Starting phenix.real_space_refine (version: dev) on Mon Apr 18 12:00:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdz_23785/04_2022/7mdz_23785_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.007 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 "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DD PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VV TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 211192 Number of models: 1 Model: "" Number of chains: 99 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 13, 'TRANS': 233, 'PCIS': 1} Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3172 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 13, 'TRANS': 378, 'PCIS': 2} Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2391 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain breaks: 3 Chain: "F" 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: "G" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1879 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain breaks: 1 Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1664 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "J" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1362 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "L" 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: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "N" 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: "O" 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: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1515 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1462 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "T" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1284 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain: "U" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "V" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1034 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "X" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Z" 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: "a" 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: "b" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Chain: "c" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 761 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f" 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: "g" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 897 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "h" 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: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "l" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 438 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "m" 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: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "p" 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: "r" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "AA" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1712 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "BB" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "CC" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "DD" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "EE" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "FF" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1471 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "GG" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "HH" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1480 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain breaks: 2 Chain: "II" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "JJ" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "KK" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "LL" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1175 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "MM" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "NN" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "OO" 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: "PP" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "QQ" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135, 'PCIS': 1} Chain: "RR" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "SS" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "TT" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "UU" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "VV" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "WW" 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: "XX" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "YY" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "ZZ" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "aa" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "bb" 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: "cc" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "dd" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "ee" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "ff" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "gg" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "5" Number of atoms: 75929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3541, 75929 Classifications: {'RNA': 3541} Modifications used: {'rna3p_pyr': 1380, 'rna2p_pur': 360, 'rna3p_pur': 1585, 'rna2p_pyr': 216} Link IDs: {'rna3p': 2964, 'rna2p': 576} Chain breaks: 24 Chain: "7" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2538 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 6, 'rna3p_pyr': 52} Link IDs: {'rna3p': 106, 'rna2p': 12} Chain: "8" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3208 Classifications: {'RNA': 151} Modifications used: {'rna3p_pyr': 63, 'rna2p_pur': 14, 'rna3p_pur': 59, 'rna2p_pyr': 15, '5*END': 1} Link IDs: {'rna3p': 122, 'rna2p': 28} Chain breaks: 1 Chain: "2" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'rna2p_pyr': 4, 'rna3p_pyr': 33, 'p5*END': 1, 'rna3p_pur': 33, 'rna2p_pur': 6} Link IDs: {'rna3p': 66, 'rna2p': 9} Chain: "9" Number of atoms: 36229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36229 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 144, 'rna3p_pur': 754, 'rna2p_pyr': 112, 'rna3p_pyr': 687} Link IDs: {'rna3p': 1441, 'rna2p': 255} Chain breaks: 11 Chain: "6" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'RNA': 10} Modifications used: {'rna3p_pyr': 5, 'rna3p_pur': 4, 'rna2p_pyr': 1} Link IDs: {'rna3p': 8, 'rna2p': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "aa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "dd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "ff" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 218 Unusual residues: {'Z2V': 1, ' MG': 189} Classifications: {'undetermined': 190} Link IDs: {None: 189} Chain: "7" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "8" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Unusual residues: {' MG': 69} Classifications: {'undetermined': 69} Link IDs: {None: 68} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45064 SG CYS g 46 173.899 169.215 194.966 1.00 13.66 S ATOM 45081 SG CYS g 49 174.972 172.294 193.086 1.00 16.92 S ATOM 45344 SG CYS g 83 175.830 172.380 196.523 1.00 11.12 S ATOM 45364 SG CYS g 86 172.217 172.208 196.127 1.00 11.99 S ATOM 47578 SG CYS j 19 202.184 123.091 173.817 1.00 12.12 S ATOM 47606 SG CYS j 22 204.017 120.633 171.490 1.00 13.28 S ATOM 47697 SG CYS j 34 200.827 122.536 170.451 1.00 12.05 S ATOM 47716 SG CYS j 37 200.711 119.751 173.093 1.00 14.92 S ATOM 49312 SG CYS m 70 183.787 136.761 60.880 1.00 12.11 S ATOM 49338 SG CYS m 73 186.883 138.233 62.491 1.00 11.75 S ATOM 49428 SG CYS m 84 187.168 137.136 59.056 1.00 11.88 S ATOM 49472 SG CYS m 89 186.834 134.497 61.785 1.00 12.56 S ATOM 49909 SG CYS o 12 137.098 67.636 133.963 1.00 12.79 S ATOM 49933 SG CYS o 15 135.057 64.396 134.690 1.00 12.09 S ATOM 50402 SG CYS o 72 133.413 67.938 134.531 1.00 11.83 S ATOM 50439 SG CYS o 77 136.024 66.778 137.262 1.00 14.23 S ATOM 50969 SG CYS p 39 161.254 174.584 183.863 1.00 10.11 S ATOM 50992 SG CYS p 42 163.023 177.656 185.195 1.00 11.04 S ATOM 51114 SG CYS p 57 164.799 175.224 182.850 1.00 9.69 S ATOM 51130 SG CYS p 60 164.168 174.306 186.447 1.00 10.98 S ATOM 85459 SG CYSaa 23 110.364 161.105 150.115 1.00 17.53 S ATOM 85863 SG CYSaa 74 110.712 163.279 147.365 1.00 17.74 S ATOM 85882 SG CYSaa 77 109.321 160.700 146.813 1.00 16.68 S ATOM 87400 SG CYSdd 21 73.684 166.704 82.538 1.00 31.58 S ATOM 87424 SG CYSdd 24 77.006 168.722 83.118 1.00 33.72 S ATOM 87545 SG CYSdd 39 75.895 165.865 85.585 1.00 29.34 S ATOM 87571 SG CYSdd 42 74.682 169.217 85.492 1.00 30.93 S ATOM 88482 SG CYSff 121 71.974 161.225 32.940 1.00 43.80 S ATOM 88636 SG CYSff 141 74.046 162.431 34.527 1.00 44.01 S ATOM 88655 SG CYSff 144 71.347 160.090 37.121 1.00 44.79 S Time building chain proxies: 73.96, per 1000 atoms: 0.35 Number of scatterers: 211192 At special positions: 0 Unit cell: (291.51, 298.89, 263.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 411 16.00 P 5591 15.00 Mg 277 11.99 O 54512 8.00 N 39397 7.00 C 110996 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: 65.25 Conformation dependent library (CDL) restraints added in 9.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb=" ZN m 200 " pdb="ZN ZN m 200 " - pdb=" SG CYS m 73 " pdb="ZN ZN m 200 " - pdb=" SG CYS m 84 " pdb="ZN ZN m 200 " - pdb=" SG CYS m 70 " pdb="ZN ZN m 200 " - pdb=" SG CYS m 89 " pdb=" ZN o 200 " pdb="ZN ZN o 200 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 200 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 200 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 200 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " pdb=" ZNaa 201 " pdb="ZN ZNaa 201 " - pdb=" SG CYSaa 77 " pdb="ZN ZNaa 201 " - pdb=" SG CYSaa 23 " pdb="ZN ZNaa 201 " - pdb=" SG CYSaa 74 " pdb=" ZNdd 100 " pdb="ZN ZNdd 100 " - pdb=" SG CYSdd 42 " pdb="ZN ZNdd 100 " - pdb=" SG CYSdd 39 " pdb="ZN ZNdd 100 " - pdb=" SG CYSdd 24 " pdb="ZN ZNdd 100 " - pdb=" SG CYSdd 21 " pdb=" ZNff 200 " pdb="ZN ZNff 200 " - pdb=" SG CYSff 141 " pdb="ZN ZNff 200 " - pdb=" SG CYSff 121 " pdb="ZN ZNff 200 " - pdb=" SG CYSff 144 " Number of angles added : 36 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21038 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 370 helices and 114 sheets defined 40.5% alpha, 15.4% beta 1621 base pairs and 2870 stacking pairs defined. Time for finding SS restraints: 75.86 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.623A pdb=" N GLY A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.976A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 4.951A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.973A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.292A pdb=" N LEU B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Proline residue: B 18 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.998A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 