A) Processing helix chain 'S2' and resid 146 through 151 removed outlier: 3.542A pdb=" N TYRS2 149 " --> pdb=" O ARGS2 146 " (cutoff:3.500A) Processing helix chain 'S2' and resid 171 through 176 removed outlier: 4.062A pdb=" N GLUS2 175 " --> pdb=" O GLYS2 171 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARGS2 176 " --> pdb=" O ARGS2 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'S2' and resid 171 through 176' Processing helix chain 'S2' and resid 181 through 185 removed outlier: 3.539A pdb=" N GLYS2 185 " --> pdb=" O ALAS2 182 " (cutoff:3.500A) Processing helix chain '32' and resid 4 through 16 removed outlier: 3.640A pdb=" N LEU32 15 " --> pdb=" O ALA32 11 " (cutoff:3.500A) Processing helix chain '32' and resid 28 through 34 removed outlier: 3.654A pdb=" N ILE32 32 " --> pdb=" O GLU32 28 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA32 33 " --> pdb=" O THR32 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN32 34 " --> pdb=" O ASN32 30 " (cutoff:3.500A) No H-bonds generated for 'chain '32' and resid 28 through 34' Processing helix chain '32' and resid 37 through 47 removed outlier: 3.678A pdb=" N ARG32 42 " --> pdb=" O ARG32 38 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS32 43 " --> pdb=" O GLN32 39 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS32 46 " --> pdb=" O ARG32 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP32 47 " --> pdb=" O LYS32 43 " (cutoff:3.500A) Processing helix chain '32' and resid 60 through 71 removed outlier: 3.901A pdb=" N ASN32 66 " --> pdb=" O ARG32 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA32 69 " --> pdb=" O LYS32 65 " (cutoff:3.500A) Processing helix chain '32' and resid 84 through 89 removed outlier: 3.763A pdb=" N MET32 89 " --> pdb=" O ALA32 85 " (cutoff:3.500A) Processing helix chain '32' and resid 90 through 103 removed outlier: 3.705A pdb=" N ILE32 101 " --> pdb=" O ARG32 97 " (cutoff:3.500A) Processing helix chain '32' and resid 103 through 111 removed outlier: 3.825A pdb=" N GLU32 111 " --> pdb=" O ARG32 107 " (cutoff:3.500A) Processing helix chain '32' and resid 116 through 129 removed outlier: 3.524A pdb=" N SER32 122 " --> pdb=" O HIS32 118 " (cutoff:3.500A) Processing helix chain '32' and resid 135 through 155 removed outlier: 3.576A pdb=" N HIS32 143 " --> pdb=" O MET32 139 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA32 147 " --> pdb=" O HIS32 143 " (cutoff:3.500A) Processing helix chain '32' and resid 158 through 181 removed outlier: 3.538A pdb=" N LYS32 167 " --> pdb=" O ARG32 163 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS32 180 " --> pdb=" O ARG32 176 " (cutoff:3.500A) Processing helix chain '52' and resid 13 through 17 removed outlier: 3.620A pdb=" N PHE52 16 " --> pdb=" O SER52 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU52 17 " --> pdb=" O LEU52 14 " (cutoff:3.500A) No H-bonds generated for 'chain '52' and resid 13 through 17' Processing helix chain '52' and resid 111 through 116 removed outlier: 3.599A pdb=" N ARG52 116 " --> pdb=" O ASP52 112 " (cutoff:3.500A) Processing helix chain '52' and resid 139 through 157 removed outlier: 3.851A pdb=" N LYS52 143 " --> pdb=" O ASP52 139 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS52 148 " --> pdb=" O ARG52 144 " (cutoff:3.500A) Processing helix chain '52' and resid 189 through 201 Processing helix chain '52' and resid 230 through 236 Processing helix chain '52' and resid 381 through 390 removed outlier: 3.758A pdb=" N ALA52 387 " --> pdb=" O GLU52 383 " (cutoff:3.500A) Processing helix chain '62' and resid 36 through 52 removed outlier: 3.748A pdb=" N TRP62 45 " --> pdb=" O LYS62 41 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER62 49 " --> pdb=" O TRP62 45 " (cutoff:3.500A) Processing helix chain '62' and resid 101 through 118 removed outlier: 3.825A pdb=" N GLN62 108 " --> pdb=" O GLY62 104 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA62 115 " --> pdb=" O ARG62 111 " (cutoff:3.500A) Processing helix chain '62' and resid 133 through 137 removed outlier: 3.730A pdb=" N CYS62 137 " --> pdb=" O ALA62 134 " (cutoff:3.500A) Processing helix chain '62' and resid 139 through 144 Processing helix chain '72' and resid 54 through 58 Processing helix chain '72' and resid 99 through 119 removed outlier: 4.327A pdb=" N ASP72 103 " --> pdb=" O SER72 99 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE72 105 " --> pdb=" O SER72 101 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG72 108 " --> pdb=" O SER72 104 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS72 110 " --> pdb=" O LEU72 106 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU72 111 " --> pdb=" O LYS72 107 " (cutoff:3.500A) Processing helix chain '82' and resid 25 through 31 removed outlier: 3.983A pdb=" N VAL82 29 " --> pdb=" O CYS82 25 " (cutoff:3.500A) Processing helix chain '82' and resid 35 through 47 removed outlier: 3.541A pdb=" N GLU82 40 " --> pdb=" O ALA82 36 " (cutoff:3.500A) Processing helix chain '82' and resid 79 through 95 removed outlier: 4.176A pdb=" N LEU82 83 " --> pdb=" O SER82 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS82 84 " --> pdb=" O LYS82 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS82 88 " --> pdb=" O LYS82 84 " (cutoff:3.500A) Processing helix chain 'k2' and resid 123 through 129 removed outlier: 3.506A pdb=" N LEUk2 128 " --> pdb=" O GLUk2 124 " (cutoff:3.500A) Processing helix chain 'k2' and resid 129 through 136 removed outlier: 3.806A pdb=" N ASNk2 135 " --> pdb=" O ARGk2 131 " (cutoff:3.500A) Processing helix chain 'l2' and resid 36 through 41 removed outlier: 3.833A pdb=" N PHEl2 40 " --> pdb=" O CYSl2 36 " (cutoff:3.500A) Processing helix chain 'l2' and resid 52 through 59 Processing helix chain 'm2' and resid 72 through 77 removed outlier: 3.730A pdb=" N ILEm2 77 " --> pdb=" O HISm2 73 " (cutoff:3.500A) Processing helix chain 'm2' and resid 83 through 92 removed outlier: 3.822A pdb=" N LYSm2 88 " --> pdb=" O GLUm2 84 " (cutoff:3.500A) Processing helix chain 'm2' and resid 105 through 118 removed outlier: 3.865A pdb=" N GLNm2 111 " --> pdb=" O HISm2 107 " (cutoff:3.500A) Processing helix chain 'm2' and resid 145 through 153 removed outlier: 3.717A pdb=" N LYSm2 152 " --> pdb=" O ASPm2 148 " (cutoff:3.500A) Processing helix chain 'o2' and resid 10 through 20 Processing helix chain 'o2' and resid 22 through 30 removed outlier: 4.537A pdb=" N LYSo2 28 " --> pdb=" O HISo2 24 " (cutoff:3.500A) Processing helix chain 'o2' and resid 35 through 43 removed outlier: 3.853A pdb=" N GLNo2 40 " --> pdb=" O LYSo2 36 " (cutoff:3.500A) Processing helix chain 'o2' and resid 113 through 118 Processing helix chain 'o2' and resid 118 through 134 removed outlier: 3.915A pdb=" N LYSo2 124 " --> pdb=" O GLUo2 120 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLNo2 127 " --> pdb=" O ALAo2 123 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLYo2 133 " --> pdb=" O GLYo2 129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYSo2 134 " --> pdb=" O LYSo2 130 " (cutoff:3.500A) Processing helix chain 'q2' and resid 7 through 11 Processing helix chain 'q2' and resid 41 through 46 Processing helix chain 'q2' and resid 64 through 69 Processing helix chain 'q2' and resid 76 through 79 removed outlier: 4.569A pdb=" N TRPq2 79 " --> pdb=" O ASPq2 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'q2' and resid 76 through 79' Processing helix chain 'q2' and resid 83 through 89 removed outlier: 3.700A pdb=" N ARGq2 87 " --> pdb=" O SERq2 83 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASNq2 89 " --> pdb=" O GLNq2 85 " (cutoff:3.500A) Processing helix chain 'q2' and resid 130 through 141 removed outlier: 3.777A pdb=" N ILEq2 137 " --> pdb=" O ALAq2 133 " (cutoff:3.500A) Processing helix chain 'r2' and resid 13 through 19 removed outlier: 4.350A pdb=" N ASNr2 19 " --> pdb=" O LYSr2 15 " (cutoff:3.500A) Processing helix chain 'r2' and resid 36 through 49 removed outlier: 3.735A pdb=" N ASNr2 42 " --> pdb=" O LYSr2 38 " (cutoff:3.500A) Processing helix chain 'r2' and resid 57 through 74 removed outlier: 3.658A pdb=" N ILEr2 72 " --> pdb=" O ARGr2 68 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYSr2 73 " --> pdb=" O ALAr2 69 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALAr2 74 " --> pdb=" O GLUr2 70 " (cutoff:3.500A) Processing helix chain '13' and resid 14 through 25 removed outlier: 3.526A pdb=" N VAL13 21 " --> pdb=" O ARG13 17 " (cutoff:3.500A) Processing helix chain '13' and resid 31 through 40 removed outlier: 3.631A pdb=" N LEU13 35 " --> pdb=" O TYR13 31 " (cutoff:3.500A) Processing helix chain '13' and resid 53 through 68 removed outlier: 3.729A pdb=" N SER13 58 " --> pdb=" O ALA13 54 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU13 61 " --> pdb=" O LYS13 57 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU13 66 " --> pdb=" O TYR13 62 " (cutoff:3.500A) Processing helix chain '13' and resid 77 through 86 Processing helix chain 't2' and resid 25 through 30 Processing helix chain 't2' and resid 33 through 40 removed outlier: 3.726A pdb=" N VALt2 37 " --> pdb=" O ARGt2 33 " (cutoff:3.500A) Processing helix chain 't2' and resid 40 through 45 removed outlier: 3.587A pdb=" N LEUt2 44 " --> pdb=" O VALt2 40 " (cutoff:3.500A) Processing helix chain 't2' and resid 116 through 128 removed outlier: 3.770A pdb=" N ILEt2 124 " --> pdb=" O LYSt2 120 " (cutoff:3.500A) Processing helix chain 't2' and resid 133 through 138 Processing helix chain 't2' and resid 157 through 161 Processing helix chain 't2' and resid 163 through 174 Processing helix chain 't2' and resid 177 through 187 removed outlier: 3.533A pdb=" N ALAt2 185 " --> pdb=" O LYSt2 181 " (cutoff:3.500A) Processing helix chain 't2' and resid 192 through 197 Processing helix chain 't2' and resid 216 through 221 Processing helix chain 't2' and resid 254 through 259 Processing helix chain 't2' and resid 259 through 265 Processing helix chain 't2' and resid 288 through 293 Processing helix chain 't2' and resid 295 through 300 Processing helix chain 't2' and resid 321 through 329 removed outlier: 3.954A pdb=" N LYSt2 327 " --> pdb=" O ARGt2 323 " (cutoff:3.500A) Processing helix chain 't2' and resid 331 through 338 removed outlier: 3.957A pdb=" N ASNt2 338 " --> pdb=" O THRt2 334 " (cutoff:3.500A) Processing helix chain 't2' and resid 340 through 363 removed outlier: 3.807A pdb=" N LEUt2 358 " --> pdb=" O ALAt2 354 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SERt2 362 " --> pdb=" O LEUt2 358 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASPt2 363 " --> pdb=" O ALAt2 359 " (cutoff:3.500A) Processing helix chain 'u2' and resid 41 through 57 removed outlier: 3.906A pdb=" N LYSu2 47 " --> pdb=" O PROu2 43 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHEu2 52 " --> pdb=" O GLUu2 48 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYSu2 55 " --> pdb=" O LYSu2 51 " (cutoff:3.500A) Processing helix chain 'u2' and resid 65 through 74 Processing helix chain 'v2' and resid 81 through 90 removed outlier: 3.522A pdb=" N GLUv2 84 " --> pdb=" O ASNv2 81 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLUv2 86 " --> pdb=" O LYSv2 83 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VALv2 87 " --> pdb=" O GLUv2 84 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N METv2 90 " --> pdb=" O VALv2 87 " (cutoff:3.500A) Processing helix chain 'v2' and resid 107 through 119 removed outlier: 3.538A pdb=" N GLNv2 117 " --> pdb=" O GLUv2 113 " (cutoff:3.500A) Processing helix chain 'y2' and resid 15 through 18 removed outlier: 3.851A pdb=" N ASNy2 18 " --> pdb=" O THRy2 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'y2' and resid 15 through 18' Processing helix chain 'y2' and resid 60 through 66 removed outlier: 3.524A pdb=" N METy2 65 " --> pdb=" O LYSy2 62 " (cutoff:3.500A) Processing helix chain 'y2' and resid 68 through 72 Processing helix chain 'y2' and resid 83 through 89 Processing helix chain 'y2' and resid 89 through 115 removed outlier: 3.735A pdb=" N PHEy2 95 " --> pdb=" O ILEy2 91 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLNy2 100 " --> pdb=" O LEUy2 96 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SERy2 113 " --> pdb=" O ALAy2 109 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYSy2 115 " --> pdb=" O ALAy2 111 " (cutoff:3.500A) Processing helix chain '92' and resid 33 through 39 Processing helix chain '92' and resid 181 through 191 removed outlier: 3.622A pdb=" N ALA92 185 " --> pdb=" O LYS92 181 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS92 188 " --> pdb=" O ARG92 184 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA92 191 " --> pdb=" O HIS92 187 " (cutoff:3.500A) Processing helix chain '92' and resid 200 through 204 Processing helix chain 'A2' and resid 13 through 37 removed outlier: 4.092A pdb=" N LEUA2 18 " --> pdb=" O LYSA2 14 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYSA2 19 " --> pdb=" O GLUA2 15 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VALA2 33 " --> pdb=" O SERA2 29 " (cutoff:3.500A) Processing helix chain 'A2' and resid 40 through 73 removed outlier: 3.511A pdb=" N SERA2 45 " --> pdb=" O ALAA2 41 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYSA2 46 " --> pdb=" O SERA2 42 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILEA2 47 " --> pdb=" O LYSA2 43 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARGA2 48 " --> pdb=" O LEUA2 44 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VALA2 49 " --> pdb=" O SERA2 45 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALAA2 55 " --> pdb=" O ARGA2 51 " (cutoff:3.500A) Processing helix chain 'A2' and resid 89 through 94 removed outlier: 3.859A pdb=" N ARGA2 93 " --> pdb=" O ARGA2 89 " (cutoff:3.500A) Processing helix chain 'A2' and resid 104 through 114 Processing helix chain 'B2' and resid 25 through 29 Processing helix chain 'B2' and resid 34 through 44 removed outlier: 3.544A pdb=" N ARGB2 41 " --> pdb=" O THRB2 37 " (cutoff:3.500A) Processing helix chain 'B2' and resid 44 through 49 Processing helix chain 'B2' and resid 51 through 64 Processing helix chain 'B2' and resid 65 through 77 removed outlier: 3.811A pdb=" N LYSB2 75 " --> pdb=" O LYSB2 71 " (cutoff:3.500A) Processing helix chain 'B2' and resid 79 through 91 removed outlier: 3.735A pdb=" N ARGB2 85 " --> pdb=" O ILEB2 81 " (cutoff:3.500A) Processing helix chain 'B2' and resid 93 through 103 removed outlier: 3.786A pdb=" N LYSB2 103 " --> pdb=" O LYSB2 99 " (cutoff:3.500A) Processing helix chain 'C2' and resid 4 through 11 removed outlier: 4.669A pdb=" N GLYC2 9 " --> pdb=" O SERC2 6 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYSC2 10 " --> pdb=" O SERC2 7 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARGC2 11 " --> pdb=" O PHEC2 8 " (cutoff:3.500A) Processing helix chain 'C2' and resid 50 through 55 removed outlier: 3.513A pdb=" N ARGC2 55 " --> pdb=" O ALAC2 51 " (cutoff:3.500A) Processing helix chain 'C2' and resid 66 through 75 removed outlier: 3.877A pdb=" N TYRC2 71 " --> pdb=" O LEUC2 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARGC2 72 " --> pdb=" O LYSC2 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARGC2 75 " --> pdb=" O TYRC2 71 " (cutoff:3.500A) Processing helix chain 'D2' and resid 6 through 19 removed outlier: 3.532A pdb=" N LYSD2 16 " --> pdb=" O PHED2 12 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLND2 17 " --> pdb=" O LEUD2 13 " (cutoff:3.500A) Processing helix chain 'D2' and resid 24 through 30 Processing helix chain 'E2' and resid 79 through 91 removed outlier: 4.011A pdb=" N TYRE2 89 " --> pdb=" O LEUE2 85 " (cutoff:3.500A) Processing helix chain 'F2' and resid 41 through 46 Processing helix chain 'G2' and resid 9 through 15 removed outlier: 3.561A pdb=" N PHEG2 13 " --> pdb=" O ASNG2 9 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYSG2 14 " --> pdb=" O LYSG2 10 " (cutoff:3.500A) Processing helix chain 'G2' and resid 20 through 25 Processing helix chain 'G2' and resid 79 through 83 removed outlier: 4.064A pdb=" N GLUG2 82 " --> pdb=" O TYRG2 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEUG2 83 " --> pdb=" O ALAG2 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G2' and resid 79 through 83' Processing helix chain 'G2' and resid 94 through 114 removed outlier: 3.703A pdb=" N ALAG2 106 " --> pdb=" O GLYG2 102 " (cutoff:3.500A) Processing helix chain 'G2' and resid 158 through 170 removed outlier: 3.707A pdb=" N ALAG2 162 " --> pdb=" O LYSG2 158 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYSG2 164 " --> pdb=" O PHEG2 160 " (cutoff:3.500A) Processing helix chain 'G2' and resid 193 through 200 Processing helix chain 'G2' and resid 201 through 215 removed outlier: 3.761A pdb=" N GLUG2 213 " --> pdb=" O ARGG2 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLUG2 214 " --> pdb=" O TYRG2 210 " (cutoff:3.500A) Processing helix chain 'G2' and resid 215 through 228 removed outlier: 7.063A pdb=" N GLNG2 225 " --> pdb=" O LYSG2 221 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYRG2 226 " --> pdb=" O GLNG2 222 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYSG2 228 " --> pdb=" O SERG2 224 " (cutoff:3.500A) Processing helix chain 'G2' and resid 232 through 234 No H-bonds generated for 'chain 'G2' and resid 232 through 234' Processing helix chain 'G2' and resid 235 through 250 removed outlier: 3.668A pdb=" N ARGG2 248 " --> pdb=" O HISG2 244 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLUG2 249 " --> pdb=" O ALAG2 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASNG2 250 " --> pdb=" O ALAG2 246 " (cutoff:3.500A) Processing helix chain 'G2' and resid 272 through 292 removed outlier: 4.042A pdb=" N ARGG2 279 " --> pdb=" O GLNG2 275 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALAG2 285 " --> pdb=" O ALAG2 281 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARGG2 289 " --> pdb=" O ALAG2 285 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLNG2 291 " --> pdb=" O PHEG2 287 " (cutoff:3.500A) Processing helix chain 'I2' and resid 8 through 15 removed outlier: 4.085A pdb=" N VALI2 11 " --> pdb=" O VALI2 8 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYSI2 13 " --> pdb=" O ILEI2 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYRI2 14 " --> pdb=" O VALI2 11 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLYI2 15 " --> pdb=" O GLYI2 12 " (cutoff:3.500A) Processing helix chain 'I2' and resid 20 through 28 removed outlier: 3.919A pdb=" N LYSI2 28 " --> pdb=" O LYSI2 24 " (cutoff:3.500A) Processing helix chain 'I2' and resid 73 through 91 removed outlier: 3.514A pdb=" N ARGI2 84 " --> pdb=" O LYSI2 80 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLUI2 88 " --> pdb=" O ARGI2 84 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEUI2 89 " --> pdb=" O ARGI2 85 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASPI2 91 " --> pdb=" O LYSI2 87 " (cutoff:3.500A) Processing helix chain 'J2' and resid 4 through 9 Processing helix chain 'J2' and resid 72 through 75 Processing helix chain 'J2' and resid 85 through 100 Processing helix chain 'J2' and resid 103 through 105 No H-bonds generated for 'chain 'J2' and resid 103 through 105' Processing helix chain 'J2' and resid 106 through 120 Processing helix chain 'K2' and resid 7 through 24 removed outlier: 3.672A pdb=" N ASPK2 22 " --> pdb=" O ILEK2 18 " (cutoff:3.500A) Processing helix chain 'K2' and resid 38 through 48 removed outlier: 3.552A pdb=" N ILEK2 43 " --> pdb=" O GLNK2 39 " (cutoff:3.500A) Processing helix chain 'K2' and resid 61 through 69 removed outlier: 4.091A pdb=" N ILEK2 65 " --> pdb=" O METK2 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEUK2 69 " --> pdb=" O ILEK2 65 " (cutoff:3.500A) Processing helix chain 'K2' and resid 74 through 78 Processing helix chain 'K2' and resid 94 through 106 removed outlier: 3.631A pdb=" N ARGK2 99 " --> pdb=" O LEUK2 95 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYSK2 106 " --> pdb=" O LEUK2 102 " (cutoff:3.500A) Processing helix chain 'K2' and resid 135 through 140 Processing helix chain 'K2' and resid 168 through 178 removed outlier: 3.610A pdb=" N ALAK2 172 " --> pdb=" O GLYK2 168 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THRK2 173 " --> pdb=" O ALAK2 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEUK2 175 " --> pdb=" O GLUK2 171 " (cutoff:3.500A) Processing helix chain 'L2' and resid 62 through 80 removed outlier: 3.557A pdb=" N GLUL2 66 " --> pdb=" O SERL2 62 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALAL2 67 " --> pdb=" O GLUL2 63 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYSL2 78 " --> pdb=" O LYSL2 74 " (cutoff:3.500A) Processing helix chain 'M2' and resid 33 through 37 removed outlier: 3.694A pdb=" N LEUM2 37 " --> pdb=" O PROM2 34 " (cutoff:3.500A) Processing helix chain 'M2' and resid 40 through 48 removed outlier: 3.711A pdb=" N ILEM2 46 " --> pdb=" O VALM2 42 " (cutoff:3.500A) Processing helix chain 'M2' and resid 77 through 83 removed outlier: 3.513A pdb=" N ILEM2 81 " --> pdb=" O ALAM2 77 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYSM2 83 " --> pdb=" O ALAM2 79 " (cutoff:3.500A) Processing helix chain 'M2' and resid 105 through 117 removed outlier: 3.730A pdb=" N VALM2 110 " --> pdb=" O PHEM2 106 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASNM2 111 " --> pdb=" O ASPM2 107 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILEM2 112 " --> pdb=" O GLUM2 108 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALAM2 113 " --> pdb=" O ILEM2 109 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARGM2 114 " --> pdb=" O VALM2 110 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLNM2 115 " --> pdb=" O ASNM2 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N METM2 116 " --> pdb=" O ILEM2 112 " (cutoff:3.500A) Processing helix chain 'M2' and resid 128 through 136 Processing helix chain 'R2' and resid 54 through 62 Processing helix chain 'T2' and resid 135 through 139 Processing helix chain 'T2' and resid 181 through 186 Processing helix chain 'T2' and resid 247 through 255 Processing helix chain 'T2' and resid 256 through 266 Proline residue: T2 262 - end of helix Processing helix chain 'T2' and resid 269 through 276 Processing helix chain 'U2' and resid 24 through 78 removed outlier: 3.541A pdb=" N ALAU2 53 " --> pdb=" O ILEU2 49 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLUU2 67 " --> pdb=" O METU2 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N METU2 70 " --> pdb=" O THRU2 66 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALAU2 77 " --> pdb=" O METU2 73 " (cutoff:3.500A) Processing helix chain 'U2' and resid 101 through 108 Processing helix chain 'U2' and resid 125 through 135 removed outlier: 3.817A pdb=" N ASNU2 130 " --> pdb=" O LYSU2 126 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N METU2 131 " --> pdb=" O ALAU2 127 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALU2 135 " --> pdb=" O METU2 131 " (cutoff:3.500A) Processing helix chain 'U2' and resid 145 through 155 Processing helix chain 'U2' and resid 170 through 179 removed outlier: 4.204A pdb=" N ILEU2 174 " --> pdb=" O ASPU2 170 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SERU2 177 " --> pdb=" O LEUU2 173 " (cutoff:3.500A) Processing helix chain 'U2' and resid 180 through 182 No H-bonds generated for 'chain 'U2' and resid 180 through 182' Processing helix chain 'U2' and resid 185 through 195 removed outlier: 3.890A pdb=" N ILEU2 193 " --> pdb=" O LEUU2 189 " (cutoff:3.500A) Processing helix chain 'U2' and resid 199 through 206 removed outlier: 3.680A pdb=" N ALAU2 203 " --> pdb=" O HISU2 199 " (cutoff:3.500A) Processing helix chain 'U2' and resid 225 through 229 Processing helix chain 'U2' and resid 238 through 245 Processing helix chain 'V2' and resid 60 through 74 removed outlier: 3.706A pdb=" N GLNV2 64 " --> pdb=" O TYRV2 60 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLNV2 66 " --> pdb=" O ARGV2 62 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALAV2 68 " --> pdb=" O GLNV2 64 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILEV2 69 " --> pdb=" O ARGV2 65 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYRV2 71 " --> pdb=" O ARGV2 67 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYSV2 72 " --> pdb=" O ALAV2 68 " (cutoff:3.500A) Processing helix chain 'V2' and resid 77 through 82 Processing helix chain 'V2' and resid 88 through 102 removed outlier: 3.873A pdb=" N GLNV2 94 " --> pdb=" O GLNV2 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYSV2 101 " --> pdb=" O LYSV2 97 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYRV2 102 " --> pdb=" O LEUV2 98 " (cutoff:3.500A) Processing helix chain 'V2' and resid 109 through 120 removed outlier: 3.659A pdb=" N LYSV2 120 " --> pdb=" O ALAV2 116 " (cutoff:3.500A) Processing helix chain 'V2' and resid 139 through 144 Processing helix chain 'V2' and resid 145 through 147 No H-bonds generated for 'chain 'V2' and resid 145 through 147' Processing helix chain 'V2' and resid 163 through 167 removed outlier: 3.603A pdb=" N VALV2 167 " --> pdb=" O ILEV2 164 " (cutoff:3.500A) Processing helix chain 'V2' and resid 169 through 178 Processing helix chain 'V2' and resid 211 through 223 removed outlier: 3.503A pdb=" N ALAV2 216 " --> pdb=" O LYSV2 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUV2 218 " --> pdb=" O ALAV2 214 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALAV2 221 " --> pdb=" O LYSV2 217 " (cutoff:3.500A) Processing helix chain 'V2' and resid 229 through 235 removed outlier: 3.636A pdb=" N ARGV2 235 " --> pdb=" O ASPV2 231 " (cutoff:3.500A) Processing helix chain 'V2' and resid 243 through 258 removed outlier: 3.659A pdb=" N ARGV2 249 " --> pdb=" O LYSV2 245 " (cutoff:3.500A) Processing helix chain 'W2' and resid 60 through 63 Processing helix chain 'W2' and resid 74 through 79 Processing helix chain 'W2' and resid 79 through 97 removed outlier: 4.098A pdb=" N THRW2 83 " --> pdb=" O ALAW2 79 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VALW2 95 " --> pdb=" O METW2 91 " (cutoff:3.500A) Processing helix chain 'W2' and resid 127 through 131 Processing helix chain 'W2' and resid 161 through 175 removed outlier: 3.974A pdb=" N ILEW2 172 " --> pdb=" O SERW2 168 " (cutoff:3.500A) Processing helix chain 'X2' and resid 144 through 157 removed outlier: 3.839A pdb=" N ARGX2 153 " --> pdb=" O VALX2 149 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHEX2 157 " --> pdb=" O ARGX2 153 " (cutoff:3.500A) Processing helix chain 'X2' and resid 180 through 188 removed outlier: 3.763A pdb=" N METX2 184 " --> pdb=" O GLUX2 180 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 10 through 14 removed outlier: 3.994A pdb=" N GLUY2 14 " --> pdb=" O PROY2 11 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 31 through 45 removed outlier: 4.545A pdb=" N LYSY2 38 " --> pdb=" O THRY2 34 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALY2 39 " --> pdb=" O ARGY2 35 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEUY2 40 " --> pdb=" O ALAY2 36 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 75 through 90 removed outlier: 3.665A pdb=" N VALY2 89 " --> pdb=" O LYSY2 85 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARGY2 90 " --> pdb=" O GLYY2 86 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 112 through 116 Processing helix chain 'Y2' and resid 138 through 143 removed outlier: 3.751A pdb=" N ALAY2 142 " --> pdb=" O PHEY2 139 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 158 through 171 removed outlier: 3.695A pdb=" N ALAY2 162 " --> pdb=" O SERY2 158 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N METY2 163 " --> pdb=" O LYSY2 159 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRPY2 165 " --> pdb=" O GLUY2 161 " (cutoff:3.500A) Processing helix chain 'a7' and resid 27 through 46 removed outlier: 3.955A pdb=" N ILEa7 33 " --> pdb=" O PROa7 29 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGa7 34 " --> pdb=" O ALAa7 30 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARGa7 44 " --> pdb=" O GLNa7 40 " (cutoff:3.500A) Processing helix chain 'a7' and resid 77 through 84 removed outlier: 3.556A pdb=" N ALAa7 84 " --> pdb=" O GLUa7 80 " (cutoff:3.500A) Processing helix chain 'a7' and resid 107 through 121 removed outlier: 3.741A pdb=" N GLNa7 111 " --> pdb=" O THRa7 107 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALAa7 112 " --> pdb=" O GLUa7 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLNa7 115 " --> pdb=" O GLNa7 111 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARGa7 116 " --> pdb=" O ALAa7 112 " (cutoff:3.500A) Processing helix chain 'a7' and resid 139 through 145 removed outlier: 3.659A pdb=" N GLUa7 143 " --> pdb=" O SERa7 139 " (cutoff:3.500A) Processing helix chain 'a7' and resid 170 through 175 removed outlier: 3.677A pdb=" N LYSa7 174 " --> pdb=" O THRa7 170 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASNa7 175 " --> pdb=" O GLUa7 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'a7' and resid 170 through 175' Processing helix chain 'a7' and resid 177 through 191 Processing helix chain 'a7' and resid 191 through 210 removed outlier: 3.641A pdb=" N ARGa7 195 " --> pdb=" O LEUa7 191 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALAa7 196 " --> pdb=" O PHEa7 192 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALAa7 202 " --> pdb=" O ARGa7 198 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALAa7 203 " --> pdb=" O ALAa7 199 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VALa7 207 " --> pdb=" O ALAa7 203 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYSa7 209 " --> pdb=" O GLNa7 205 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYSa7 210 " --> pdb=" O ASPa7 206 " (cutoff:3.500A) Processing helix chain '12' and resid 3 through 12 removed outlier: 3.543A pdb=" N ARG12 12 " --> pdb=" O GLN12 8 " (cutoff:3.500A) Processing helix chain '12' and resid 19 through 33 removed outlier: 4.217A pdb=" N ARG12 24 " --> pdb=" O ARG12 20 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL12 25 " --> pdb=" O PHE12 21 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN12 29 " --> pdb=" O VAL12 25 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR12 30 " --> pdb=" O ARG12 26 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG12 31 " --> pdb=" O CYS12 27 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN12 32 " --> pdb=" O TRP12 28 " (cutoff:3.500A) Processing helix chain '12' and resid 44 through 51 Processing helix chain '12' and resid 75 through 79 removed outlier: 3.538A pdb=" N GLY12 78 " --> pdb=" O VAL12 75 " (cutoff:3.500A) Processing helix chain '12' and resid 97 through 110 removed outlier: 3.592A pdb=" N ALA12 106 " --> pdb=" O ALA12 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS12 110 " --> pdb=" O ALA12 106 " (cutoff:3.500A) Processing