4.744A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 removed outlier: 4.508A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.353A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Proline residue: B 172 - end of helix No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.707A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.034A pdb=" N LYS C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 49 removed outlier: 4.107A pdb=" N LYS C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ARG C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 134 removed outlier: 3.729A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 135 through 141 removed outlier: 3.536A pdb=" N GLY C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.520A pdb=" N GLY C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.980A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.976A pdb=" N ARG C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 198' Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 236 through 242 Proline residue: C 242 - end of helix Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.678A pdb=" N LYS C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 4.593A pdb=" N SER C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 removed outlier: 4.260A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 329 Processing helix chain 'C' and resid 330 through 363 removed outlier: 4.352A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.819A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.569A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.597A pdb=" N TYR D 119 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 115 through 120' Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.827A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.591A pdb=" N TYR D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 250 removed outlier: 4.759A pdb=" N GLU D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.767A pdb=" N ALA D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 69 Processing helix chain 'E' and resid 193 through 198 removed outlier: 3.624A pdb=" N VAL E 197 " --> pdb=" O HIS E 193 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE E 198 " --> pdb=" O GLN E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 193 through 198' Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 246 through 268 removed outlier: 3.936A pdb=" N GLN E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Proline residue: E 262 - end of helix removed outlier: 4.197A pdb=" N VAL E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Proline residue: E 268 - end of helix Processing helix chain 'E' and resid 269 through 277 removed outlier: 5.095A pdb=" N VAL E 277 " --> pdb=" O TYR E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 removed outlier: 5.024A pdb=" N VAL E 290 " --> pdb=" O PRO E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 78 removed outlier: 4.159A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU F 67 " --> pdb=" O MET F 63 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE F 68 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 112 Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 145 through 156 Processing helix chain 'F' and resid 170 through 178 removed outlier: 4.164A pdb=" N ILE F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER F 177 " --> pdb=" O LEU F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.187A pdb=" N VAL F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 208 removed outlier: 3.560A pdb=" N LEU F 207 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TRP F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 247 removed outlier: 3.521A pdb=" N LEU F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG F 245 " --> pdb=" O ARG F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 127 removed outlier: 3.757A pdb=" N ALA G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 removed outlier: 4.659A pdb=" N PHE G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN G 138 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL G 139 " --> pdb=" O GLN G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 156 removed outlier: 4.087A pdb=" N LYS G 154 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 176 removed outlier: 3.563A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 203 Processing helix chain 'G' and resid 220 through 231 Proline residue: G 224 - end of helix Processing helix chain 'G' and resid 239 through 248 removed outlier: 3.540A pdb=" N LEU G 246 " --> pdb=" O ARG G 242 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL G 247 " --> pdb=" O LEU G 243 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 287 removed outlier: 4.919A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG G 282 " --> pdb=" O ASN G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 319 removed outlier: 4.386A pdb=" N ARG G 302 " --> pdb=" O LYS G 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU G 318 " --> pdb=" O LEU G 314 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY G 319 " --> pdb=" O ALA G 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 86 removed outlier: 3.927A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.675A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.256A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 10 removed outlier: 4.311A pdb=" N TYR I 9 " --> pdb=" O PRO I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 47 removed outlier: 4.125A pdb=" N PHE I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix No H-bonds generated for 'chain 'I' and resid 42 through 47' Processing helix chain 'I' and resid 61 through 80 Processing helix chain 'I' and resid 144 through 160 removed outlier: 4.181A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 177 through 188 removed outlier: 4.396A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 214 removed outlier: 4.092A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 45 Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 111 through 116 removed outlier: 4.774A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY J 116 " --> pdb=" O HIS J 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 116' Processing helix chain 'J' and resid 139 through 144 removed outlier: 4.403A pdb=" N ASP J 143 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'J' and resid 95 through 100 removed outlier: 4.281A pdb=" N PHE J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER J 100 " --> pdb=" O ASN J 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.054A pdb=" N ARG L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 removed outlier: 4.218A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 87 through 95 removed outlier: 4.745A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 125 removed outlier: 3.703A pdb=" N ASN L 113 " --> pdb=" O SER L 109 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER L 122 " --> pdb=" O LYS L 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS L 123 " --> pdb=" O GLU L 119 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL L 125 " --> pdb=" O ARG L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 148 removed outlier: 3.803A pdb=" N LEU L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA L 147 " --> pdb=" O GLU L 143 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR L 148 " --> pdb=" O LEU L 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 140 through 148' Processing helix chain 'L' and resid 170 through 176 removed outlier: 3.731A pdb=" N PHE L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 192 Processing helix chain 'L' and resid 193 through 211 removed outlier: 3.966A pdb=" N VAL L 207 " --> pdb=" O ALA L 203 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU L 208 " --> pdb=" O GLU L 204 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS L 209 " --> pdb=" O GLN L 205 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS L 210 " --> pdb=" O ASP L 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 56 removed outlier: 4.235A pdb=" N MET M 55 " --> pdb=" O PRO M 51 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLN M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 51 through 56' Processing helix chain 'M' and resid 69 through 81 Processing helix chain 'M' and resid 82 through 90 removed outlier: 3.603A pdb=" N ALA M 87 " --> pdb=" O ASN M 83 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR M 89 " --> pdb=" O LYS M 85 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG M 90 " --> pdb=" O TRP M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 Processing helix chain 'M' and resid 106 through 135 Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.929A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.612A pdb=" N LEU N 33 " --> pdb=" O GLN N 29 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 83 through 88 removed outlier: 4.066A pdb=" N HIS N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLY N 88 " --> pdb=" O PRO N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 88' Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.705A pdb=" N GLY N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 145 removed outlier: 3.737A pdb=" N ASN N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 153 removed outlier: 4.884A pdb=" N THR N 152 " --> pdb=" O THR N 148 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS N 153 " --> pdb=" O GLN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 148 through 153' Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.662A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY N 173 " --> pdb=" O ARG N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 197 removed outlier: 3.756A pdb=" N THR N 197 " --> pdb=" O ARG N 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.672A pdb=" N ILE O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY O 30 " --> pdb=" O GLN O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.515A pdb=" N LYS O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.695A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.689A pdb=" N MET O 87 " --> pdb=" O THR O 83 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 92 through 103 removed outlier: 3.830A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 116 removed outlier: 3.993A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 149 through 190 removed outlier: 4.942A pdb=" N LYS O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS O 188 " --> pdb=" O ASN O 184 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER O 190 " --> pdb=" O GLU O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 200 removed outlier: 3.897A pdb=" N VAL O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU O 196 " --> pdb=" O PHE O 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 54 removed outlier: 3.501A pdb=" N LYS P 46 " --> pdb=" O ARG P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 77 removed outlier: 4.620A pdb=" N TRP P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 54 removed outlier: 4.602A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 146 through 153 removed outlier: 4.482A pdb=" N ARG Q 150 " --> pdb=" O ARG Q 146 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS Q 151 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLY Q 153 " --> pdb=" O TYR Q 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 146 through 153' Processing helix chain 'Q' and resid 171 through 176 removed outlier: 5.288A pdb=" N GLU Q 175 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG Q 176 " --> pdb=" O ARG Q 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 171 through 176' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 5.802A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 35 removed outlier: 3.596A pdb=" N ASN R 34 " --> pdb=" O ASN R 30 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.585A pdb=" N VAL R 93 " --> pdb=" O MET R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 181 removed outlier: 3.504A pdb=" N ARG R 173 " --> pdb=" O ALA R 169 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS R 180 " --> pdb=" O ARG R 176 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 117 Processing helix chain 'S' and resid 120 through 125 removed outlier: 3.583A pdb=" N ILE S 124 " --> pdb=" O ARG S 120 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN S 125 " --> pdb=" O ALA S 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 120 through 125' Processing helix chain 'S' and resid 139 through 147 removed outlier: 5.107A pdb=" N PHE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS S 146 " --> pdb=" O VAL S 142 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP S 147 " --> pdb=" O LYS S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 166 Proline residue: S 165 - end of helix No H-bonds generated for 'chain 'S' and resid 161 through 166' Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.443A pdb=" N TYR T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.152A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS T 97 " --> pdb=" O ILE T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 100 through 123 removed outlier: 3.945A pdb=" N SER T 104 " --> pdb=" O LYS T 100 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE T 105 " --> pdb=" O SER T 101 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS T 107 " --> pdb=" O ASP T 103 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG T 108 " --> pdb=" O SER T 104 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU T 118 " --> pdb=" O GLN T 114 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU T 121 " --> pdb=" O LYS T 117 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS T 122 " --> pdb=" O GLU T 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.992A pdb=" N VAL U 29 " --> pdb=" O CYS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 54 through 59 removed outlier: 4.564A pdb=" N GLY U 58 " --> pdb=" O GLY U 54 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY U 59 " --> pdb=" O ASN U 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 54 through 59' Processing helix chain 'U' and resid 79 through 95 removed outlier: 3.708A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS U 93 " --> pdb=" O LYS U 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 74 removed outlier: 5.407A pdb=" N LYS V 74 " --> pdb=" O PRO V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 130 Proline residue: V 130 - end of helix Processing helix chain 'V' and resid 131 through 136 removed outlier: 4.490A pdb=" N ASN V 135 " --> pdb=" O ARG V 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 43 Processing helix chain 'W' and resid 45 through 50 removed outlier: 3.820A pdb=" N ILE W 49 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASN W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 45 through 50' Processing helix chain 'W' and resid 52 through 60 Processing helix chain 'X' and resid 72 through 78 removed outlier: 4.973A pdb=" N LYS X 78 " --> pdb=" O TYR X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 93 removed outlier: 3.606A pdb=" N LYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 118 Processing helix chain 'X' and resid 145 through 154 Processing helix chain 'Y' and resid 10 through 21 Processing helix chain 'Y' and resid 22 through 31 removed outlier: 4.313A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER Y 31 " --> pdb=" O ARG Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 3.969A pdb=" N VAL Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 134 removed outlier: 3.965A pdb=" N GLU Y 120 " --> pdb=" O LYS Y 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 67 removed outlier: 3.835A pdb=" N LYS Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.807A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N MET Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 4.261A pdb=" N ASN Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 125 removed outlier: 3.589A pdb=" N THR Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 3.838A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN Z 132 " --> pdb=" O LYS Z 128 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 127 through 133' Processing helix chain 'a' and resid 2 through 7 removed outlier: 3.583A pdb=" N ARG a 6 " --> pdb=" O PRO a 2 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS a 7 " --> pdb=" O SER a 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 2 through 7' Processing helix chain 'a' and resid 41 through 48 Processing helix chain 'a' and resid 64 through 69 removed outlier: 4.073A pdb=" N SER a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE a 69 " --> pdb=" O ARG a 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 64 through 69' Processing helix chain 'a' and resid 74 through 83 removed outlier: 4.274A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER a 83 " --> pdb=" O TRP a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 93 Processing helix chain 'a' and resid 102 through 107 removed outlier: 3.578A pdb=" N SER a 106 " --> pdb=" O ASP a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 141 removed outlier: 4.069A pdb=" N GLY a 141 " --> pdb=" O ILE a 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 20 removed outlier: 4.302A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY b 20 " --> pdb=" O TRP b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 55 removed outlier: 3.630A pdb=" N ASN b 42 " --> pdb=" O LYS b 38 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY b 53 " --> pdb=" O HIS b 49 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU b 54 " --> pdb=" O ASN b 50 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 76 removed outlier: 3.599A pdb=" N LEU b 75 " --> pdb=" O ALA b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 101 removed outlier: 3.527A pdb=" N HIS b 101 " --> pdb=" O ALA b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 117 Processing helix chain 'c' and resid 10 through 24 removed outlier: 4.535A pdb=" N SER c 16 " --> pdb=" O GLU c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 41 Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 Processing helix chain 'd' and resid 28 through 34 removed outlier: 3.579A pdb=" N ARG d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 58 removed outlier: 4.076A pdb=" N GLY d 58 " --> pdb=" O MET d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'e' and resid 24 through 29 removed outlier: 3.897A pdb=" N TYR e 28 " --> pdb=" O GLN e 24 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL e 29 " --> pdb=" O SER e 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 24 through 29' Processing helix chain 'e' and resid 43 through 48 Processing helix chain 'e' and resid 81 through 90 removed outlier: 4.307A pdb=" N LEU e 85 " --> pdb=" O ASN e 81 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU e 86 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU e 88 " --> pdb=" O GLU e 84 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET e 90 " --> pdb=" O GLU e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 119 removed outlier: 3.871A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 40 removed outlier: 3.804A pdb=" N THR f 39 " --> pdb=" O ALA f 35 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU f 40 " --> pdb=" O ARG f 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 35 through 40' Processing helix chain 'g' and resid 60 through 68 removed outlier: 3.665A pdb=" N LEU g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N MET g 65 " --> pdb=" O PRO g 61 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARG g 66 " --> pdb=" O LYS g 62 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER g 68 " --> pdb=" O LEU g 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 60 through 68' Processing helix chain 'g' and resid 83 through 114 Processing helix chain 'h' and resid 5 through 13 removed outlier: 3.639A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG h 10 " --> pdb=" O ALA h 6 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 5 through 13' Processing helix chain 'h' and resid 14 through 38 Processing helix chain 'h' and resid 40 through 74 removed outlier: 3.806A pdb=" N LYS h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS h 74 " --> pdb=" O ARG h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 85 Proline residue: h 85 - end of helix Processing helix chain 'h' and resid 88 through 95 removed outlier: 6.311A pdb=" N LEU h 95 " --> pdb=" O MET h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 102 Processing helix chain 'h' and resid 104 through 114 Processing helix chain 'i' and resid 25 through 30 removed outlier: 3.958A pdb=" N ARG i 29 " --> pdb=" O ARG i 25 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG i 30 " --> pdb=" O HIS i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 103 Processing helix chain 'j' and resid 4 through 11 removed outlier: 4.282A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.861A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 4.405A pdb=" N ILE j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG j 75 " --> pdb=" O TYR j 71 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 Processing helix chain 'k' and resid 49 through 60 removed outlier: 3.958A pdb=" N ALA k 53 " --> pdb=" O ASP k 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.682A pdb=" N ASN l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG l 21 " --> pdb=" O GLN l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.420A pdb=" N TRP l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 53 through 65 removed outlier: 3.566A pdb=" N TYR m 63 " --> pdb=" O LEU m 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 25 Processing helix chain 'o' and resid 35 through 47 removed outlier: 5.820A pdb=" N GLY o 47 " --> pdb=" O ARG o 43 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.879A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 