helix chain '12' and resid 139 through 144 Processing helix chain '12' and resid 149 through 157 Proline residue: 12 154 - end of helix Processing helix chain '12' and resid 158 through 162 removed outlier: 3.513A pdb=" N MET12 161 " --> pdb=" O HIS12 158 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG12 162 " --> pdb=" O ARG12 159 " (cutoff:3.500A) No H-bonds generated for 'chain '12' and resid 158 through 162' Processing helix chain '12' and resid 165 through 170 removed outlier: 3.735A pdb=" N LYS12 170 " --> pdb=" O SER12 166 " (cutoff:3.500A) Processing helix chain '12' and resid 171 through 173 No H-bonds generated for 'chain '12' and resid 171 through 173' Processing helix chain '12' and resid 189 through 194 Processing helix chain '22' and resid 58 through 66 removed outlier: 3.735A pdb=" N LYS22 64 " --> pdb=" O LYS22 60 " (cutoff:3.500A) Processing helix chain '22' and resid 97 through 101 removed outlier: 3.871A pdb=" N PHE22 101 " --> pdb=" O LYS22 98 " (cutoff:3.500A) Processing helix chain '22' and resid 103 through 123 removed outlier: 4.050A pdb=" N ARG22 108 " --> pdb=" O PRO22 104 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS22 109 " --> pdb=" O ALA22 105 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG22 121 " --> pdb=" O LYS22 117 " (cutoff:3.500A) Processing helix chain '22' and resid 124 through 126 No H-bonds generated for 'chain '22' and resid 124 through 126' Processing helix chain '42' and resid 17 through 21 removed outlier: 3.809A pdb=" N GLY42 20 " --> pdb=" O VAL42 17 " (cutoff:3.500A) Processing helix chain '42' and resid 73 through 78 Processing helix chain '42' and resid 86 through 91 removed outlier: 3.815A pdb=" N LYS42 91 " --> pdb=" O ILE42 87 " (cutoff:3.500A) Processing helix chain '42' and resid 115 through 118 Processing helix chain '42' and resid 119 through 124 Processing helix chain '42' and resid 125 through 132 removed outlier: 4.303A pdb=" N ASN42 129 " --> pdb=" O GLY42 125 " (cutoff:3.500A) Processing helix chain '42' and resid 136 through 140 removed outlier: 3.628A pdb=" N THR42 139 " --> pdb=" O SER42 136 " (cutoff:3.500A) Processing helix chain '42' and resid 147 through 152 removed outlier: 3.513A pdb=" N LYS42 152 " --> pdb=" O VAL42 148 " (cutoff:3.500A) Processing helix chain '42' and resid 178 through 187 removed outlier: 4.211A pdb=" N HIS42 184 " --> pdb=" O VAL42 180 " (cutoff:3.500A) Processing helix chain '42' and resid 187 through 192 removed outlier: 3.918A pdb=" N VAL42 191 " --> pdb=" O VAL42 187 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER42 192 " --> pdb=" O ASN42 188 " (cutoff:3.500A) No H-bonds generated for 'chain '42' and resid 187 through 192' Processing helix chain 'I3' and resid 28 through 47 removed outlier: 3.670A pdb=" N LYSI3 34 " --> pdb=" O LYSI3 30 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VALI3 35 " --> pdb=" O SERI3 31 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYSI3 36 " --> pdb=" O LEUI3 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALAI3 43 " --> pdb=" O LEUI3 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYSI3 44 " --> pdb=" O ILEI3 40 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLUI3 45 " --> pdb=" O ARGI3 41 " (cutoff:3.500A) Processing helix chain 'I3' and resid 95 through 104 removed outlier: 3.576A pdb=" N LYSI3 99 " --> pdb=" O SERI3 95 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILEI3 104 " --> pdb=" O GLNI3 100 " (cutoff:3.500A) Processing helix chain 's3' and resid 31 through 42 removed outlier: 4.214A pdb=" N ARGs3 41 " --> pdb=" O GLNs3 37 " (cutoff:3.500A) Processing helix chain 'G3' and resid 48 through 53 Processing helix chain 'P3' and resid 257 through 268 Processing helix chain 'P3' and resid 269 through 275 removed outlier: 6.597A pdb=" N SERP3 272 " --> pdb=" O GLUP3 269 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASPP3 273 " --> pdb=" O METP3 270 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYSP3 275 " --> pdb=" O SERP3 272 " (cutoff:3.500A) Processing helix chain 'P3' and resid 306 through 311 Processing helix chain 'P3' and resid 313 through 324 removed outlier: 4.099A pdb=" N ARGP3 319 " --> pdb=" O VALP3 315 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLUP3 320 " --> pdb=" O ARGP3 316 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYSP3 323 " --> pdb=" O ARGP3 319 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYSP3 324 " --> pdb=" O GLUP3 320 " (cutoff:3.500A) Processing helix chain 'P3' and resid 360 through 365 removed outlier: 3.813A pdb=" N ASPP3 365 " --> pdb=" O THRP3 361 " (cutoff:3.500A) Processing helix chain 'P3' and resid 365 through 372 removed outlier: 3.808A pdb=" N VALP3 372 " --> pdb=" O LEUP3 368 " (cutoff:3.500A) Processing helix chain 'P3' and resid 404 through 406 No H-bonds generated for 'chain 'P3' and resid 404 through 406' Processing helix chain 'P3' and resid 407 through 420 removed outlier: 3.914A pdb=" N SERP3 412 " --> pdb=" O VALP3 408 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLYP3 413 " --> pdb=" O GLUP3 409 " (cutoff:3.500A) Processing helix chain 'a5' and resid 57 through 61 removed outlier: 3.591A pdb=" N METa5 60 " --> pdb=" O THRa5 57 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYSa5 61 " --> pdb=" O GLYa5 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'a5' and resid 57 through 61' Processing helix chain 'a5' and resid 64 through 68 removed outlier: 3.778A pdb=" N GLUa5 68 " --> pdb=" O ASPa5 65 " (cutoff:3.500A) Processing helix chain 'a5' and resid 70 through 86 removed outlier: 3.521A pdb=" N ALAa5 77 " --> pdb=" O ALAa5 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALAa5 82 " --> pdb=" O ALAa5 78 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSa5 86 " --> pdb=" O ALAa5 82 " (cutoff:3.500A) Processing helix chain 'a5' and resid 111 through 123 removed outlier: 3.924A pdb=" N GLYa5 123 " --> pdb=" O LEUa5 119 " (cutoff:3.500A) Processing helix chain 'A3' and resid 16 through 20 Processing helix chain 'A3' and resid 29 through 35 Processing helix chain 'A3' and resid 38 through 46 removed outlier: 3.595A pdb=" N ARGA3 42 " --> pdb=" O SERA3 38 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARGA3 43 " --> pdb=" O ALAA3 39 " (cutoff:3.500A) Processing helix chain 'A3' and resid 53 through 67 Processing helix chain 'A3' and resid 86 through 90 removed outlier: 3.579A pdb=" N META3 89 " --> pdb=" O LEUA3 86 " (cutoff:3.500A) Processing helix chain 'A3' and resid 115 through 120 Processing helix chain 'B3' and resid 64 through 68 Processing helix chain 'B3' and resid 73 through 85 removed outlier: 3.695A pdb=" N LEUB3 77 " --> pdb=" O LEUB3 73 " (cutoff:3.500A) Proline residue: B3 80 - end of helix Processing helix chain 'B3' and resid 102 through 126 removed outlier: 4.067A pdb=" N GLNB3 112 " --> pdb=" O TYRB3 108 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SERB3 115 " --> pdb=" O ARGB3 111 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLNB3 123 " --> pdb=" O VALB3 119 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYSB3 124 " --> pdb=" O ALAB3 120 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYRB3 125 " --> pdb=" O TYRB3 121 " (cutoff:3.500A) Processing helix chain 'B3' and resid 127 through 140 removed outlier: 3.666A pdb=" N LYSB3 131 " --> pdb=" O ASPB3 127 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILEB3 134 " --> pdb=" O SERB3 130 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILEB3 137 " --> pdb=" O GLUB3 133 " (cutoff:3.500A) Processing helix chain 'C3' and resid 6 through 20 Processing helix chain 'C3' and resid 27 through 39 removed outlier: 3.694A pdb=" N ARGC3 33 " --> pdb=" O HISC3 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLUC3 36 " --> pdb=" O LYSC3 32 " (cutoff:3.500A) Processing helix chain 'C3' and resid 43 through 62 removed outlier: 3.501A pdb=" N GLYC3 52 " --> pdb=" O ASNC3 48 " (cutoff:3.500A) Processing helix chain 'C3' and resid 71 through 83 removed outlier: 4.123A pdb=" N GLUC3 77 " --> pdb=" O LEUC3 73 " (cutoff:3.500A) Processing helix chain 'C3' and resid 99 through 110 removed outlier: 3.677A pdb=" N LYSC3 103 " --> pdb=" O ASPC3 99 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLUC3 104 " --> pdb=" O PROC3 100 " (cutoff:3.500A) Processing helix chain 'D3' and resid 56 through 63 removed outlier: 3.632A pdb=" N ARGD3 60 " --> pdb=" O CYSD3 56 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARGD3 61 " --> pdb=" O GLYD3 57 " (cutoff:3.500A) Processing helix chain 'D3' and resid 64 through 76 removed outlier: 3.549A pdb=" N ARGD3 71 " --> pdb=" O ASPD3 67 " (cutoff:3.500A) Processing helix chain 'G5' and resid 25 through 31 removed outlier: 3.821A pdb=" N THRG5 31 " --> pdb=" O ALAG5 27 " (cutoff:3.500A) Processing helix chain 'G5' and resid 37 through 48 removed outlier: 3.725A pdb=" N ARGG5 46 " --> pdb=" O HISG5 42 " (cutoff:3.500A) Processing helix chain 'G5' and resid 60 through 73 removed outlier: 3.736A pdb=" N VALG5 64 " --> pdb=" O THRG5 60 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARGG5 66 " --> pdb=" O ASPG5 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VALG5 67 " --> pdb=" O GLUG5 63 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THRG5 69 " --> pdb=" O GLUG5 65 " (cutoff:3.500A) Processing helix chain 'G5' and resid 74 through 78 removed outlier: 3.527A pdb=" N LYSG5 78 " --> pdb=" O ARGG5 75 " (cutoff:3.500A) Processing helix chain 'G5' and resid 80 through 84 Processing helix chain 'G5' and resid 101 through 118 removed outlier: 3.505A pdb=" N LYSG5 106 " --> pdb=" O GLYG5 102 " (cutoff:3.500A) Processing helix chain 'G5' and resid 119 through 126 Processing helix chain 'H5' and resid 5 through 9 Processing helix chain 'H5' and resid 10 through 26 removed outlier: 4.021A pdb=" N ARGH5 16 " --> pdb=" O GLNH5 12 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEH5 21 " --> pdb=" O ALAH5 17 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYSH5 23 " --> pdb=" O ALAH5 19 " (cutoff:3.500A) Processing helix chain 'H5' and resid 52 through 65 removed outlier: 3.533A pdb=" N ALAH5 61 " --> pdb=" O ALAH5 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYRH5 65 " --> pdb=" O ALAH5 61 " (cutoff:3.500A) Processing helix chain 'H5' and resid 71 through 79 removed outlier: 3.520A pdb=" N METH5 75 " --> pdb=" O GLYH5 71 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILEH5 78 " --> pdb=" O SERH5 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYRH5 79 " --> pdb=" O METH5 75 " (cutoff:3.500A) Processing helix chain 'H5' and resid 97 through 110 removed outlier: 3.764A pdb=" N VALH5 103 " --> pdb=" O VALH5 99 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEUH5 104 " --> pdb=" O ALAH5 100 " (cutoff:3.500A) Processing helix chain 'H5' and resid 117 through 119 No H-bonds generated for 'chain 'H5' and resid 117 through 119' Processing helix chain 'H5' and resid 126 through 139 removed outlier: 3.557A pdb=" N ASPH5 130 " --> pdb=" O GLNH5 126 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEUH5 131 " --> pdb=" O GLYH5 127 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALAH5 135 " --> pdb=" O LEUH5 131 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLNH5 137 " --> pdb=" O ARGH5 133 " (cutoff:3.500A) Processing helix chain 'H5' and resid 140 through 142 No H-bonds generated for 'chain 'H5' and resid 140 through 142' Processing helix chain 'J5' and resid 5 through 21 removed outlier: 3.774A pdb=" N ALAJ5 10 " --> pdb=" O VALJ5 6 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARGJ5 20 " --> pdb=" O ASNJ5 16 " (cutoff:3.500A) Processing helix chain 'J5' and resid 31 through 43 removed outlier: 3.785A pdb=" N VALJ5 40 " --> pdb=" O ARGJ5 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N METJ5 41 " --> pdb=" O PHEJ5 37 " (cutoff:3.500A) Processing helix chain 'J5' and resid 85 through 93 removed outlier: 3.628A pdb=" N ASNJ5 91 " --> pdb=" O GLUJ5 87 " (cutoff:3.500A) Processing helix chain 'J5' and resid 113 through 120 removed outlier: 3.577A pdb=" N ARGJ5 118 " --> pdb=" O GLUJ5 114 " (cutoff:3.500A) Processing helix chain 'I5' and resid 36 through 49 removed outlier: 3.718A pdb=" N ALAI5 45 " --> pdb=" O ARGI5 41 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYSI5 46 " --> pdb=" O GLUI5 42 " (cutoff:3.500A) Processing helix chain 'I5' and resid 78 through 86 removed outlier: 3.617A pdb=" N LYSI5 83 " --> pdb=" O LEUI5 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYSI5 84 " --> pdb=" O ASPI5 80 " (cutoff:3.500A) Processing helix chain 'I5' and resid 87 through 93 Processing helix chain 'I5' and resid 104 through 116 removed outlier: 3.536A pdb=" N LYSI5 115 " --> pdb=" O LYSI5 111 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYSI5 116 " --> pdb=" O ASNI5 112 " (cutoff:3.500A) Processing helix chain 'I5' and resid 120 through 127 removed outlier: 3.866A pdb=" N ALAI5 127 " --> pdb=" O ALAI5 123 " (cutoff:3.500A) Processing helix chain 'M3' and resid 53 through 62 removed outlier: 3.781A pdb=" N LYSM3 60 " --> pdb=" O ASPM3 56 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLUM3 61 " --> pdb=" O LYSM3 57 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VALM3 62 " --> pdb=" O LEUM3 58 " (cutoff:3.500A) Processing helix chain 'M3' and resid 63 through 65 No H-bonds generated for 'chain 'M3' and resid 63 through 65' Processing helix chain 'M3' and resid 69 through 77 Processing helix chain 'M3' and resid 80 through 95 removed outlier: 3.582A pdb=" N LYSM3 94 " --> pdb=" O GLUM3 90 " (cutoff:3.500A) Processing helix chain 'O3' and resid 46 through 48 No H-bonds generated for 'chain 'O3' and resid 46 through 48' Processing helix chain 'O3' and resid 49 through 56 removed outlier: 3.985A pdb=" N ALAO3 56 " --> pdb=" O ASPO3 52 " (cutoff:3.500A) Processing helix chain 'O3' and resid 74 through 82 removed outlier: 3.592A pdb=" N HISO3 80 " --> pdb=" O SERO3 76 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SERO3 81 " --> pdb=" O CYSO3 77 " (cutoff:3.500A) Processing helix chain 'T3' and resid 11 through 21 removed outlier: 3.631A pdb=" N ARGT3 17 " --> pdb=" O LEUT3 13 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASPT3 19 " --> pdb=" O SERT3 15 " (cutoff:3.500A) Processing helix chain 'T3' and resid 24 through 32 removed outlier: 4.363A pdb=" N ALAT3 30 " --> pdb=" O GLNT3 26 " (cutoff:3.500A) Processing helix chain 'T3' and resid 32 through 38 removed outlier: 4.079A pdb=" N LEUT3 36 " --> pdb=" O LEUT3 32 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALAT3 38 " --> pdb=" O THRT3 34 " (cutoff:3.500A) Processing helix chain 'T3' and resid 129 through 136 Processing helix chain 'U3' and resid 11 through 21 Processing helix chain 'U3' and resid 34 through 36 No H-bonds generated for 'chain 'U3' and resid 34 through 36' Processing helix chain 'U3' and resid 50 through 68 removed outlier: 3.652A pdb=" N ALAU3 67 " --> pdb=" O ARGU3 63 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILEU3 68 " --> pdb=" O ALAU3 64 " (cutoff:3.500A) Processing helix chain 'U3' and resid 70 through 72 No H-bonds generated for 'chain 'U3' and resid 70 through 72' Processing helix chain 'U3' and resid 83 through 95 removed outlier: 3.674A pdb=" N LEUU3 88 " --> pdb=" O GLNU3 84 " (cutoff:3.500A) Processing helix chain 'U3' and resid 131 through 137 removed outlier: 3.672A pdb=" N THRU3 135 " --> pdb=" O HISU3 131 " (cutoff:3.500A) Processing helix chain 'U3' and resid 167 through 185 removed outlier: 3.728A pdb=" N VALU3 171 " --> pdb=" O GLYU3 167 " (cutoff:3.500A) Processing helix chain 'U3' and resid 198 through 203 Processing helix chain 'V3' and resid 23 through 26 Processing helix chain 'V3' and resid 57 through 63 removed outlier: 3.975A pdb=" N LYSV3 63 " --> pdb=" O SERV3 59 " (cutoff:3.500A) Processing helix chain 'V3' and resid 72 through 74 No H-bonds generated for 'chain 'V3' and resid 72 through 74' Processing helix chain 'V3' and resid 106 through 114 removed outlier: 3.519A pdb=" N METV3 110 " --> pdb=" O THRV3 106 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SERV3 112 " --> pdb=" O ASPV3 108 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N METV3 113 " --> pdb=" O LYSV3 109 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VALV3 114 " --> pdb=" O METV3 110 " (cutoff:3.500A) Processing helix chain 'V3' and resid 157 through 178 removed outlier: 3.651A pdb=" N GLNV3 163 " --> pdb=" O GLNV3 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYSV3 166 " --> pdb=" O ARGV3 162 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYSV3 167 " --> pdb=" O GLNV3 163 " (cutoff:3.500A) Processing helix chain 'V3' and resid 180 through 189 removed outlier: 3.665A pdb=" N ASNV3 186 " --> pdb=" O LYSV3 182 " (cutoff:3.500A) Processing helix chain 'V3' and resid 191 through 201 removed outlier: 3.968A pdb=" N LYSV3 195 " --> pdb=" O ASPV3 191 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASPV3 196 " --> pdb=" O SERV3 192 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILEV3 197 " --> pdb=" O ILEV3 193 " (cutoff:3.500A) Processing helix chain 'V3' and resid 224 through 233 Processing helix chain 'W3' and resid 64 through 72 removed outlier: 4.007A pdb=" N ASPW3 72 " --> pdb=" O ARGW3 68 " (cutoff:3.500A) Processing helix chain 'W3' and resid 77 through 84 removed outlier: 3.568A pdb=" N ILEW3 81 " --> pdb=" O SERW3 77 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHEW3 84 " --> pdb=" O GLUW3 80 " (cutoff:3.500A) Processing helix chain 'W3' and resid 91 through 99 removed outlier: 3.640A pdb=" N ASPW3 95 " --> pdb=" O SERW3 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHEW3 97 " --> pdb=" O ILEW3 93 " (cutoff:3.500A) Processing helix chain 'W3' and resid 146 through 161 removed outlier: 3.849A pdb=" N ILEW3 155 " --> pdb=" O ILEW3 151 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILEW3 156 " --> pdb=" O ARGW3 152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SERW3 161 " --> pdb=" O LEUW3 157 " (cutoff:3.500A) Processing helix chain 'W3' and resid 209 through 217 removed outlier: 3.710A pdb=" N LEUW3 213 " --> pdb=" O VALW3 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALAW3 217 " --> pdb=" O LEUW3 213 " (cutoff:3.500A) Processing helix chain 'W3' and resid 232 through 246 removed outlier: 4.023A pdb=" N LYSW3 238 " --> pdb=" O GLYW3 234 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILEW3 244 " --> pdb=" O THRW3 240 " (cutoff:3.500A) Processing helix chain 'W3' and resid 264 through 269 removed outlier: 3.853A pdb=" N GLUW3 268 " --> pdb=" O SERW3 264 " (cutoff:3.500A) Processing helix chain 'X3' and resid 3 through 20 removed outlier: 3.554A pdb=" N LYSX3 7 " --> pdb=" O ALAX3 3 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARGX3 15 " --> pdb=" O ARGX3 11 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 6 through 26 removed outlier: 3.514A pdb=" N GLYY3 15 " --> pdb=" O PHEY3 11 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASNY3 22 " --> pdb=" O LYSY3 18 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 27 through 32 removed outlier: 4.940A pdb=" N ALAY3 30 " --> pdb=" O ARGY3 27 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLUY3 31 " --> pdb=" O GLUY3 28 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 55 through 60 removed outlier: 4.184A pdb=" N GLYY3 60 " --> pdb=" O GLNY3 56 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 63 through 78 removed outlier: 3.602A pdb=" N ARGY3 67 " --> pdb=" O GLYY3 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALAY3 71 " --> pdb=" O ARGY3 67 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALY3 72 " --> pdb=" O GLUY3 68 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARGY3 76 " --> pdb=" O VALY3 72 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 97 through 112 removed outlier: 3.754A pdb=" N GLYY3 112 " --> pdb=" O LYSY3 108 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 114 through 129 removed outlier: 3.613A pdb=" N TYRY3 120 " --> pdb=" O ARGY3 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLYY3 121 " --> pdb=" O ARGY3 117 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 161 through 166 removed outlier: 3.611A pdb=" N VALY3 164 " --> pdb=" O GLYY3 161 " (cutoff:3.500A) Processing helix chain 'j3' and resid 15 through 19 Processing helix chain 'j3' and resid 37 through 41 removed outlier: 3.526A pdb=" N GLUj3 40 " --> pdb=" O LYSj3 37 " (cutoff:3.500A) Processing helix chain 'j3' and resid 45 through 50 removed outlier: 3.502A pdb=" N ASNj3 50 " --> pdb=" O ILEj3 46 " (cutoff:3.500A) Processing helix chain 'j3' and resid 57 through 67 Processing helix chain 'j3' and resid 132 through 136 Processing helix chain 'j3' and resid 247 through 258 removed outlier: 3.679A pdb=" N ALAj3 258 " --> pdb=" O LYSj3 254 " (cutoff:3.500A) Processing helix chain 'N3' and resid 61 through 65 removed outlier: 3.561A pdb=" N ALAN3 64 " --> pdb=" O PHEN3 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLNN3 65 " --> pdb=" O ARGN3 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N3' and resid 61 through 65' Processing helix chain 'N3' and resid 67 through 75 Processing helix chain 'N3' and resid 85 through 104 removed outlier: 3.988A pdb=" N THRN3 89 " --> pdb=" O LYSN3 85 " (cutoff:3.500A) Processing helix chain 'N3' and resid 107 through 117 Processing helix chain 'N3' and resid 118 through 120 No H-bonds generated for 'chain 'N3' and resid 118 through 120' Processing helix chain 'N3' and resid 142 through 162 removed outlier: 3.523A pdb=" N ALAN3 150 " --> pdb=" O ARGN3 146 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYSN3 155 " --> pdb=" O ILEN3 151 " (cutoff:3.500A) Processing helix chain 'N3' and resid 168 through 182 removed outlier: 3.501A pdb=" N ALAN3 174 " --> pdb=" O ALAN3 170 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALAN3 180 " --> pdb=" O GLUN3 176 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYSN3 182 " --> pdb=" O ILEN3 178 " (cutoff:3.500A) Processing helix chain 'N3' and resid 187 through 203 removed outlier: 3.542A pdb=" N ASPN3 194 " --> pdb=" O ILEN3 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLUN3 195 " --> pdb=" O LYSN3 191 " (cutoff:3.500A) Processing helix chain 'b3' and resid 20 through 25 removed outlier: 3.727A pdb=" N LEUb3 24 " --> pdb=" O ASPb3 20 " (cutoff:3.500A) Processing helix chain 'b3' and resid 26 through 28 No H-bonds generated for 'chain 'b3' and resid 26 through 28' Processing helix chain 'b3' and resid 137 through 146 Processing helix chain 'b3' and resid 181 through 219 removed outlier: 3.537A pdb=" N HISb3 187 " --> pdb=" O ARGb3 183 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYSb3 188 " --> pdb=" O VALb3 184 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYSb3 215 " --> pdb=" O LYSb3 211 " (cutoff:3.500A) Processing helix chain 'b3' and resid 220 through 236 removed outlier: 3.581A pdb=" N ARGb3 224 " --> pdb=" O ALAb3 220 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLUb3 226 " --> pdb=" O GLUb3 222 " (cutoff:3.500A) Processing helix chain 'c3' and resid 88 through 93 removed outlier: 3.880A pdb=" N ARGc3 92 " --> pdb=" O ASNc3 88 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THRc3 93 " --> pdb=" O GLUc3 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'c3' and resid 88 through 93' Processing helix chain 'c3' and resid 106 through 117 Processing helix chain 'c3' and resid 130 through 138 removed outlier: 3.744A pdb=" N GLUc3 134 " --> pdb=" O THRc3 130 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLUc3 135 " --> pdb=" O PROc3 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEUc3 137 " --> pdb=" O GLUc3 133 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASNc3 138 " --> pdb=" O GLUc3 134 " (cutoff:3.500A) Processing helix chain 'c3' and resid 143 through 154 removed outlier: 3.726A pdb=" N LYSc3 147 " --> pdb=" O LYSc3 143 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYSc3 148 " --> pdb=" O LYSc3 144 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASPc3 150 " --> pdb=" O GLNc3 146 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYSc3 154 " --> pdb=" O ASPc3 150 " (cutoff:3.500A) Processing helix chain 'c3' and resid 159 through 169 removed outlier: 4.742A pdb=" N GLNc3 165 " --> pdb=" O LEUc3 161 " (cutoff:3.500A) Processing helix chain 'c3' and resid 191 through 204 removed outlier: 3.562A pdb=" N LYSc3 201 " --> pdb=" O PHEc3 197 " (cutoff:3.500A) Processing helix chain 'd3' and resid 23 through 36 removed outlier: 3.563A pdb=" N LYSd3 30 " --> pdb=" O ASPd3 26 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLUd3 34 " --> pdb=" O LYSd3 30 " (cutoff:3.500A) Processing helix chain 'd3' and resid 40 through 63 removed outlier: 4.433A pdb=" N VALd3 46 " --> pdb=" O GLUd3 42 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLUd3 59 " --> pdb=" O LYSd3 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEUd3 60 " --> pdb=" O ALAd3 56 " (cutoff:3.500A) Processing helix chain 'd3' and resid 67 through 85 removed outlier: 3.754A pdb=" N PHEd3 72 " --> pdb=" O PROd3 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEUd3 81 " --> pdb=" O LEUd3 77 " (cutoff:3.500A) Processing helix chain 'd3' and resid 95 through 101 removed outlier: 6.034A pdb=" N LYSd3 101 " --> pdb=" O LEUd3 98 " (cutoff:3.500A) Processing helix chain 'd3' and resid 102 through 108 removed outlier: 3.655A pdb=" N LEUd3 106 " --> pdb=" O ILEd3 102 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARGd3 108 " --> pdb=" O ASPd3 104 " (cutoff:3.500A) Processing helix chain 'd3' and resid 109 through 117 removed outlier: 3.644A pdb=" N PHEd3 115 " --> pdb=" O GLNd3 111 " (cutoff:3.500A) Processing helix chain 'd3' and resid 122 through 132 removed outlier: 3.821A pdb=" N ARGd3 127 " --> pdb=" O ILEd3 123 " (cutoff:3.500A) Processing helix chain 'd3' and resid 151 through 155 removed outlier: 4.032A pdb=" N LYSd3 155 " --> pdb=" O ASPd3 152 " (cutoff:3.500A) Processing helix chain 'd3' and resid 171 through 186 removed outlier: 3.506A pdb=" N LYSd3 179 " --> pdb=" O ARGd3 175 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLYd3 183 " --> pdb=" O LYSd3 179 " (cutoff:3.500A) Processing helix chain 'e3' and resid 15 through 29 removed outlier: 3.884A pdb=" N GLNe3 19 " --> pdb=" O ASNe3 15 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILEe3 27 " --> pdb=" O LYSe3 23 " (cutoff:3.500A) Processing helix chain 'e3' and resid 34 through 44 Processing helix chain 'e3' and resid 62 through 71 removed outlier: 3.640A pdb=" N ALAe3 67 " --> pdb=" O LYSe3 63 " (cutoff:3.500A) Processing helix chain 'e3' and resid 81 through 90 Processing helix chain 'e3' and resid 121 through 129 removed outlier: 3.808A pdb=" N GLUe3 125 " --> pdb=" O LYSe3 121 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYRe3 127 " --> pdb=" O VALe3 123 " (cutoff:3.500A) Processing helix chain 'F3' and resid 79 through 94 removed outlier: 3.781A pdb=" N TYRF3 88 " --> pdb=" O LYSF3 84 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYSF3 89 " --> pdb=" O GLUF3 85 " (cutoff:3.500A) Processing helix chain 'F3' and resid 96 through 107 removed outlier: 4.069A pdb=" N GLYF3 101 " --> pdb=" O PROF3 97 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VALF3 102 " --> pdb=" O SERF3 98 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEF3 103 " --> pdb=" O GLNF3 99 " (cutoff:3.500A) Processing helix chain 'F3' and resid 112 through 117 Processing helix chain 'F3' and resid 120 through 129 removed outlier: 3.578A pdb=" N SERF3 127 " --> pdb=" O ARGF3 123 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSF3 128 " --> pdb=" O ILEF3 124 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLYF3 129 " --> pdb=" O LEUF3 125 " (cutoff:3.500A) Processing helix chain 'F3' and resid 135 through 155 removed outlier: 3.678A pdb=" N HISF3 140 " --> pdb=" O GLUF3 136 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARGF3 154 " --> pdb=" O LYSF3 150 " (cutoff:3.500A) Processing helix chain 'F3' and resid 158 through 180 removed outlier: 3.938A pdb=" N ILEF3 166 " --> pdb=" O LYSF3 162 " (cutoff:3.500A) Processing helix chain 'F3' and resid 196 through 200 Processing helix chain 'E3' and resid 8 through 18 removed outlier: 4.026A pdb=" N TYRE3 12 " --> pdb=" O ARGE3 8 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEUE3 14 " --> pdb=" O ALAE3 10 " (cutoff:3.500A) Processing helix chain 'E3' and resid 48 through 55 Processing helix chain 'E3' and resid 74 through 82 removed outlier: 4.277A pdb=" N TYRE3 78 " --> pdb=" O GLUE3 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASPE3 81 " --> pdb=" O GLNE3 77 " (cutoff:3.500A) Processing helix chain 'H3' and resid 39 through 45 Processing helix chain 'H3' and resid 46 through 51 Processing sheet with id=AA1, first strand: chain 'Z2' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'Z2' and resid 48 through 51 removed outlier: 3.504A pdb=" N VALZ2 38 " --> pdb=" O GLNZ2 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALAZ2 36 " --> pdb=" O METZ2 50 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ARGZ2 35 " --> pdb=" O VALZ2 30 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VALZ2 30 " --> pdb=" O ARGZ2 35 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEUZ2 37 " --> pdb=" O VALZ2 28 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARGZ2 11 " --> pdb=" O ILEZ2 27 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VALZ2 12 " --> pdb=" O THRZ2 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'p2' and resid 3 through 5 removed outlier: 5.961A pdb=" N ARGp2 3 " --> pdb=" O THRp2 44 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VALp2 46 " --> pdb=" O ARGp2 3 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILEp2 5 " --> pdb=" O VALp2 46 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SERp2 22 " --> pdb=" O ARGp2 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'w2' and resid 7 through 10 removed outlier: 6.242A pdb=" N LEUw2 7 " --> pdb=" O VALw2 34 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VALw2 36 " --> pdb=" O LEUw2 7 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEUw2 9 " --> pdb=" O VALw2 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H2' and resid 16 through 22 removed outlier: 5.712A pdb=" N LYSH2 16 " --> pdb=" O LEUH2 150 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEUH2 150 " --> pdb=" O LYSH2 16 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARGH2 18 " --> pdb=" O METH2 148 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N METH2 148 " --> pdb=" O ARGH2 18 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SERH2 20 " --> pdb=" O ILEH2 146 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILEH2 146 " --> pdb=" O SERH2 20 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HISH2 116 " --> pdb=" O ILEH2 149 