removed outlier: 3.503A pdb=" N SER p 81 " --> pdb=" O VAL p 77 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 13 removed outlier: 5.768A pdb=" N ASN r 12 " --> pdb=" O MET r 8 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS r 13 " --> pdb=" O VAL r 9 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 101 Processing helix chain 'r' and resid 103 through 123 removed outlier: 4.759A pdb=" N ARG r 107 " --> pdb=" O HIS r 103 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N MET r 108 " --> pdb=" O PRO r 104 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALA r 109 " --> pdb=" O ASP r 105 " (cutoff:3.500A) Proline residue: r 123 - end of helix Processing helix chain 'AA' and resid 11 through 22 removed outlier: 3.931A pdb=" N VALAA 15 " --> pdb=" O LYSAA 11 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEUAA 16 " --> pdb=" O GLUAA 12 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYSAA 17 " --> pdb=" O GLUAA 13 " (cutoff:3.500A) Processing helix chain 'AA' and resid 50 through 69 removed outlier: 3.575A pdb=" N ILEAA 68 " --> pdb=" O ALAAA 64 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLUAA 69 " --> pdb=" O ILEAA 65 " (cutoff:3.500A) Processing helix chain 'AA' and resid 80 through 95 removed outlier: 4.719A pdb=" N ARGAA 85 " --> pdb=" O ASNAA 81 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALAAA 86 " --> pdb=" O THRAA 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUAA 88 " --> pdb=" O GLNAA 84 " (cutoff:3.500A) Processing helix chain 'AA' and resid 126 through 131 Processing helix chain 'AA' and resid 132 through 141 removed outlier: 3.720A pdb=" N VALAA 140 " --> pdb=" O GLUAA 136 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASNAA 141 " --> pdb=" O ALAAA 137 " (cutoff:3.500A) Processing helix chain 'AA' and resid 167 through 187 removed outlier: 3.951A pdb=" N GLYAA 172 " --> pdb=" O ALAAA 168 " (cutoff:3.500A) Processing helix chain 'AA' and resid 198 through 204 removed outlier: 4.767A pdb=" N TYRAA 202 " --> pdb=" O METAA 198 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHEAA 203 " --> pdb=" O PROAA 199 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYRAA 204 " --> pdb=" O ASPAA 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 198 through 204' Processing helix chain 'AA' and resid 206 through 218 removed outlier: 3.880A pdb=" N ALAAA 216 " --> pdb=" O LYSAA 212 " (cutoff:3.500A) Processing helix chain 'AA' and resid 32 through 37 removed outlier: 3.651A pdb=" N GLUAA 35 " --> pdb=" O PHEAA 32 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLNAA 36 " --> pdb=" O GLNAA 33 " (cutoff:3.500A) Processing helix chain 'BB' and resid 23 through 29 removed outlier: 4.560A pdb=" N LYSBB 27 " --> pdb=" O ASPBB 23 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYSBB 28 " --> pdb=" O PROBB 24 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASPBB 29 " --> pdb=" O PHEBB 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 23 through 29' Processing helix chain 'BB' and resid 57 through 65 removed outlier: 4.195A pdb=" N GLYBB 61 " --> pdb=" O ILEBB 57 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEUBB 62 " --> pdb=" O ALABB 58 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLYBB 64 " --> pdb=" O ASPBB 60 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARGBB 65 " --> pdb=" O GLYBB 61 " (cutoff:3.500A) Processing helix chain 'BB' and resid 70 through 76 removed outlier: 3.746A pdb=" N LEUBB 74 " --> pdb=" O SERBB 70 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASNBB 76 " --> pdb=" O ALABB 72 " (cutoff:3.500A) Processing helix chain 'BB' and resid 106 through 114 removed outlier: 4.630A pdb=" N SERBB 112 " --> pdb=" O ASPBB 108 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N METBB 113 " --> pdb=" O LYSBB 109 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALBB 114 " --> pdb=" O METBB 110 " (cutoff:3.500A) Processing helix chain 'BB' and resid 157 through 179 removed outlier: 4.413A pdb=" N THRBB 178 " --> pdb=" O ARGBB 174 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASNBB 179 " --> pdb=" O GLUBB 175 " (cutoff:3.500A) Processing helix chain 'BB' and resid 180 through 191 Proline residue: BB 190 - end of helix Processing helix chain 'BB' and resid 192 through 203 removed outlier: 3.579A pdb=" N LYSBB 199 " --> pdb=" O LYSBB 195 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLNBB 202 " --> pdb=" O GLUBB 198 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SERBB 203 " --> pdb=" O LYSBB 199 " (cutoff:3.500A) Processing helix chain 'BB' and resid 224 through 233 Processing helix chain 'CC' and resid 64 through 73 Processing helix chain 'CC' and resid 77 through 85 removed outlier: 4.360A pdb=" N ILECC 81 " --> pdb=" O SERCC 77 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHECC 84 " --> pdb=" O GLUCC 80 " (cutoff:3.500A) Processing helix chain 'CC' and resid 90 through 98 removed outlier: 3.886A pdb=" N ILECC 94 " --> pdb=" O GLUCC 90 " (cutoff:3.500A) Processing helix chain 'CC' and resid 146 through 162 removed outlier: 3.587A pdb=" N ILECC 162 " --> pdb=" O ALACC 158 " (cutoff:3.500A) Processing helix chain 'CC' and resid 207 through 218 removed outlier: 3.528A pdb=" N LEUCC 213 " --> pdb=" O VALCC 209 " (cutoff:3.500A) Processing helix chain 'CC' and resid 232 through 250 removed outlier: 3.697A pdb=" N THRCC 240 " --> pdb=" O PHECC 236 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THRCC 247 " --> pdb=" O ALACC 243 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYRCC 248 " --> pdb=" O ILECC 244 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SERCC 249 " --> pdb=" O SERCC 245 " (cutoff:3.500A) Processing helix chain 'CC' and resid 252 through 257 removed outlier: 5.685A pdb=" N LYSCC 257 " --> pdb=" O PROCC 253 " (cutoff:3.500A) Processing helix chain 'CC' and resid 264 through 270 removed outlier: 3.717A pdb=" N PHECC 269 " --> pdb=" O PROCC 265 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THRCC 270 " --> pdb=" O TYRCC 266 " (cutoff:3.500A) Processing helix chain 'CC' and resid 271 through 277 Processing helix chain 'DD' and resid 6 through 30 removed outlier: 3.933A pdb=" N ALADD 30 " --> pdb=" O THRDD 26 " (cutoff:3.500A) Processing helix chain 'DD' and resid 54 through 60 Processing helix chain 'DD' and resid 63 through 78 removed outlier: 3.685A pdb=" N ALADD 71 " --> pdb=" O ARGDD 67 " (cutoff:3.500A) Processing helix chain 'DD' and resid 93 through 98 removed outlier: 4.202A pdb=" N CYSDD 97 " --> pdb=" O THRDD 93 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALADD 98 " --> pdb=" O ARGDD 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'DD' and resid 93 through 98' Processing helix chain 'DD' and resid 99 through 112 removed outlier: 3.716A pdb=" N GLYDD 112 " --> pdb=" O LYSDD 108 " (cutoff:3.500A) Processing helix chain 'DD' and resid 114 through 130 Processing helix chain 'DD' and resid 161 through 167 removed outlier: 4.610A pdb=" N ASNDD 165 " --> pdb=" O GLYDD 161 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYRDD 166 " --> pdb=" O ASPDD 162 " (cutoff:3.500A) Processing helix chain 'EE' and resid 21 through 26 removed outlier: 4.954A pdb=" N GLYEE 25 " --> pdb=" O ASPEE 21 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VALEE 26 " --> pdb=" O LYSEE 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'EE' and resid 21 through 26' Processing helix chain 'EE' and resid 43 through 49 Processing helix chain 'EE' and resid 57 through 68 removed outlier: 3.629A pdb=" N VALEE 61 " --> pdb=" O THREE 57 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLNEE 67 " --> pdb=" O LYSEE 63 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARGEE 68 " --> pdb=" O ILEEE 64 " (cutoff:3.500A) Processing helix chain 'EE' and resid 115 through 120 Processing helix chain 'EE' and resid 221 through 226 removed outlier: 3.604A pdb=" N ILEEE 225 " --> pdb=" O ARGEE 221 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHEEE 226 " --> pdb=" O LEUEE 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'EE' and resid 221 through 226' Processing helix chain 'EE' and resid 247 through 263 removed outlier: 3.755A pdb=" N ALAEE 258 " --> pdb=" O LYSEE 254 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLYEE 263 " --> pdb=" O LYSEE 259 " (cutoff:3.500A) Processing helix chain 'FF' and resid 35 through 40 removed outlier: 4.424A pdb=" N ALAFF 40 " --> pdb=" O GLNFF 36 " (cutoff:3.500A) Processing helix chain 'FF' and resid 61 through 66 removed outlier: 4.554A pdb=" N GLNFF 65 " --> pdb=" O PHEFF 61 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N CYSFF 66 " --> pdb=" O ARGFF 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'FF' and resid 61 through 66' Processing helix chain 'FF' and resid 67 through 78 removed outlier: 4.969A pdb=" N METFF 78 " --> pdb=" O ASNFF 74 " (cutoff:3.500A) Processing helix chain 'FF' and resid 85 through 104 removed outlier: 3.619A pdb=" N LEUFF 102 " --> pdb=" O GLUFF 98 " (cutoff:3.500A) Processing helix chain 'FF' and resid 107 through 120 Processing helix chain 'FF' and resid 142 through 164 removed outlier: 6.156A pdb=" N ARGFF 164 " --> pdb=" O GLUFF 160 " (cutoff:3.500A) Processing helix chain 'FF' and resid 168 through 183 Processing helix chain 'FF' and resid 187 through 204 removed outlier: 4.415A pdb=" N GLUFF 195 " --> pdb=" O LYSFF 191 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASNFF 203 " --> pdb=" O VALFF 199 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARGFF 204 " --> pdb=" O ALAFF 200 " (cutoff:3.500A) Processing helix chain 'GG' and resid 20 through 31 removed outlier: 4.189A pdb=" N LYSGG 30 " --> pdb=" O THRGG 26 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARGGG 31 " --> pdb=" O PHEGG 27 " (cutoff:3.500A) Processing helix chain 'GG' and resid 137 through 146 Processing helix chain 'GG' and resid 152 through 157 removed outlier: 4.442A pdb=" N TYRGG 156 " --> pdb=" O ASPGG 152 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VALGG 157 " --> pdb=" O VALGG 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'GG' and resid 152 through 157' Processing helix chain 'GG' and resid 181 through 237 removed outlier: 4.293A pdb=" N GLUGG 222 " --> pdb=" O LYSGG 218 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEUGG 237 " --> pdb=" O ARGGG 233 " (cutoff:3.500A) Processing helix chain 'HH' and resid 17 through 34 removed outlier: 4.002A pdb=" N ASNHH 33 " --> pdb=" O GLUHH 29 " (cutoff:3.500A) Processing helix chain 'HH' and resid 36 through 44 removed outlier: 3.686A pdb=" N LEUHH 40 " --> pdb=" O LEUHH 36 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLUHH 42 " --> pdb=" O ALAHH 38 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEUHH 43 " --> pdb=" O GLNHH 39 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASNHH 44 " --> pdb=" O LEUHH 40 " (cutoff:3.500A) Processing helix chain 'HH' and resid 65 through 76 removed outlier: 4.017A pdb=" N LYSHH 70 " --> pdb=" O VALHH 66 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SERHH 71 " --> pdb=" O PROHH 67 " (cutoff:3.500A) Processing helix chain 'HH' and resid 77 through 88 removed outlier: 3.845A pdb=" N ARGHH 81 " --> pdb=" O VALHH 77 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYSHH 85 " --> pdb=" O ARGHH 81 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYSHH 86 " --> pdb=" O GLUHH 82 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SERHH 88 " --> pdb=" O GLUHH 84 " (cutoff:3.500A) Processing helix chain 'HH' and resid 117 through 122 removed outlier: 3.613A pdb=" N THRHH 121 " --> pdb=" O PROHH 117 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEUHH 122 " --> pdb=" O ARGHH 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'HH' and resid 117 through 122' Processing helix chain 'HH' and resid 123 through 135 removed outlier: 3.872A pdb=" N ASPHH 127 " --> pdb=" O THRHH 123 " (cutoff:3.500A) Processing helix chain 'HH' and resid 165 through 181 removed outlier: 4.312A pdb=" N LYSHH 169 " --> pdb=" O ASNHH 165 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLUHH 171 " --> pdb=" O GLUHH 167 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THRHH 172 " --> pdb=" O HISHH 168 " (cutoff:3.500A) Processing helix chain 'II' and resid 87 through 94 removed outlier: 4.159A pdb=" N VALII 91 " --> pdb=" O ASNII 87 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARGII 92 " --> pdb=" O ASNII 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYSII 94 " --> pdb=" O LEUII 90 " (cutoff:3.500A) Processing helix chain 'II' and resid 106 through 117 Processing helix chain 'II' and resid 132 through 139 removed outlier: 3.983A pdb=" N LEUII 137 " --> pdb=" O GLUII 133 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASNII 138 " --> pdb=" O GLUII 134 " (cutoff:3.500A) Processing helix chain 'II' and resid 142 through 157 removed outlier: 3.579A pdb=" N LYSII 154 " --> pdb=" O ASPII 150 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASNII 155 " --> pdb=" O GLUII 151 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYSII 157 " --> pdb=" O LYSII 153 " (cutoff:3.500A) Processing helix chain 'II' and resid 159 through 169 Processing helix chain 'II' and resid 192 through 207 Processing helix chain 'JJ' and resid 21 through 36 removed outlier: 3.934A pdb=" N LYSJJ 30 " --> pdb=" O ASPJJ 26 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEUJJ 31 " --> pdb=" O GLNJJ 27 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 39 through 64 removed outlier: 3.773A pdb=" N VALJJ 43 " --> pdb=" O ASNJJ 39 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VALJJ 46 " --> pdb=" O GLUJJ 42 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASPJJ 64 " --> pdb=" O LEUJJ 60 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 67 through 85 Processing helix chain 'JJ' and resid 93 through 100 removed outlier: 4.266A pdb=" N ILEJJ 97 " --> pdb=" O LYSJJ 93 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEUJJ 98 " --> pdb=" O LEUJJ 94 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLYJJ 99 " --> pdb=" O ASPJJ 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEUJJ 100 " --> pdb=" O TYRJJ 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'JJ' and resid 93 through 100' Processing helix chain 'JJ' and resid 101 through 109 removed outlier: 3.513A pdb=" N PHEJJ 105 " --> pdb=" O LYSJJ 101 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARGJJ 108 " --> pdb=" O ASPJJ 104 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARGJJ 109 " --> pdb=" O PHEJJ 105 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 110 through 118 Processing helix chain 'JJ' and resid 122 through 133 removed outlier: 3.730A pdb=" N ARGJJ 133 " --> pdb=" O LEUJJ 129 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 150 through 155 removed outlier: 4.099A pdb=" N LYSJJ 155 " --> pdb=" O LEUJJ 151 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 171 through 186 Processing helix chain 'KK' and resid 4 through 19 removed outlier: 3.959A pdb=" N GLYKK 19 " --> pdb=" O LEUKK 15 " (cutoff:3.500A) Processing helix chain 'KK' and resid 41 through 56 Processing helix chain 'KK' and resid 72 through 84 Processing helix chain 'KK' and resid 91 through 96 removed outlier: 3.680A pdb=" N ARGKK 95 " --> pdb=" O PROKK 91 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARGKK 96 " --> pdb=" O ALAKK 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'KK' and resid 91 through 96' Processing helix chain 'LL' and resid 47 through 53 Processing helix chain 'MM' and resid 15 through 29 removed outlier: 4.043A pdb=" N GLNMM 19 " --> pdb=" O ASNMM 15 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLUMM 20 " --> pdb=" O THRMM 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HISMM 28 " --> pdb=" O THRMM 24 " (cutoff:3.500A) Processing helix chain 'MM' and resid 34 through 45 removed outlier: 3.770A pdb=" N ARGMM 45 " --> pdb=" O ALAMM 41 " (cutoff:3.500A) Processing helix chain 'MM' and resid 58 through 72 removed outlier: 3.605A pdb=" N LYSMM 63 " --> pdb=" O PROMM 59 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALAMM 70 " --> pdb=" O GLUMM 66 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLUMM 71 " --> pdb=" O ALAMM 67 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N HISMM 72 " --> pdb=" O LEUMM 68 " (cutoff:3.500A) Processing helix chain 'MM' and resid 81 through 90 Processing helix chain 'MM' and resid 118 through 130 removed outlier: 4.121A pdb=" N ASPMM 122 " --> pdb=" O SERMM 118 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VALMM 123 " --> pdb=" O GLNMM 119 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILEMM 124 " --> pdb=" O ALAMM 120 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLUMM 125 " --> pdb=" O LYSMM 121 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLUMM 126 " --> pdb=" O ASPMM 122 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYSMM 130 " --> pdb=" O GLUMM 126 " (cutoff:3.500A) Processing helix chain 'NN' and resid 29 through 44 removed outlier: 3.760A pdb=" N LYSNN 43 " --> pdb=" O LYSNN 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLYNN 44 " --> pdb=" O LEUNN 40 " (cutoff:3.500A) Processing helix chain 'NN' and resid 46 through 57 Processing helix chain 'NN' and resid 62 through 67 Processing helix chain 'NN' and resid 70 through 79 Processing helix chain 'NN' and resid 85 through 106 Processing helix chain 'NN' and resid 108 through 133 removed outlier: 3.624A pdb=" N TYRNN 128 " --> pdb=" O ARGNN 124 " (cutoff:3.500A) Processing helix chain 'NN' and resid 145 through 150 removed outlier: 4.235A pdb=" N LEUNN 149 " --> pdb=" O THRNN 145 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALNN 150 " --> pdb=" O ALANN 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'NN' and resid 145 through 150' Processing helix chain 'OO' and resid 57 through 62 removed outlier: 3.578A pdb=" N LYSOO 61 " --> pdb=" O THROO 57 " (cutoff:3.500A) Processing helix chain 'OO' and resid 64 through 69 removed outlier: 4.029A pdb=" N GLUOO 68 " --> pdb=" O ALAOO 64 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SEROO 69 " --> pdb=" O ASPOO 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'OO' and resid 64 through 69' Processing helix chain 'OO' and resid 70 through 89 Processing helix chain 'OO' and resid 110 through 123 removed outlier: 4.202A pdb=" N SEROO 114 " --> pdb=" O PROOO 110 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLYOO 123 " --> pdb=" O LEUOO 119 " (cutoff:3.500A) Processing helix chain 'PP' and resid 21 through 28 removed outlier: 3.655A pdb=" N METPP 28 " --> pdb=" O GLNPP 24 " (cutoff:3.500A) Processing helix chain 'PP' and resid 29 through 38 removed outlier: 5.331A pdb=" N SERPP 38 " --> pdb=" O METPP 34 " (cutoff:3.500A) Processing helix chain 'PP' and resid 39 through 48 Processing helix chain 'PP' and resid 50 through 68 removed outlier: 3.619A pdb=" N LYSPP 65 " --> pdb=" O ARGPP 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLUPP 66 " --> pdb=" O LYSPP 62 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALAPP 67 " --> pdb=" O ALAPP 63 " (cutoff:3.500A) Proline residue: PP 68 - end of helix Processing helix chain 'PP' and resid 115 through 121 removed outlier: 4.492A pdb=" N PHEPP 119 " --> pdb=" O TYRPP 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SERPP 120 " --> pdb=" O LEUPP 116 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILEPP 121 " --> pdb=" O GLYPP 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'PP' and resid 115 through 121' Processing helix chain 'QQ' and resid 38 through 43 removed outlier: 3.621A pdb=" N ILEQQ 42 " --> pdb=" O PROQQ 38 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLUQQ 43 " --> pdb=" O LEUQQ 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'QQ' and resid 38 through 43' Processing helix chain 'QQ' and resid 44 through 56 removed outlier: 4.228A pdb=" N GLNQQ 48 " --> pdb=" O PROQQ 44 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYRQQ 49 " --> pdb=" O ARGQQ 45 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYSQQ 50 " --> pdb=" O THRQQ 46 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEUQQ 51 " --> pdb=" O LEUQQ 47 " (cutoff:3.500A) Proline residue: QQ 54 - end of helix Processing helix chain 'QQ' and resid 59 through 65 removed outlier: 4.539A pdb=" N PHEQQ 63 " --> pdb=" O GLYQQ 59 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLYQQ 65 " --> pdb=" O GLUQQ 61 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 76 through 99 removed outlier: 3.981A pdb=" N VALQQ 93 " --> pdb=" O SERQQ 89 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYSQQ 98 " --> pdb=" O ALAQQ 94 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 101 through 116 removed outlier: 3.699A pdb=" N GLNQQ 114 " --> pdb=" O ASPQQ 110 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYRQQ 115 " --> pdb=" O ILEQQ 111 " (cutoff:3.500A) Processing helix chain 'RR' and resid 6 through 20 Processing helix chain 'RR' and resid 27 through 39 removed outlier: 3.680A pdb=" N ASNRR 31 " --> pdb=" O ASPRR 27 " (cutoff:3.500A) Processing helix chain 'RR' and resid 43 through 64 removed outlier: 3.982A pdb=" N ARGRR 47 " --> pdb=" O SERRR 43 " (cutoff:3.500A) Processing helix chain 'RR' and resid 71 through 84 removed outlier: 4.556A pdb=" N GLURR 76 " --> pdb=" O LYSRR 72 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARGRR 78 " --> pdb=" O GLNRR 74 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYRRR 84 " --> pdb=" O ARGRR 80 " (cutoff:3.500A) Processing helix chain 'RR' and resid 99 through 110 removed outlier: 3.606A pdb=" N LEURR 109 " --> pdb=" O METRR 105 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASPRR 110 " --> pdb=" O LEURR 106 " (cutoff:3.500A) Processing helix chain 'SS' and resid 37 through 49 removed outlier: 4.056A pdb=" N HISSS 42 " --> pdb=" O ARGSS 38 