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THRH2 151 " --> pdb=" O ILEH2 114 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILEH2 114 " --> pdb=" O THRH2 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H2' and resid 58 through 59 Processing sheet with id=AA7, first strand: chain 'H2' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'S2' and resid 61 through 62 removed outlier: 4.844A pdb=" N VALS2 100 " --> pdb=" O ALAS2 80 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VALS2 82 " --> pdb=" O VALS2 100 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALAS2 102 " --> pdb=" O VALS2 82 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLYS2 84 " --> pdb=" O ALAS2 102 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARGS2 104 " --> pdb=" O GLYS2 84 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VALS2 100 " --> pdb=" O LEUS2 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S2' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain '32' and resid 22 through 24 removed outlier: 3.705A pdb=" N ILE32 51 " --> pdb=" O TRP32 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '52' and resid 42 through 43 removed outlier: 5.229A pdb=" N ILE52 160 " --> pdb=" O VAL52 185 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL52 159 " --> pdb=" O TYR52 92 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS52 165 " --> pdb=" O VAL52 86 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL52 86 " --> pdb=" O HIS52 165 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL52 87 " --> pdb=" O PHE52 106 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE52 106 " --> pdb=" O VAL52 87 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE52 89 " --> pdb=" O THR52 104 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR52 104 " --> pdb=" O ILE52 89 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY52 91 " --> pdb=" O PHE52 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '52' and resid 42 through 43 removed outlier: 5.229A pdb=" N ILE52 160 " --> pdb=" O VAL52 185 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL52 159 " --> pdb=" O TYR52 92 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS52 165 " --> pdb=" O VAL52 86 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL52 86 " --> pdb=" O HIS52 165 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '52' and resid 276 through 278 removed outlier: 3.545A pdb=" N ARG52 277 " --> pdb=" O GLY52 221 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL52 222 " --> pdb=" O VAL52 344 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL52 344 " --> pdb=" O VAL52 222 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG52 343 " --> pdb=" O LYS52 50 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE52 330 " --> pdb=" O ILE52 287 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE52 287 " --> pdb=" O PHE52 330 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET52 332 " --> pdb=" O TYR52 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '52' and resid 57 through 58 Processing sheet with id=AB6, first strand: chain '52' and resid 225 through 228 removed outlier: 5.980A pdb=" N LYS52 272 " --> pdb=" O LYS52 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '52' and resid 292 through 293 removed outlier: 3.837A pdb=" N LEU52 292 " --> pdb=" O LEU52 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '62' and resid 59 through 66 removed outlier: 6.521A pdb=" N VAL62 13 " --> pdb=" O VAL62 62 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS62 64 " --> pdb=" O LYS62 11 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LYS62 11 " --> pdb=" O CYS62 64 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN62 66 " --> pdb=" O GLU62 9 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLU62 9 " --> pdb=" O GLN62 66 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG62 8 " --> pdb=" O ALA62 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '62' and resid 90 through 99 removed outlier: 3.656A pdb=" N LYS62 76 " --> pdb=" O ASP62 99 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN62 77 " --> pdb=" O ILE62 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '72' and resid 84 through 92 removed outlier: 3.794A pdb=" N VAL72 91 " --> pdb=" O VAL72 72 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN72 66 " --> pdb=" O GLY72 73 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL72 75 " --> pdb=" O VAL72 64 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL72 64 " --> pdb=" O VAL72 75 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASN72 77 " --> pdb=" O GLY72 62 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY72 62 " --> pdb=" O ASN72 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '72' and resid 139 through 141 removed outlier: 3.644A pdb=" N HIS72 139 " --> pdb=" O VALU2 82 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHEU2 80 " --> pdb=" O VAL72 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '82' and resid 21 through 24 Processing sheet with id=AC4, first strand: chain '82' and resid 48 through 49 removed outlier: 3.524A pdb=" N VAL82 49 " --> pdb=" O LYS82 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '82' and resid 101 through 103 Processing sheet with id=AC6, first strand: chain 'k2' and resid 20 through 21 Processing sheet with id=AC7, first strand: chain 'k2' and resid 25 through 28 removed outlier: 7.087A pdb=" N METk2 62 " --> pdb=" O ILEk2 40 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VALk2 42 " --> pdb=" O METk2 60 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N METk2 60 " --> pdb=" O VALk2 42 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLYk2 103 " --> pdb=" O VALk2 25 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASNk2 27 " --> pdb=" O GLYk2 103 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILEk2 105 " --> pdb=" O ASNk2 27 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'k2' and resid 88 through 89 removed outlier: 3.506A pdb=" N ALAl2 22 " --> pdb=" O TYRk2 97 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'k2' and resid 121 through 122 removed outlier: 5.416A pdb=" N VALk2 121 " --> pdb=" O ALAk2 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'l2' and resid 4 through 5 removed outlier: 3.704A pdb=" N GLUl2 4 " --> pdb=" O ILEl2 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILEl2 13 " --> pdb=" O GLUl2 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'm2' and resid 79 through 80 removed outlier: 3.829A pdb=" N PHEm2 79 " --> pdb=" O ILEm2 99 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYSm2 134 " --> pdb=" O VALm2 100 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYSm2 123 " --> pdb=" O ARGm2 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'o2' and resid 31 through 33 Processing sheet with id=AD4, first strand: chain 'o2' and resid 79 through 82 removed outlier: 7.258A pdb=" N VALo2 79 " --> pdb=" O VALo2 73 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VALo2 73 " --> pdb=" O VALo2 79 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYRo2 81 " --> pdb=" O VALo2 71 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASPo2 53 " --> pdb=" O VALo2 70 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLUo2 54 " --> pdb=" O THRo2 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'o2' and resid 86 through 88 Processing sheet with id=AD6, first strand: chain 'q2' and resid 72 through 74 Processing sheet with id=AD7, first strand: chain 'q2' and resid 100 through 102 removed outlier: 6.651A pdb=" N ILEq2 101 " --> pdb=" O LYSq2 125 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VALq2 124 " --> pdb=" O VALq2 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '13' and resid 26 through 29 removed outlier: 6.624A pdb=" N LYS13 26 " --> pdb=" O ILE13 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU13 94 " --> pdb=" O ILE13 47 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU13 45 " --> pdb=" O ILE13 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 't2' and resid 7 through 9 Processing sheet with id=AE1, first strand: chain 't2' and resid 64 through 66 Processing sheet with id=AE2, first strand: chain 't2' and resid 152 through 154 removed outlier: 6.374A pdb=" N LEUt2 152 " --> pdb=" O TRPt2 252 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 't2' and resid 188 through 189 Processing sheet with id=AE4, first strand: chain 'u2' and resid 22 through 28 Processing sheet with id=AE5, first strand: chain 'v2' and resid 78 through 79 Processing sheet with id=AE6, first strand: chain 'x2' and resid 6 through 7 Processing sheet with id=AE7, first strand: chain 'x2' and resid 9 through 16 removed outlier: 5.614A pdb=" N PHEx2 11 " --> pdb=" O LYSx2 29 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYSx2 29 " --> pdb=" O PHEx2 11 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLYx2 13 " --> pdb=" O LEUx2 27 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THRx2 25 " --> pdb=" O LYSx2 15 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N METx2 83 " --> pdb=" O HISx2 78 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARGx2 76 " --> pdb=" O ARGx2 85 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'y2' and resid 20 through 25 removed outlier: 3.846A pdb=" N ARGy2 29 " --> pdb=" O THRy2 25 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '92' and resid 71 through 77 removed outlier: 7.043A pdb=" N LEU92 58 " --> pdb=" O ILE92 48 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE92 48 " --> pdb=" O LEU92 58 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS92 60 " --> pdb=" O LYS92 46 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG92 64 " --> pdb=" O LYS92 42 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS92 42 " --> pdb=" O ARG92 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '92' and resid 102 through 103 removed outlier: 3.748A pdb=" N LEU92 102 " --> pdb=" O ALA92 164 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA92 164 " --> pdb=" O LEU92 102 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG92 147 " --> pdb=" O ILE92 137 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N HIS92 139 " --> pdb=" O LYS92 145 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS92 145 " --> pdb=" O HIS92 139 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E2' and resid 102 through 103 Processing sheet with id=AF3, first strand: chain 'F2' and resid 7 through 11 removed outlier: 3.564A pdb=" N THRF2 24 " --> pdb=" O ARGF2 69 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G2' and resid 72 through 77 removed outlier: 5.301A pdb=" N ILEG2 74 " --> pdb=" O TYRG2 66 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYRG2 66 " --> pdb=" O ILEG2 74 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I2' and resid 48 through 51 removed outlier: 7.063A pdb=" N ILEI2 54 " --> pdb=" O ARGI2 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J2' and resid 17 through 20 Processing sheet with id=AF7, first strand: chain 'J2' and resid 50 through 53 Processing sheet with id=AF8, first strand: chain 'K2' and resid 51 through 54 removed outlier: 3.528A pdb=" N LEUK2 54 " --> pdb=" O PHEK2 88 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHEK2 88 " --> pdb=" O LEUK2 54 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRK2 91 " --> pdb=" O LYSK2 26 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYSK2 26 " --> pdb=" O THRK2 91 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N CYSK2 27 " --> pdb=" O VALK2 192 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VALK2 192 " --> pdb=" O CYSK2 27 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILEK2 29 " --> pdb=" O GLNK2 190 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLNK2 190 " --> pdb=" O ILEK2 29 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K2' and resid 146 through 147 Processing sheet with id=AG1, first strand: chain 'L2' and resid 35 through 37 removed outlier: 3.638A pdb=" N METX2 136 " --> pdb=" O METL2 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HISX2 166 " --> pdb=" O HISL2 51 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L2' and resid 59 through 61 removed outlier: 4.202A pdb=" N ILEL2 97 " --> pdb=" O GLNX2 123 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THRX2 125 " --> pdb=" O HISL2 95 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HISL2 95 " --> pdb=" O THRX2 125 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M2' and resid 15 through 17 removed outlier: 3.950A pdb=" N LEUM2 62 " --> pdb=" O VALM2 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VALM2 73 " --> pdb=" O LEUM2 62 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILEM2 64 " --> pdb=" O ILEM2 71 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R2' and resid 45 through 47 removed outlier: 3.677A pdb=" N VALR2 47 " --> pdb=" O ILER2 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T2' and resid 190 through 192 removed outlier: 4.111A pdb=" N LYST2 169 " --> pdb=" O LEUT2 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THRT2 179 " --> pdb=" O PHET2 167 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHET2 167 " --> pdb=" O THRT2 179 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VALT2 165 " --> pdb=" O LEUT2 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THRT2 151 " --> pdb=" O PHET2 167 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILET2 152 " --> pdb=" O THRT2 200 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U2' and resid 139 through 142 removed outlier: 4.194A pdb=" N ASNU2 118 " --> pdb=" O ARGU2 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'U2' and resid 158 through 161 removed outlier: 3.728A pdb=" N ILEU2 161 " --> pdb=" O LYSU2 164 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V2' and resid 181 through 184 removed outlier: 5.844A pdb=" N VALV2 155 " --> pdb=" O CYSV2 182 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILEV2 184 " --> pdb=" O VALV2 155 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILEV2 157 " --> pdb=" O ILEV2 184 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W2' and resid 19 through 22 removed outlier: 3.727A pdb=" N GLNW2 19 " --> pdb=" O VALW2 68 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W2' and resid 28 through 31 removed outlier: 3.578A pdb=" N GLYW2 43 " --> pdb=" O GLYW2 40 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W2' and resid 144 through 147 removed outlier: 3.514A pdb=" N METW2 103 " --> pdb=" O LEUW2 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEUW2 157 " --> pdb=" O TYRW2 101 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARGW2 100 " --> pdb=" O LYSW2 195 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYSW2 195 " --> pdb=" O ARGW2 100 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYSW2 102 " --> pdb=" O SERW2 193 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'W2' and resid 113 through 116 Processing sheet with id=AH4, first strand: chain 'X2' and resid 190 through 193 removed outlier: 3.502A pdb=" N ILEX2 191 " --> pdb=" O LYSX2 198 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y2' and resid 49 through 51 removed outlier: 3.623A pdb=" N VALY2 49 " --> pdb=" O HISY2 71 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VALY2 133 " --> pdb=" O ARGY2 18 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEUY2 20 " --> pdb=" O TYRY2 131 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYRY2 131 " --> pdb=" O LEUY2 20 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEUY2 22 " --> pdb=" O ASPY2 129 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASPY2 129 " --> pdb=" O LEUY2 22 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y2' and resid 93 through 94 Processing sheet with id=AH7, first strand: chain 'a7' and resid 58 through 60 Processing sheet with id=AH8, first strand: chain '12' and resid 36 through 38 removed outlier: 6.344A pdb=" N GLU12 131 " --> pdb=" O TRP12 120 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TRP12 120 " --> pdb=" O GLU12 131 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE12 133 " --> pdb=" O SER12 118 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER12 118 " --> pdb=" O ILE12 133 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ILE12 135 " --> pdb=" O LEU12 116 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU12 116 " --> pdb=" O ILE12 135 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '22' and resid 71 through 76 removed outlier: 7.589A pdb=" N HIS22 40 " --> pdb=" O ASN22 28 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASN22 28 " --> pdb=" O HIS22 40 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU22 42 " --> pdb=" O VAL22 26 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL22 26 " --> pdb=" O LEU22 42 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS22 9 " --> pdb=" O ILE22 25 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL22 10 " --> pdb=" O THR22 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR22 83 " --> pdb=" O VAL22 10 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '42' and resid 166 through 168 Processing sheet with id=AI2, first strand: chain '42' and resid 50 through 52 Processing sheet with id=AI3, first strand: chain 'I3' and resid 50 through 51 removed outlier: 3.595A pdb=" N ASPI3 90 " --> pdb=" O LYSI3 51 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I3' and resid 50 through 51 removed outlier: 3.595A pdb=" N ASPI3 90 " --> pdb=" O LYSI3 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SERI3 26 " --> pdb=" O HISI3 85 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILEI3 20 " --> pdb=" O LEUI3 91 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G3' and resid 109 through 112 removed outlier: 6.868A pdb=" N VALG3 87 " --> pdb=" O THRG3 78 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILEG3 125 " --> pdb=" O VALG3 145 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VALG3 145 " --> pdb=" O ILEG3 125 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THRG3 127 " --> pdb=" O LEUG3 143 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G3' and resid 91 through 95 removed outlier: 3.669A pdb=" N TYRG3 92 " --> pdb=" O ARGG3 105 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'f3' and resid 10 through 13 removed outlier: 3.512A pdb=" N LEUf3 58 " --> pdb=" O LYSf3 10 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'f3' and resid 17 through 19 removed outlier: 6.835A pdb=" N GLNf3 29 " --> pdb=" O LEUf3 18 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'f3' and resid 46 through 47 Processing sheet with id=AJ1, first strand: chain 'P3' and resid 285 through 289 removed outlier: 3.547A pdb=" N ALAP3 297 " --> pdb=" O ILEP3 289 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILEP3 298 " --> pdb=" O VALP3 331 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILEP3 333 " --> pdb=" O ILEP3 298 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILEP3 300 " --> pdb=" O ILEP3 333 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P3' and resid 423 through 426 removed outlier: 6.007A pdb=" N ILEP3 392 " --> pdb=" O ASNP3 424 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLUP3 426 " --> pdb=" O ILEP3 392 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VALP3 394 " --> pdb=" O GLUP3 426 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYSP3 393 " --> pdb=" O ARGP3 381 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'a5' and resid 44 through 45 removed outlier: 3.615A pdb=" N HISa5 94 " --> pdb=" O GLYa5 29 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'A3' and resid 93 through 97 Processing sheet with id=AJ5, first strand: chain 'B3' and resid 39 through 40 Processing sheet with id=AJ6, first strand: chain 'B3' and resid 39 through 40 removed outlier: 7.107A pdb=" N LYSB3 59 " --> pdb=" O VALB3 96 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VALB3 98 " --> pdb=" O LYSB3 59 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D3' and resid 32 through 39 removed outlier: 3.634A pdb=" N GLUD3 38 " --> pdb=" O GLND3 49 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLND3 49 " --> pdb=" O GLUD3 38 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'G5' and resid 13 through 15 removed outlier: 3.837A pdb=" N LEUG5 13 " --> pdb=" O ILEG5 20 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H5' and resid 80 through 82 removed outlier: 4.120A pdb=" N GLYH5 81 " --> pdb=" O SERH5 93 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SERH5 93 " --> pdb=" O GLYH5 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'H5' and resid 113 through 116 removed outlier: 3.563A pdb=" N GLYH5 120 " --> pdb=" O ASPH5 116 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'J5' and resid 71 through 74 removed outlier: 3.745A pdb=" N METJ5 111 " --> pdb=" O LEUJ5 104 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J5' and resid 80 through 81 removed outlier: 3.698A pdb=" N GLYJ5 123 " --> pdb=" O VALJ5 81 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I5' and resid 8 through 14 removed outlier: 4.401A pdb=" N PHEI5 12 " --> pdb=" O GLNI5 22 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLNI5 22 " --> pdb=" O PHEI5 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N METI5 23 " --> pdb=" O GLYI5 73 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLYI5 73 " --> pdb=" O METI5 23 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LYSI5 68 " --> pdb=" O THRI5 62 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THRI5 62 " --> pdb=" O LYSI5 68 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THRI5 70 " --> pdb=" O PHEI5 60 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHEI5 60 " --> pdb=" O THRI5 70 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'L3' and resid 32 through 35 Processing sheet with id=AK6, first strand: chain 'L3' and resid 54 through 55 removed outlier: 6.784A pdb=" N VALL3 54 " --> pdb=" O LEUL3 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THRL3 67 " --> pdb=" O LYSL3 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYSL3 70 " --> pdb=" O THRL3 67 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'M3' and resid 98 through 102 removed outlier: 6.180A pdb=" N LEUM3 99 " --> pdb=" O THRM3 110 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THRM3 110 " --> pdb=" O LEUM3 99 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'O3' and resid 20 through 22 Processing sheet with id=AK9, first strand: chain 'O3' and resid 36 through 43 removed outlier: 3.565A pdb=" N VALO3 69 " --> pdb=" O VALO3 40 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Q3' and resid 25 through 26 removed outlier: 4.284A pdb=" N SERQ3 34 " --> pdb=" O LYSQ3 26 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'a3' and resid 4 through 11 removed outlier: 6.829A pdb=" N VALa3 309 " --> pdb=" O ARGa3 8 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THRa3 10 " --> pdb=" O VALa3 307 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VALa3 307 " --> pdb=" O THRa3 10 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'a3' and resid 20 through 22 removed outlier: 3.541A pdb=" N GLNa3 20 " --> pdb=" O ALAa3 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEUa3 32 " --> pdb=" O ALAa3 22 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILEa3 31 " --> pdb=" O TRPa3 43 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARGa3 57 " --> pdb=" O METa3 42 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYSa3 44 " --> pdb=" O PROa3 55 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'a3' and resid 68 through 70 removed outlier: 3.703A pdb=" N SERa3 80 " --> pdb=" O ARGa3 88 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARGa3 88 " --> pdb=" O SERa3 80 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARGa3 99 " --> pdb=" O LEUa3 89 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASPa3 91 " --> pdb=" O THRa3 97 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THRa3 97 " --> pdb=" O ASPa3 91 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'a3' and resid 108 through 113 removed outlier: 4.205A pdb=" N SERa3 122 " --> pdb=" O LYSa3 130 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYSa3 130 " --> pdb=" O SERa3 122 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILEa3 129 " --> pdb=" O THRa3 141 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THRa3 141 " --> pdb=" O ILEa3 129 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEUa3 131 " --> pdb=" O LYSa3 139 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'a3' and resid 151 through 156 removed outlier: 4.326A pdb=" N CYSa3 153 " --> pdb=" O CYSa3 168 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLYa3 169 " --> pdb=" O LEUa3 173 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEUa3 173 " --> pdb=" O GLYa3 169 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VALa3 174 " --> pdb=" O ASNa3 187 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASNa3 187 " --> pdb=" O VALa3 174 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VALa3 176 " --> pdb=" O LYSa3 185 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'a3' and resid 197 through 198 removed outlier: 4.026A pdb=" N THRa3 197 " --> pdb=" O GLYa3 210 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLYa3 210 " --> pdb=" O THRa3 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'a3' and resid 215 through 217 Processing sheet with id=AL9, first strand: chain 'a3' and resid 238 through 241 removed outlier: 3.504A pdb=" N LYSa3 257 " --> pdb=" O ALAa3 250 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASPa3 260 " --> pdb=" O ILEa3 266 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILEa3 266 " --> pdb=" O ASPa3 260 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'T3' and resid 72 through 74 removed outlier: 6.731A pdb=" N LEUT3 101 " --> pdb=" O VALT3 123 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'T3' and resid 56 through 58 Processing sheet with id=AM3, first strand: chain 'U3' and resid 38 through 41 removed outlier: 6.910A pdb=" N ILEU3 48 " --> pdb=" O TYRU3 39 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'U3' and resid 97 through 99 removed outlier: 6.682A pdb=" N VALU3 74 " --> pdb=" O THRU3 97 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILEU3 99 " --> pdb=" O VALU3 74 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VALU3 76 " --> pdb=" O ILEU3 99 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'V3' and resid 28 through 34 removed outlier: 6.753A pdb=" N ASPV3 29 " --> pdb=" O LEUV3 48 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEUV3 48 " --> pdb=" O ASPV3 29 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYRV3 31 " --> pdb=" O LYSV3 46 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYSV3 46 " --> pdb=" O TYRV3 31 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VALV3 33 " --> pdb=" O ILEV3 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILEV3 44 " --> pdb=" O VALV3 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM5 Processing sheet with id=AM6, first strand: chain 'V3' and resid 69 through 70 removed outlier: 3.545A pdb=" N LYSV3 83 " --> pdb=" O ASPV3 104 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VALV3 210 " --> pdb=" O PHEV3 142 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHEV3 142 " --> pdb=" O VALV3 210 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VALV3 212 " --> pdb=" O VALV3 140 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VALV3 140 " --> pdb=" O VALV3 212 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYSV3 214 " --> pdb=" O PHEV3 138 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEUV3 134 " --> pdb=" O LEUV3 218 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'V3' and resid 87 through 92 removed outlier: 5.918A pdb=" N THRV3 88 " --> pdb=" O ASNV3 99 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASNV3 99 " --> pdb=" O THRV3 88 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'W3' and resid 108 through 114 removed outlier: 3.814A pdb=" N LYSW3 108 " --> pdb=" O PHEW3 127 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'W3' and resid 184 through 188 removed outlier: 3.501A pdb=" N GLYW3 186 " --> pdb=" O VALW3 193 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VALW3 191 " --> pdb=" O CYSW3 188 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'Y3' and resid 34 through 40 removed outlier: 3.972A pdb=" N GLYY3 36 " --> pdb=" O LEUY3 51 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEUY3 51 " --> pdb=" O GLYY3 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLUY3 38 " --> pdb=" O ILEY3 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARGY3 40 " --> pdb=" O GLUY3 47 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLUY3 47 " --> pdb=" O ARGY3 40 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILEY3 48 " --> pdb=" O GLUY3 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLUY3 89 " --> pdb=" O ILEY3 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALAY3 52 " --> pdb=" O GLUY3 89 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'Y3' and resid 148 through 155 removed outlier: 4.223A pdb=" N GLYY3 133 " --> pdb=" O METY3 189 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SERY3 139 " --> pdb=" O GLYY3 183 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'j3' and resid 9 through 10 removed outlier: 4.183A pdb=" N LEUj3 9 " --> pdb=" O ALAj3 28 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'j3' and resid 75 through 76 removed outlier: 4.028A pdb=" N ILEj3 72 " --> pdb=" O LYSj3 75 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'j3' and resid 123 through 125 Processing sheet with id=AN6, first strand: chain 'j3' and resid 192 through 194 Processing sheet with id=AN7, first strand: chain 'j3' and resid 207 through 211 Processing sheet with id=AN8, first strand: chain 'j3' and resid 229 through 230 Processing sheet with id=AN9, first strand: chain 'b3' and resid 12 through 17 removed outlier: 8.014A pdb=" N LEUb3 111 " --> pdb=" O LYSb3 2 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASNb3 4 " --> pdb=" O LEUb3 111 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILEb3 113 " --> pdb=" O ASNb3 4 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SERb3 6 " --> pdb=" O ILEb3 113 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N LYSb3 115 " --> pdb=" O SERb3 6 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VALb3 49 " --> pdb=" O VALb3 114 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'b3' and resid 56 through 57 Processing sheet with id=AO2, first strand: chain 'b3' and resid 72 through 77 removed outlier: 3.560A pdb=" N VALb3 97 " --> pdb=" O VALb3 73 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'c3' and resid 37 through 38 removed outlier: 4.770A pdb=" N TYRc3 55 " --> pdb=" O VALc3 46 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VALc3 46 " --> pdb=" O TYRc3 55 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALAc3 57 " --> pdb=" O HISc3 44 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HISc3 44 " --> pdb=" O ALAc3 57 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'c3' and resid 62 through 63 removed outlier: 7.046A pdb=" N ILEc3 78 " --> pdb=" O ASPc3 105 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASPc3 105 " --> pdb=" O ILEc3 78 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASPc3 80 " --> pdb=" O LEUc3 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUc3 103 " --> pdb=" O ASPc3 80 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILEc3 101 " --> pdb=" O VALc3 82 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYSc3 100 " --> pdb=" O ILEc3 175 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILEc3 175 " --> pdb=" O CYSc3 100 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'c3' and resid 66 through 67 removed outlier: 3.695A pdb=" N CYSc3 72 " --> pdb=" O TRPc3 67 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'd3' and resid 140 through 141 removed outlier: 3.819A pdb=" N GLNd3 140 " --> pdb=" O VALd3 137 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASPd3 158 " --> pdb=" O ARGd3 136 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'e3' and resid 31 through 33 Processing sheet with id=AO8, first strand: chain 'e3' and resid 50 through 53 removed outlier: 6.544A pdb=" N CYSe3 50 " --> pdb=" O ILEe3 77 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VALe3 79 " --> pdb=" O CYSe3 50 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEUe3 52 " --> pdb=" O VALe3 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO8 Processing sheet with id=AO9, first strand: chain 'E3' and resid 20 through 24 removed outlier: 3.629A pdb=" N TRPE3 69 " --> pdb=" O METE3 21 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHEE3 67 " --> pdb=" O ALAE3 23 " (cutoff:3.500A) 2855 hydrogen bonds defined for protein. 