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALASS 48 " --> pdb=" O VALSS 44 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASPSS 49 " --> pdb=" O LEUSS 45 " (cutoff:3.500A) Processing helix chain 'SS' and resid 60 through 74 Proline residue: SS 74 - end of helix Processing helix chain 'SS' and resid 100 through 118 removed outlier: 4.765A pdb=" N ASPSS 104 " --> pdb=" O ALASS 100 " (cutoff:3.500A) Processing helix chain 'SS' and resid 119 through 128 Processing helix chain 'SS' and resid 140 through 145 removed outlier: 4.203A pdb=" N ARGSS 144 " --> pdb=" O GLYSS 140 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THRSS 145 " --> pdb=" O ARGSS 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 140 through 145' Processing helix chain 'SS' and resid 27 through 34 removed outlier: 5.165A pdb=" N ILESS 30 " --> pdb=" O ALASS 27 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYSSS 34 " --> pdb=" O THRSS 31 " (cutoff:3.500A) Processing helix chain 'TT' and resid 10 through 26 removed outlier: 4.239A pdb=" N ARGTT 16 " --> pdb=" O GLNTT 12 " (cutoff:3.500A) Processing helix chain 'TT' and resid 51 through 68 removed outlier: 4.293A pdb=" N THRTT 55 " --> pdb=" O ASNTT 51 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLYTT 68 " --> pdb=" O LEUTT 64 " (cutoff:3.500A) Processing helix chain 'TT' and resid 71 through 80 Processing helix chain 'TT' and resid 96 through 111 removed outlier: 4.465A pdb=" N LYSTT 111 " --> pdb=" O LEUTT 107 " (cutoff:3.500A) Processing helix chain 'TT' and resid 124 through 143 removed outlier: 3.841A pdb=" N LYSTT 143 " --> pdb=" O ALATT 139 " (cutoff:3.500A) Processing helix chain 'UU' and resid 28 through 47 removed outlier: 4.122A pdb=" N GLYUU 42 " --> pdb=" O ASPUU 38 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASNUU 47 " --> pdb=" O ALAUU 43 " (cutoff:3.500A) Processing helix chain 'UU' and resid 94 through 105 removed outlier: 4.607A pdb=" N VALUU 98 " --> pdb=" O PROUU 94 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLNUU 100 " --> pdb=" O GLUUU 96 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILEUU 101 " --> pdb=" O ILEUU 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERUU 103 " --> pdb=" O LYSUU 99 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SERUU 105 " --> pdb=" O ILEUU 101 " (cutoff:3.500A) Processing helix chain 'VV' and resid 56 through 63 Processing helix chain 'VV' and resid 64 through 77 Processing helix chain 'WW' and resid 5 through 21 Processing helix chain 'WW' and resid 31 through 45 Processing helix chain 'WW' and resid 83 through 94 removed outlier: 5.139A pdb=" N GLUWW 87 " --> pdb=" O LEUWW 83 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYSWW 88 " --> pdb=" O LYSWW 84 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASNWW 92 " --> pdb=" O LYSWW 88 " (cutoff:3.500A) Processing helix chain 'WW' and resid 112 through 120 Processing helix chain 'XX' and resid 9 through 24 removed outlier: 4.218A pdb=" N TRPXX 22 " --> pdb=" O ARGXX 18 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N HISXX 23 " --> pdb=" O ASPXX 19 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASPXX 24 " --> pdb=" O GLNXX 20 " (cutoff:3.500A) Processing helix chain 'XX' and resid 25 through 32 removed outlier: 3.721A pdb=" N ALAXX 30 " --> pdb=" O GLNXX 26 " (cutoff:3.500A) Processing helix chain 'XX' and resid 33 through 40 Proline residue: XX 40 - end of helix Processing helix chain 'XX' and resid 89 through 95 removed outlier: 4.310A pdb=" N PHEXX 93 " --> pdb=" O GLYXX 89 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLUXX 95 " --> pdb=" O LEUXX 91 " (cutoff:3.500A) Processing helix chain 'XX' and resid 129 through 136 Processing helix chain 'YY' and resid 36 through 49 Processing helix chain 'YY' and resid 51 through 56 removed outlier: 4.513A pdb=" N ILEYY 55 " --> pdb=" O THRYY 51 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHEYY 56 " --> pdb=" O PROYY 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'YY' and resid 51 through 56' Processing helix chain 'YY' and resid 78 through 86 Processing helix chain 'YY' and resid 87 through 95 removed outlier: 3.758A pdb=" N LEUYY 91 " --> pdb=" O PROYY 87 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALAYY 92 " --> pdb=" O LYSYY 88 " (cutoff:3.500A) Processing helix chain 'YY' and resid 103 through 118 removed outlier: 3.696A pdb=" N VALYY 117 " --> pdb=" O ARGYY 113 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARGYY 118 " --> pdb=" O METYY 114 " (cutoff:3.500A) Processing helix chain 'YY' and resid 120 through 126 removed outlier: 3.624A pdb=" N ASNYY 124 " --> pdb=" O THRYY 120 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLYYY 126 " --> pdb=" O LYSYY 122 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 51 through 61 removed outlier: 4.292A pdb=" N LYSZZ 57 " --> pdb=" O ALAZZ 53 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 69 through 78 Processing helix chain 'ZZ' and resid 80 through 95 removed outlier: 3.551A pdb=" N SERZZ 93 " --> pdb=" O GLNZZ 89 " (cutoff:3.500A) Processing helix chain 'aa' and resid 47 through 57 removed outlier: 4.928A pdb=" N ARGaa 51 " --> pdb=" O ALAaa 47 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASPaa 52 " --> pdb=" O ALAaa 48 " (cutoff:3.500A) Processing helix chain 'aa' and resid 74 through 82 Processing helix chain 'aa' and resid 88 through 94 removed outlier: 4.430A pdb=" N LYSaa 93 " --> pdb=" O ARGaa 89 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASPaa 94 " --> pdb=" O GLUaa 90 " (cutoff:3.500A) Processing helix chain 'bb' and resid 11 through 19 removed outlier: 4.243A pdb=" N LYSbb 16 " --> pdb=" O PRObb 12 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARGbb 17 " --> pdb=" O GLUbb 13 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HISbb 19 " --> pdb=" O GLUbb 15 " (cutoff:3.500A) Processing helix chain 'dd' and resid 2 through 9 removed outlier: 5.631A pdb=" N TRPdd 8 " --> pdb=" O GLNdd 4 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SERdd 9 " --> pdb=" O GLNdd 5 " (cutoff:3.500A) Processing helix chain 'dd' and resid 39 through 47 Processing helix chain 'ee' and resid 83 through 89 Processing helix chain 'ee' and resid 103 through 115 Processing helix chain 'ff' and resid 101 through 106 removed outlier: 4.682A pdb=" N TYRff 105 " --> pdb=" O ALAff 101 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYRff 106 " --> pdb=" O VALff 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'ff' and resid 101 through 106' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.912A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.751A pdb=" N THR A 111 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 65 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'A' and resid 145 through 150 removed outlier: 3.821A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 41 through 44 removed outlier: 3.609A pdb=" N HIS B 42 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN B 184 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 53 through 58 removed outlier: 6.684A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.634A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 286 through 290 removed outlier: 4.120A pdb=" N GLY B 290 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN B 328 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 291 through 294 removed outlier: 3.655A pdb=" N LEU B 292 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 76 through 80 Processing sheet with id= 11, first strand: chain 'B' and resid 88 through 93 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'C' and resid 226 through 232 removed outlier: 5.463A pdb=" N PHE C 249 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 60 through 66 removed outlier: 3.761A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 93 through 98 removed outlier: 6.072A pdb=" N ALA E 93 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 150 through 156 removed outlier: 4.086A pdb=" N THR E 151 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS E 163 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL E 165 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY E 180 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE E 167 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL E 178 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS E 169 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU E 176 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU E 171 " --> pdb=" O GLY E 174 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 138 through 143 removed outlier: 6.980A pdb=" N TYR F 138 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LYS F 87 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN F 118 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE F 117 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 232 through 237 removed outlier: 3.707A pdb=" N LEU G 207 " --> pdb=" O PHE G 257 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 5 through 12 removed outlier: 5.944A pdb=" N LYS H 53 " --> pdb=" O ILE H 12 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 20, first strand: chain 'H' and resid 102 through 106 removed outlier: 7.499A pdb=" N SER H 110 " --> pdb=" O MET H 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET H 128 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 132 through 136 removed outlier: 5.977A pdb=" N ASP H 142 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.580A pdb=" N PHE I 34 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE I 135 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET I 136 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N CYS I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG I 162 " --> pdb=" O ASP I 55 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 95 through 98 removed outlier: 3.705A pdb=" N GLY I 124 " --> pdb=" O ILE I 97 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 189 through 192 removed outlier: 5.614A pdb=" N ARG I 189 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 48 through 52 removed outlier: 7.978A pdb=" N ILE J 68 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N CYS J 25 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLY J 127 " --> pdb=" O CYS J 25 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 57 through 60 Processing sheet with id= 27, first strand: chain 'M' and resid 11 through 16 removed outlier: 4.356A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS M 23 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.533A pdb=" N ARG M 35 " --> pdb=" O ILE M 31 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 113 through 116 removed outlier: 6.833A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 31, first strand: chain 'P' and resid 13 through 20 removed outlier: 7.273A pdb=" N LYS P 13 " --> pdb=" O GLU P 152 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 124 through 132 removed outlier: 4.140A