7923 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4493 hydrogen bonds 7812 hydrogen bond angles 0 basepair planarities 1714 basepair parallelities 2706 stacking parallelities Total time for adding SS restraints: 458.57 Time building geometry restraints manager: 89.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 1219 1.22 - 1.37: 71065 1.37 - 1.52: 123106 1.52 - 1.67: 49608 1.67 - 1.82: 686 Bond restraints: 245684 Sorted by residual: bond pdb=" CG PROA3 87 " pdb=" CD PROA3 87 " ideal model delta sigma weight residual 1.503 1.073 0.430 3.40e-02 8.65e+02 1.60e+02 bond pdb=" CG PROY3 80 " pdb=" CD PROY3 80 " ideal model delta sigma weight residual 1.503 1.097 0.406 3.40e-02 8.65e+02 1.43e+02 bond pdb=" C METW3 61 " pdb=" N PROW3 62 " ideal model delta sigma weight residual 1.329 1.398 -0.070 1.20e-02 6.94e+03 3.37e+01 bond pdb=" C THR62 24 " pdb=" N PRO62 25 " ideal model delta sigma weight residual 1.329 1.394 -0.064 1.18e-02 7.18e+03 2.99e+01 bond pdb=" CG PROE3 41 " pdb=" CD PROE3 41 " ideal model delta sigma weight residual 1.503 1.354 0.149 3.40e-02 8.65e+02 1.92e+01 ... (remaining 245679 not shown) Histogram of bond angle deviations from ideal: 76.94 - 88.80: 4 88.80 - 100.65: 446 100.65 - 112.51: 168927 112.51 - 124.37: 166546 124.37 - 136.22: 25867 Bond angle restraints: 361790 Sorted by residual: angle pdb=" N PROY3 80 " pdb=" CD PROY3 80 " pdb=" CG PROY3 80 " ideal model delta sigma weight residual 103.20 76.94 26.26 1.50e+00 4.44e-01 3.06e+02 angle pdb=" N PROA3 87 " pdb=" CD PROA3 87 " pdb=" CG PROA3 87 " ideal model delta sigma weight residual 103.20 78.87 24.33 1.50e+00 4.44e-01 2.63e+02 angle pdb=" CA PROY3 80 " pdb=" CB PROY3 80 " pdb=" CG PROY3 80 " ideal model delta sigma weight residual 104.50 82.51 21.99 1.90e+00 2.77e-01 1.34e+02 angle pdb=" CA PROA3 87 " pdb=" CB PROA3 87 " pdb=" CG PROA3 87 " ideal model delta sigma weight residual 104.50 85.53 18.97 1.90e+00 2.77e-01 9.97e+01 angle pdb=" CA PROE3 41 " pdb=" N PROE3 41 " pdb=" CD PROE3 41 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.14e+01 ... (remaining 361785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 128251 35.99 - 71.98: 5899 71.98 - 107.98: 589 107.98 - 143.97: 106 143.97 - 179.96: 157 Dihedral angle restraints: 135002 sinusoidal: 100809 harmonic: 34193 Sorted by residual: dihedral pdb=" CA VALM2 143 " pdb=" C VALM2 143 " pdb=" N ASPM2 144 " pdb=" CA ASPM2 144 " ideal model delta harmonic sigma weight residual -180.00 -116.79 -63.21 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA GLUC3 94 " pdb=" C GLUC3 94 " pdb=" N ILEC3 95 " pdb=" CA ILEC3 95 " ideal model delta harmonic sigma weight residual 180.00 -122.51 -57.49 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" C4' CK31574 " pdb=" C3' CK31574 " pdb=" C2' CK31574 " pdb=" C1' CK31574 " ideal model delta sinusoidal sigma weight residual -35.00 36.12 -71.12 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 134999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 42615 0.088 - 0.176: 2376 0.176 - 0.264: 203 0.264 - 0.352: 28 0.352 - 0.440: 2 Chirality restraints: 45224 Sorted by residual: chirality pdb=" C3' Ue21440 " pdb=" C4' Ue21440 " pdb=" O3' Ue21440 " pdb=" C2' Ue21440 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA PHED3 8 " pdb=" N PHED3 8 " pdb=" C PHED3 8 " pdb=" CB PHED3 8 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILET3 66 " pdb=" CA ILET3 66 " pdb=" CG1 ILET3 66 " pdb=" CG2 ILET3 66 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 45221 not shown) Planarity restraints: 22751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPr2 16 " -0.062 2.00e-02 2.50e+03 4.64e-02 5.38e+01 pdb=" CG TRPr2 16 " 0.122 2.00e-02 2.50e+03 pdb=" CD1 TRPr2 16 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRPr2 16 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRPr2 16 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRPr2 16 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRPr2 16 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRPr2 16 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRPr2 16 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRPr2 16 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASNG5 73 " 0.117 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PROG5 74 " -0.299 5.00e-02 4.00e+02 pdb=" CA PROG5 74 " 0.097 5.00e-02 4.00e+02 pdb=" CD PROG5 74 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYSa7 11 " -0.097 5.00e-02 4.00e+02 1.42e-01 3.24e+01 pdb=" N PROa7 12 " 0.246 5.00e-02 4.00e+02 pdb=" CA PROa7 12 " -0.072 5.00e-02 4.00e+02 pdb=" CD PROa7 12 " -0.076 5.00e-02 4.00e+02 ... (remaining 22748 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 2980 2.57 - 3.16: 185192 3.16 - 3.74: 412802 3.74 - 4.32: 553843 4.32 - 4.90: 813331 Nonbonded interactions: 1968148 Sorted by model distance: nonbonded pdb=" OD1 ASNp2 24 " pdb=" O LYSp2 67 " model vdw 1.992 3.040 nonbonded pdb=" O2' Ae23621 " pdb=" O2' Ge24658 " model vdw 2.008 2.440 nonbonded pdb=" OP2 Gh2 75 " pdb=" OH TYRo2 74 " model vdw 2.041 2.440 nonbonded pdb=" OG1 THRa3 252 " pdb=" O SERa3 255 " model vdw 2.044 2.440 nonbonded pdb=" O2' Ge2 930 " pdb=" OP2 Ce2 931 " model vdw 2.051 2.440 ... (remaining 1968143 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 6205 5.49 5 S 437 5.16 5 C 119510 2.51 5 N 42437 2.21 5 O 59696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 23.820 Check model and map are aligned: 2.270 Convert atoms to be neutral: 1.350 Process input model: 876.880 Find NCS groups from input model: 6.020 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 915.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.006 0.430 245684 Z= 0.349 Angle : 0.846 26.259 361790 Z= 0.443 Chirality : 0.044 0.440 45224 Planarity : 0.006 0.173 22751 Dihedral : 18.190 179.960 112946 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.55 % Favored : 89.24 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.82 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.07), residues: 11684 helix: -2.24 (0.08), residues: 3383 sheet: -2.14 (0.12), residues: 1605 loop : -2.37 (0.07), residues: 6696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1981 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1913 time to evaluate : 11.016 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 outliers start: 68 outliers final: 18 residues processed: 1956 average time/residue: 1.8238 time to fit residues: 6262.7345 Evaluate side-chains 1618 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1600 time to evaluate : 10.818 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 1.5685 time to fit residues: 65.1194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 1492 optimal weight: 10.0000 chunk 1340 optimal weight: 30.0000 chunk 743 optimal weight: 9.9990 chunk 457 optimal weight: 2.9990 chunk 903 optimal weight: 40.0000 chunk 715 optimal weight: 6.9990 chunk 1385 optimal weight: 9.9990 chunk 536 optimal weight: 2.9990 chunk 842 optimal weight: 9.9990 chunk 1031 optimal weight: 5.9990 chunk 1605 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z2 56 GLN ** Z2 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 50 ASN ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 97 ASN S2 77 ASN S2 160 HIS 62 144 GLN ** 72 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 82 17 GLN ** 82 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q2 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q2 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t2 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 62 ASN D2 17 GLN D2 25 GLN F2 18 HIS F2 25 GLN G2 45 ASN G2 229 ASN G2 244 HIS L2 86 HIS ** R2 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2 185 ASN U2 205 ASN U2 247 ASN V2 208 ASN W2 127 ASN ** X2 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 90 ASN 12 156 HIS 12 181 HIS ** 42 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 28 ASN ** I3 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 106 HIS ** f3 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 35 GLN B3 140 GLN ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 4 ASN ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U3 132 GLN ** V3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V3 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 147 ASN j3 50 ASN j3 188 ASN N3 165 ASN ** c3 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 99 GLN ** F3 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 119 ASN F3 140 HIS ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 245684 Z= 0.280 Angle : 0.758 16.769 361790 Z= 0.381 Chirality : 0.042 0.364 45224 Planarity : 0.006 0.108 22751 Dihedral : 18.179 179.906 87951 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.22 % Favored : 89.62 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.07), residues: 11684 helix: -1.52 (0.08), residues: 3552 sheet: -1.90 (0.12), residues: 1628 loop : -2.29 (0.07), residues: 6504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1950 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1765 time to evaluate : 12.043 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 outliers start: 185 outliers final: 129 residues processed: 1860 average time/residue: 1.8902 time to fit residues: 6170.0661 Evaluate side-chains 1719 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1590 time to evaluate : 10.488 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 0 residues processed: 129 average time/residue: 1.3869 time to fit residues: 354.6260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 892 optimal weight: 9.9990 chunk 498 optimal weight: 3.9990 chunk 1336 optimal weight: 10.0000 chunk 1093 optimal weight: 6.9990 chunk 442 optimal weight: 0.9990 chunk 1608 optimal weight: 2.9990 chunk 1737 optimal weight: 8.9990 chunk 1432 optimal weight: 5.9990 chunk 1595 optimal weight: 20.0000 chunk 548 optimal weight: 3.9990 chunk 1290 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z2 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 50 ASN ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 160 HIS 52 302 ASN ** 72 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 72 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q2 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t2 223 ASN t2 276 ASN B2 15 HIS ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 109 ASN G2 229 ASN M2 142 ASN V2 85 GLN V2 153 GLN W2 127 ASN X2 144 ASN X2 163 GLN ** 12 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 42 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 81 GLN G3 106 HIS f3 26 GLN ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 311 GLN ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V3 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 147 ASN ** j3 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j3 188 ASN ** d3 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 99 GLN F3 112 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H3 37 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.100 245684 Z= 0.201 Angle : 0.678 16.501 361790 Z= 0.342 Chirality : 0.038 0.359 45224 Planarity : 0.005 0.092 22751 Dihedral : 17.923 179.999 87951 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.46 % Favored : 91.42 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.07), residues: 11684 helix: -1.02 (0.08), residues: 3548 sheet: -1.63 (0.12), residues: 1614 loop : -2.17 (0.07), residues: 6522 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1928 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1775 time to evaluate : 11.332 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 outliers start: 153 outliers final: 79 residues processed: 1858 average time/residue: 1.7879 time to fit residues: 5832.4055 Evaluate side-chains 1684 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1605 time to evaluate : 10.702 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 1.5888 time to fit residues: 252.1519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 1589 optimal weight: 0.8980 chunk 1209 optimal weight: 20.0000 chunk 834 optimal weight: 10.0000 chunk 178 optimal weight: 50.0000 chunk 767 optimal weight: 6.9990 chunk 1080 optimal weight: 8.9990 chunk 1614 optimal weight: 30.0000 chunk 1708 optimal weight: 10.0000 chunk 843 optimal weight: 8.9990 chunk 1529 optimal weight: 9.9990 chunk 460 optimal weight: 10.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 52 302 ASN 62 144 GLN 72 66 ASN ** o2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u2 93 ASN D2 33 ASN E2 90 ASN ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 122 GLN G2 229 ASN ** U2 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 208 ASN W2 127 ASN Y2 42 GLN ** 12 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 42 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 28 ASN ** G3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f3 29 GLN ** A3 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 147 ASN j3 138 HIS j3 188 ASN ** c3 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d3 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 99 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 245684 Z= 0.322 Angle : 0.759 16.778 361790 Z= 0.377 Chirality : 0.041 0.371 45224 Planarity : 0.006 0.106 22751 Dihedral : 17.986 179.973 87951 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.54 % Favored : 89.30 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.07), residues: 11684 helix: -0.95 (0.08), residues: 3535 sheet: -1.70 (0.12), residues: 1651 loop : -2.20 (0.07), residues: 6498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1958 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1670 time to evaluate : 10.