pdb=" N ARG P 127 " --> pdb=" O TYR P 139 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG P 135 " --> pdb=" O ARG P 131 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 78 through 82 Processing sheet with id= 34, first strand: chain 'S' and resid 27 through 33 removed outlier: 6.729A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 91 through 99 removed outlier: 3.568A pdb=" N MET S 93 " --> pdb=" O LEU S 82 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 9 through 13 removed outlier: 4.965A pdb=" N GLU S 9 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 39 through 43 removed outlier: 3.958A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 13.521A pdb=" N GLY T 59 " --> pdb=" O GLN T 79 " (cutoff:3.500A) removed outlier: 11.585A pdb=" N GLN T 79 " --> pdb=" O GLY T 59 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR T 61 " --> pdb=" O ASN T 77 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN T 77 " --> pdb=" O THR T 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY T 73 " --> pdb=" O TYR T 65 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 61 through 65 removed outlier: 5.661A pdb=" N GLU U 108 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N TRP U 99 " --> pdb=" O PHE U 115 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 24 through 27 removed outlier: 4.300A pdb=" N ALA V 24 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET V 62 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP V 59 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP V 100 " --> pdb=" O ARG V 85 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG V 85 " --> pdb=" O ASP V 100 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 87 through 90 removed outlier: 3.607A pdb=" N VAL V 94 " --> pdb=" O ARG V 90 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 18 through 22 Processing sheet with id= 42, first strand: chain 'X' and resid 94 through 99 removed outlier: 6.970A pdb=" N ASN X 94 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU X 133 " --> pdb=" O ARG X 129 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS X 123 " --> pdb=" O ARG X 139 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Y' and resid 53 through 56 removed outlier: 4.897A pdb=" N ASP Y 53 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Y' and resid 72 through 75 removed outlier: 3.722A pdb=" N GLN Y 72 " --> pdb=" O TYR Y 81 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.578A pdb=" N THR Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 9 through 13 removed outlier: 5.102A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 48, first strand: chain 'a' and resid 98 through 101 Processing sheet with id= 49, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.143A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY c 70 " --> pdb=" O LYS c 44 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 61 through 64 removed outlier: 5.175A pdb=" N ASP d 61 " --> pdb=" O LEU d 102 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR d 22 " --> pdb=" O VAL d 122 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 74 through 80 Processing sheet with id= 52, first strand: chain 'f' and resid 8 through 12 removed outlier: 6.116A pdb=" N LYS f 8 " --> pdb=" O GLU f 31 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU f 27 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS f 87 " --> pdb=" O LYS f 73 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS f 73 " --> pdb=" O LYS f 87 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS f 66 " --> pdb=" O ALA f 53 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS f 45 " --> pdb=" O VAL f 74 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG f 46 " --> pdb=" O MET f 104 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 6 through 12 removed outlier: 4.301A pdb=" N HIS f 99 " --> pdb=" O PHE f 11 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'g' and resid 20 through 24 Processing sheet with id= 55, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.792A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER k 22 " --> pdb=" O ARG k 37 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU k 69 " --> pdb=" O ILE k 25 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS k 27 " --> pdb=" O LEU k 69 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'm' and resid 74 through 77 removed outlier: 6.255A pdb=" N LYS m 67 " --> pdb=" O LYS m 98 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ASN m 94 " --> pdb=" O ARG m 71 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'o' and resid 7 through 10 removed outlier: 5.497A pdb=" N VAL o 67 " --> pdb=" O TYR o 26 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE o 66 " --> pdb=" O ILE o 85 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER o 79 " --> pdb=" O CYS o 72 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.234A pdb=" N LYS p 46 " --> pdb=" O GLY p 58 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY p 58 " --> pdb=" O LYS p 46 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'r' and resid 48 through 53 removed outlier: 5.126A pdb=" N THR r 48 " --> pdb=" O LYS r 65 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N SER r 76 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'AA' and resid 24 through 28 removed outlier: 5.597A pdb=" N HISAA 24 " --> pdb=" O ILEAA 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYRAA 47 " --> pdb=" O GLYAA 26 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THRAA 28 " --> pdb=" O GLYAA 45 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLYAA 45 " --> pdb=" O THRAA 28 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'AA' and resid 96 through 99 Processing sheet with id= 62, first strand: chain 'BB' and resid 45 through 48 removed outlier: 4.038A pdb=" N GLYBB 45 " --> pdb=" O VALBB 33 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'BB' and resid 119 through 128 removed outlier: 5.130A pdb=" N THRBB 119 " --> pdb=" O THRBB 143 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEUBB 134 " --> pdb=" O LEUBB 218 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'BB' and resid 102 through 105 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'CC' and resid 102 through 107 removed outlier: 4.374A pdb=" N GLYCC 131 " --> pdb=" O LYSCC 103 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHECC 127 " --> pdb=" O LEUCC 107 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'CC' and resid 183 through 187 removed outlier: 4.141A pdb=" N ALACC 198 " --> pdb=" O ASPCC 221 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASPCC 221 " --> pdb=" O ALACC 198 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'CC' and resid 123 through 132 removed outlier: 4.106A pdb=" N HISCC 136 " --> pdb=" O ASPCC 132 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'DD' and resid 46 through 53 Processing sheet with id= 69, first strand: chain 'DD' and resid 148 through 155 removed outlier: 3.530A pdb=" N GLYDD 133 " --> pdb=" O METDD 189 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'EE' and resid 88 through 92 removed outlier: 3.988A pdb=" N ASPEE 88 " --> pdb=" O LEUEE 101 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'EE' and resid 121 through 126 removed outlier: 4.309A pdb=" N ASPEE 158 " --> pdb=" O VALEE 126 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASNEE 157 " --> pdb=" O PHEEE 175 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHEEE 175 " --> pdb=" O ASNEE 157 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASPEE 171 " --> pdb=" O GLNEE 161 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'EE' and resid 128 through 131 removed outlier: 4.623A pdb=" N ARGEE 145 " --> pdb=" O THREE 141 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'EE' and resid 197 through 201 removed outlier: 4.441A pdb=" N HISEE 201 " --> pdb=" O PHEEE 205 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHEEE 205 " --> pdb=" O HISEE 201 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'FF' and resid 122 through 127 removed outlier: 6.349A pdb=" N ARGFF 122 " --> pdb=" O VALFF 141 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'GG' and resid 11 through 18 removed outlier: 5.602A pdb=" N ASNGG 110 " --> pdb=" O SERGG 53 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VALGG 49 " --> pdb=" O VALGG 114 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THRGG 34 " --> pdb=" O ILEGG 52 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'GG' and resid 159 through 163 Processing sheet with id= 77, first strand: chain 'HH' and resid 47 through 53 removed outlier: 4.119A pdb=" N ALAHH 47 " --> pdb=" O PHEHH 63 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'HH' and resid 141 through 147 removed outlier: 3.808A pdb=" N SERHH 151 " --> pdb=" O LYSHH 147 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASPHH 184 " --> pdb=" O ARGHH 152 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'II' and resid 42 through 48 removed outlier: 6.443A pdb=" N ARGII 42 " --> pdb=" O LEUII 58 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'II' and resid 72 through 75 removed outlier: 4.265A pdb=" N ASNII 64 " --> pdb=" O ALAII 185 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASPII 186 " --> pdb=" O ALAII 176 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEUII 172 " --> pdb=" O LEUII 190 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYSII 100 " --> pdb=" O ILEII 175 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILEII 101 " --> pdb=" O VALII 82 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'KK' and resid 20 through 24 removed outlier: 4.510A pdb=" N METKK 21 " --> pdb=" O TRPKK 69 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRPKK 69 " --> pdb=" O METKK 21 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HISKK 66 " --> pdb=" O ALAKK 63 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'LL' and resid 71 through 76 removed outlier: 5.534A pdb=" N ARGLL 71 " --> pdb=" O GLULL 130 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THRLL 127 " --> pdb=" O LEULL 143 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'LL' and resid 84 through 95 No H-bonds generated for sheet with id= 83 Processing sheet with id= 84, first strand: chain 'MM' and resid 30 through 33 removed outlier: 5.486A pdb=" N GLYMM 30 " --> pdb=" O LYSMM 112 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASNMM 75 " --> pdb=" O HISMM 48 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYSMM 50 " --> pdb=" O ASNMM 75 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILEMM 77 " --> pdb=" O CYSMM 50 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'OO' and resid 40 through 46 removed outlier: 5.317A pdb=" N ILEOO 95 " --> pdb=" O GLYOO 127 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'OO' and resid 94 through 98 No H-bonds generated for sheet with id= 86 Processing sheet with id= 87, first strand: chain 'PP' and