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 288 outliers final: 175 residues processed: 1834 average time/residue: 1.7145 time to fit residues: 5539.3301 Evaluate side-chains 1759 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1584 time to evaluate : 12.904 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 0 residues processed: 175 average time/residue: 1.3979 time to fit residues: 480.8926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 1423 optimal weight: 30.0000 chunk 970 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 1272 optimal weight: 20.0000 chunk 705 optimal weight: 9.9990 chunk 1458 optimal weight: 1.9990 chunk 1181 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 872 optimal weight: 40.0000 chunk 1533 optimal weight: 7.9990 chunk 431 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z2 33 GLN ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w2 150 GLN ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 160 HIS 62 144 GLN 72 66 ASN 82 17 GLN l2 59 HIS ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 122 GLN ** U2 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U2 171 ASN V2 208 ASN W2 127 ASN Y2 42 GLN a7 111 GLN ** 12 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I3 28 ASN G3 106 HIS ** A3 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J5 5 ASN ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 76 ASN V3 147 ASN W3 235 ASN Y3 179 GLN j3 188 ASN ** c3 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d3 177 ASN F3 99 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H3 10 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.005 245684 Z= 0.366 Angle : 0.780 104.845 361790 Z= 0.383 Chirality : 0.041 0.364 45224 Planarity : 0.006 0.105 22751 Dihedral : 17.989 179.928 87951 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.31 % Favored : 89.52 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.07), residues: 11684 helix: -0.91 (0.08), residues: 3525 sheet: -1.68 (0.12), residues: 1622 loop : -2.20 (0.07), residues: 6537 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1870 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1659 time to evaluate : 12.118 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 outliers start: 211 outliers final: 107 residues processed: 1794 average time/residue: 1.8755 time to fit residues: 5950.8485 Evaluate side-chains 1691 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1584 time to evaluate : 11.927 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 1.6019 time to fit residues: 337.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 574 optimal weight: 2.9990 chunk 1538 optimal weight: 0.8980 chunk 337 optimal weight: 10.0000 chunk 1003 optimal weight: 6.9990 chunk 421 optimal weight: 10.0000 chunk 1710 optimal weight: 20.0000 chunk 1420 optimal weight: 30.0000 chunk 792 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 565 optimal weight: 7.9990 chunk 898 optimal weight: 0.2980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 72 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 82 17 GLN l2 59 HIS ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t2 231 ASN v2 117 GLN ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W2 127 ASN ** W2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y2 42 GLN ** 12 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 42 84 HIS I3 28 ASN ** I3 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 147 ASN W3 235 ASN j3 188 ASN ** c3 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d3 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 99 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.090 245684 Z= 0.428 Angle : 0.813 106.100 361790 Z= 0.393 Chirality : 0.040 0.495 45224 Planarity : 0.006 0.129 22751 Dihedral : 17.990 179.881 87951 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.35 % Favored : 89.49 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.61 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.07), residues: 11684 helix: -0.88 (0.08), residues: 3525 sheet: -1.67 (0.13), residues: 1617 loop : -2.20 (0.07), residues: 6542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1745 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1612 time to evaluate : 12.153 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 outliers start: 133 outliers final: 95 residues processed: 1678 average time/residue: 1.7436 time to fit residues: 5140.4477 Evaluate side-chains 1668 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1573 time to evaluate : 10.716 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 1.4413 time to fit residues: 271.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 1649 optimal weight: 3.9990 chunk 192 optimal weight: 40.0000 chunk 974 optimal weight: 10.0000 chunk 1249 optimal weight: 10.0000 chunk 967 optimal weight: 8.9990 chunk 1439 optimal weight: 7.9990 chunk 955 optimal weight: 10.0000 chunk 1704 optimal weight: 30.0000 chunk 1066 optimal weight: 0.4980 chunk 1038 optimal weight: 9.9990 chunk 786 optimal weight: 0.0030 overall best weight: 4.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 160 HIS 72 66 ASN 82 17 GLN 82 94 ASN l2 59 HIS ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t2 236 ASN ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W2 127 ASN ** W2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I3 28 ASN I3 81 GLN ** G3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 147 ASN W3 235 ASN j3 188 ASN d3 27 GLN ** e3 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 99 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.023 245684 Z= 0.383 Angle : 0.786 106.100 361790 Z= 0.378 Chirality : 0.040 0.397 45224 Planarity : 0.005 0.122 22751 Dihedral : 17.959 179.991 87951 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.90 % Favored : 89.95 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.07), residues: 11684 helix: -0.83 (0.08), residues: 3526 sheet: -1.64 (0.13), residues: 1622 loop : -2.17 (0.07), residues: 6536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1775 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1638 time to evaluate : 10.758 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 outliers start: 137 outliers final: 74 residues processed: 1720 average time/residue: 1.8964 time to fit residues: 5767.7532 Evaluate side-chains 1657 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1583 time to evaluate : 10.658 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 1.5995 time to fit residues: 236.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 1054 optimal weight: 0.7980 chunk 680 optimal weight: 3.9990 chunk 1017 optimal weight: 10.0000 chunk 513 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 1083 optimal weight: 10.0000 chunk 1160 optimal weight: 30.0000 chunk 842 optimal weight: 5.9990 chunk 158 optimal weight: 50.0000 chunk 1339 optimal weight: 20.0000 overall best weight: 4.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 72 66 ASN l2 59 HIS ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W2 127 ASN ** W2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I3 28 ASN I3 81 GLN ** G3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H5 85 ASN ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 147 ASN W3 235 ASN j3 188 ASN ** c3 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d3 27 GLN e3 46 GLN ** e3 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 99 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.030 245684 Z= 0.356 Angle : 0.772 106.097 361790 Z= 0.376 Chirality : 0.040 0.366 45224 Planarity : 0.005 0.115 22751 Dihedral : 17.942 179.952 87951 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.86 % Favored : 89.99 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.07), residues: 11684 helix: -0.81 (0.08), residues: 3533 sheet: -1.62 (0.12), residues: 1633 loop : -2.16 (0.07), residues: 6518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1704 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1609 time to evaluate : 10.703 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 outliers start: 95 outliers final: 61 residues processed: 1649 average time/residue: 1.8598 time to fit residues: 5406.8238 Evaluate side-chains 1625 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1564 time to evaluate : 10.658 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 1.3856 time to fit residues: 175.2819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 1550 optimal weight: 9.9990 chunk 1632 optimal weight: 8.9990 chunk 1489 optimal weight: 50.0000 chunk 1587 optimal weight: 0.5980 chunk 955 optimal weight: 8.9990 chunk 691 optimal weight: 9.9990 chunk 1246 optimal weight: 20.0000 chunk 487 optimal weight: 7.9990 chunk 1434 optimal weight: 0.0370 chunk 1501 optimal weight: 7.9990 chunk 1582 optimal weight: 8.9990 overall best weight: 5.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 160 HIS 72 66 ASN l2 59 HIS ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 122 GLN ** G2 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2 194 GLN W2 127 ASN ** W2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 57 GLN I3 28 ASN I3 81 GLN ** G3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 106 GLN ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 147 ASN W3 235 ASN j3 188 ASN ** c3 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d3 27 GLN F3 99 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.010 245684 Z= 0.371 Angle : 0.775 106.100 361790 Z= 0.379 Chirality : 0.040 0.370 45224 Planarity : 0.005 0.149 22751 Dihedral : 17.930 179.964 87951 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.94 % Favored : 89.91 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.07), residues: 11684 helix: -0.80 (0.08), residues: 3533 sheet: -1.61 (0.13), residues: 1616 loop : -2.16 (0.07), residues: 6535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1658 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1588 time to evaluate : 13.938 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 outliers start: 70 outliers final: 44 residues processed: 1622 average time/residue: 1.7641 time to fit residues: 5024.8229 Evaluate side-chains 1609 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1565 time to evaluate : 10.548 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 1.4895 time to fit residues: 134.9778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 1042 optimal weight: 9.9990 chunk 1679 optimal weight: 20.0000 chunk 1024 optimal weight: 6.9990 chunk 796 optimal weight: 3.9990 chunk 1167 optimal weight: 40.0000 chunk 1761 optimal weight: 8.9990 chunk 1621 optimal weight: 20.0000 chunk 1402 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 1083 optimal weight: 2.9990 chunk 860 optimal weight: 0.4980 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 52 55 HIS 72 66 ASN l2 59 HIS ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 92 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2 194 GLN U2 247 ASN W2 127 ASN ** W2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I3 28 ASN I3 81 GLN ** G3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 76 ASN V3 147 ASN W3 235 ASN ** c3 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d3 27 GLN F3 99 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 2.165 245684 Z= 0.439 Angle : 0.791 106.100 361790 Z= 0.393 Chirality : 0.040 0.370 45224 Planarity : 0.006 0.149 22751 Dihedral : 17.930 179.964 87951 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.94 % Favored : 89.91 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.07), residues: 11684 helix: -0.80 (0.08), residues: 3533 sheet: -1.61 (0.13), residues: 1616 loop : -2.16 (0.07), residues: 6535 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23368 Ramachandran restraints generated. 11684 Oldfield, 0 Emsley, 11684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1578 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1574 time to evaluate : 12.069 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 outliers start: 4 outliers final: 0 residues processed: 1575 average time/residue: 1.7626 time to fit residues: 4879.9574 Evaluate side-chains 1567 residues out of total 10204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1567 time to evaluate : 10.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 13.9696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1768 random chunks: chunk 1114 optimal weight: 6.9990 chunk 1494 optimal weight: 20.0000 chunk 429 optimal weight: 40.0000 chunk 1293 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 389 optimal weight: 20.0000 chunk 1404 optimal weight: 20.0000 chunk 587 optimal weight: 0.0060 chunk 1442 optimal weight: 9.9990 chunk 177 optimal weight: 30.0000 chunk 258 optimal weight: 10.0000 overall best weight: 7.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p2 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w2 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 160 HIS 72 66 ASN l2 59 HIS ** q2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2 194 GLN W2 127 ASN ** W2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I3 28 ASN I3 81 GLN ** G3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 76 HIS ** G5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 147 ASN W3 235 ASN j3 188 ASN ** c3 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d3 27 GLN F3 99 GLN F3 119 ASN ** E3 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.186278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.145202 restraints weight = 406311.161| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.54 r_work: 0.3910 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.3890 rms_B_bonded: 1.53 restraints_weight: 0.1250 r_work: 0.3879 rms_B_bonded: 1.64 restraints_weight: 0.0625 r_work: 0.3868 rms_B_bonded: 1.80 restraints_weight: 0.0312 r_work: 0.3855 rms_B_bonded: 1.99 restraints_weight: 0.0156 r_work: 0.3841 rms_B_bonded: 2.23 restraints_weight: 0.0078 r_work: 0.3825 rms_B_bonded: 2.51 restraints_weight: 0.0039 r_work: 0.3808 rms_B_bonded: 2.85 restraints_weight: 0.0020 r_work: 0.3788 rms_B_bonded: 3.25 restraints_weight: 0.0010 r_work: 0.3766 rms_B_bonded: 3.72 restraints_weight: 0.0005 r_work: 0.3740 rms_B_bonded: 4.29 restraints_weight: 0.0002 r_work: 0.3710 rms_B_bonded: 4.97 restraints_weight: 0.0001 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 2.165 245684 Z= 0.439 Angle : 0.791 106.100 361790 Z= 0.393 Chirality : 0.040 0.370 45224 Planarity : 0.006 0.149 22751 Dihedral : 17.930 179.964 87951 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.94 % Favored : 89.91 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.05 % Twisted Proline : 0.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.07), residues: 11684 helix: -0.80 (0.08), residues: 3533 sheet: -1.61 (0.13), residues: 1616 loop : -2.16 (0.07), residues: 6535 =============================================================================== Job complete usr+sys time: 71417.97 seconds wall clock time: 1238 minutes 13.89 seconds (74293.89 seconds total)