resid 75 through 78 removed outlier: 4.136A pdb=" N SERPP 92 " --> pdb=" O ILEPP 107 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'QQ' and resid 9 through 15 removed outlier: 5.660A pdb=" N ASPQQ 67 " --> pdb=" O LYSQQ 26 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'RR' and resid 95 through 98 removed outlier: 3.918A pdb=" N ILERR 96 " --> pdb=" O ASNRR 116 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALRR 98 " --> pdb=" O GLNRR 118 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'TT' and resid 81 through 84 Processing sheet with id= 91, first strand: chain 'TT' and resid 113 through 116 removed outlier: 4.307A pdb=" N GLYTT 120 " --> pdb=" O ASPTT 116 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'UU' and resid 84 through 92 Processing sheet with id= 93, first strand: chain 'VV' and resid 32 through 38 removed outlier: 4.754A pdb=" N GLNVV 49 " --> pdb=" O GLUVV 38 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'WW' and resid 23 through 28 removed outlier: 5.226A pdb=" N ARGWW 23 " --> pdb=" O LEUWW 65 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLUWW 49 " --> pdb=" O ASNWW 64 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'WW' and resid 79 through 82 removed outlier: 4.471A pdb=" N PHEWW 79 " --> pdb=" O ILEWW 125 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VALWW 103 " --> pdb=" O LEUWW 126 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'XX' and resid 46 through 50 removed outlier: 6.576A pdb=" N LEUXX 101 " --> pdb=" O VALXX 123 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'XX' and resid 52 through 59 removed outlier: 5.131A pdb=" N ALAXX 65 " --> pdb=" O ALAXX 59 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYSXX 79 " --> pdb=" O LEUXX 74 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'YY' and resid 5 through 10 removed outlier: 4.623A pdb=" N VALYY 24 " --> pdb=" O LYSYY 11 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYSYY 11 " --> pdb=" O VALYY 24 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'YY' and resid 58 through 62 removed outlier: 4.747A pdb=" N GLYYY 59 " --> pdb=" O PHEYY 72 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHEYY 72 " --> pdb=" O GLYYY 59 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'YY' and resid 25 through 30 No H-bonds generated for sheet with id=100 Processing sheet with id=101, first strand: chain 'aa' and resid 20 through 23 removed outlier: 4.752A pdb=" N ARGaa 28 " --> pdb=" O CYSaa 23 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'aa' and resid 36 through 43 Processing sheet with id=103, first strand: chain 'bb' and resid 33 through 36 No H-bonds generated for sheet with id=103 Processing sheet with id=104, first strand: chain 'cc' and resid 9 through 14 removed outlier: 3.604A pdb=" N LYScc 10 " --> pdb=" O LEUcc 58 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASPcc 54 " --> pdb=" O VALcc 14 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'cc' and resid 18 through 22 removed outlier: 5.540A pdb=" N ARGcc 40 " --> pdb=" O PHEcc 34 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'ff' and resid 132 through 135 removed outlier: 4.325A pdb=" N TYRff 140 " --> pdb=" O ALAff 133 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'gg' and resid 3 through 8 removed outlier: 6.868A pdb=" N GLNgg 4 " --> pdb=" O THRgg 313 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VALgg 309 " --> pdb=" O ARGgg 8 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VALgg 312 " --> pdb=" O GLNgg 296 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLNgg 296 " --> pdb=" O VALgg 312 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THRgg 297 " --> pdb=" O SERgg 292 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'gg' and resid 19 through 23 removed outlier: 6.529A pdb=" N ASPgg 29 " --> pdb=" O LEUgg 45 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEUgg 45 " --> pdb=" O ASPgg 29 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILEgg 31 " --> pdb=" O TRPgg 43 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRPgg 43 " --> pdb=" O ILEgg 31 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N METgg 42 " --> pdb=" O GLNgg 56 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYRgg 52 " --> pdb=" O THRgg 46 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'gg' and resid 67 through 72 removed outlier: 5.419A pdb=" N PHEgg 77 " --> pdb=" O SERgg 72 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N GLNgg 76 " --> pdb=" O LEUgg 92 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEUgg 92 " --> pdb=" O GLNgg 76 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAgg 78 " --> pdb=" O TRPgg 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THRgg 86 " --> pdb=" O SERgg 82 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEUgg 89 " --> pdb=" O THRgg 98 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'gg' and resid 109 through 114 removed outlier: 4.298A pdb=" N SERgg 110 " --> pdb=" O GLYgg 123 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLNgg 119 " --> pdb=" O SERgg 114 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'gg' and resid 153 through 156 removed outlier: 4.247A pdb=" N LEUgg 173 " --> pdb=" O GLYgg 169 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VALgg 174 " --> pdb=" O HISgg 188 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HISgg 188 " --> pdb=" O VALgg 174 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THRgg 186 " --> pdb=" O VALgg 176 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'gg' and resid 196 through 200 removed outlier: 3.753A pdb=" N THRgg 197 " --> pdb=" O GLYgg 210 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLYgg 210 " --> pdb=" O THRgg 197 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'gg' and resid 238 through 242 removed outlier: 4.194A pdb=" N ALAgg 238 " --> pdb=" O ALAgg 251 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TRPgg 247 " --> pdb=" O SERgg 242 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'gg' and resid 39 through 42 3516 hydrogen bonds defined for protein. 10410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4235 hydrogen bonds 7154 hydrogen bond angles 0 basepair planarities 1621 basepair parallelities 2870 stacking parallelities Total time for adding SS restraints: 420.28 Time building geometry restraints manager: 71.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 21226 1.30 - 1.44: 94650 1.44 - 1.57: 99026 1.57 - 1.70: 11149 1.70 - 1.83: 642 Bond restraints: 226693 Sorted by residual: bond pdb=" C02 Z2V 55288 " pdb=" O01 Z2V 55288 " ideal model delta sigma weight residual 1.185 1.393 -0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C09 Z2V 55288 " pdb=" O14 Z2V 55288 " ideal model delta sigma weight residual 1.184 1.372 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" C11 Z2V 55288 " pdb=" O13 Z2V 55288 " ideal model delta sigma weight residual 1.188 1.375 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C04 Z2V 55288 " pdb=" C06 Z2V 55288 " ideal model delta sigma weight residual 1.533 1.614 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C03 Z2V 55288 " pdb=" C04 Z2V 55288 " ideal model delta sigma weight residual 1.530 1.459 0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 226688 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.35: 27121 105.35 - 112.95: 133043 112.95 - 120.56: 97537 120.56 - 128.16: 66147 128.16 - 135.77: 9145 Bond angle restraints: 332993 Sorted by residual: angle pdb=" CA PROHH 65 " pdb=" N PROHH 65 " pdb=" CD PROHH 65 " ideal model delta sigma weight residual 112.00 99.57 12.43 1.40e+00 5.10e-01 7.89e+01 angle pdb=" C12 Z2V 55288 " pdb=" C11 Z2V 55288 " pdb=" O13 Z2V 55288 " ideal model delta sigma weight residual 123.51 107.83 15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" N10 Z2V 55288 " pdb=" C11 Z2V 55288 " pdb=" O13 Z2V 55288 " ideal model delta sigma weight residual 123.52 107.89 15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" N10 Z2V 55288 " pdb=" C09 Z2V 55288 " pdb=" O14 Z2V 55288 " ideal model delta sigma weight residual 123.49 108.96 14.53 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C08 Z2V 55288 " pdb=" C09 Z2V 55288 " pdb=" O14 Z2V 55288 " ideal model delta sigma weight residual 123.48 109.02 14.46 3.00e+00 1.11e-01 2.32e+01 ... (remaining 332988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 119990 35.98 - 71.96: 4200 71.96 - 107.95: 371 107.95 - 143.93: 65 143.93 - 179.91: 91 Dihedral angle restraints: 124717 sinusoidal: 92088 harmonic: 32629 Sorted by residual: dihedral pdb=" O4' C 91139 " pdb=" C1' C 91139 " pdb=" N1 C 91139 " pdb=" C2 C 91139 " ideal model delta sinusoidal sigma weight residual 200.00 21.32 178.68 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 52008 " pdb=" C1' U 52008 " pdb=" N1 U 52008 " pdb=" C2 U 52008 " ideal model delta sinusoidal sigma weight residual 200.00 22.79 177.21 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 91551 " pdb=" C1' U 91551 " pdb=" N1 U 91551 " pdb=" C2 U 91551 " ideal model delta sinusoidal sigma weight residual -160.00 15.66 -175.66 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 124714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.077: 41451 1.077 - 2.155: 0 2.155 - 3.232: 0 3.232 - 4.310: 0 4.310 - 5.387: 1 Chirality restraints: 41452 Sorted by residual: chirality pdb=" C16 Z2V 55288 " pdb=" C15 Z2V 55288 " pdb=" C26 Z2V 55288 " pdb=" C27 Z2V 55288 " both_signs ideal model delta sigma weight residual False 2.71 -2.68 5.39 2.00e-01 2.50e+01 7.25e+02 chirality pdb=" CB ILEaa 41 " pdb=" CA ILEaa 41 " pdb=" CG1 ILEaa 41 " pdb=" CG2 ILEaa 41 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C1' G 9 958 " pdb=" O4' G 9 958 " pdb=" C2' G 9 958 " pdb=" N9 G 9 958 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 41449 not shown) Planarity restraints: 21348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 Z2V 55288 " 0.012 2.00e-02 2.50e+03 2.76e-01 9.55e+02 pdb=" C09 Z2V 55288 " -0.401 2.00e-02 2.50e+03 pdb=" C11 Z2V 55288 " 0.246 2.00e-02 2.50e+03 pdb=" N10 Z2V 55288 " -0.202 2.00e-02 2.50e+03 pdb=" O14 Z2V 55288 " 0.345 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 Z2V 55288 " 0.366 2.00e-02 2.50e+03 2.11e-01 4.46e+02 pdb=" C03 Z2V 55288 " -0.115 2.00e-02 2.50e+03 pdb=" C28 Z2V 55288 " -0.118 2.00e-02 2.50e+03 pdb=" O01 Z2V 55288 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Z2V 55288 " 0.362 2.00e-02 2.50e+03 2.09e-01 4.37e+02 pdb=" C12 Z2V 55288 " -0.118 2.00e-02 2.50e+03 pdb=" N10 Z2V 55288 " -0.118 2.00e-02 2.50e+03 pdb=" O13 Z2V 55288 " -0.126 2.00e-02 2.50e+03 ... (remaining 21345 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 1202 2.39 - 3.02: 116784 3.02 - 3.65: 359596 3.65 - 4.27: 590212 4.27 - 4.90: 852521 Nonbonded interactions: 1920315 Sorted by model distance: nonbonded pdb=" OP2 U 53645 " pdb="MG MG 55158 " model vdw 1.763 2.170 nonbonded pdb=" O6 G 91605 " pdb="MG MG 91955 " model vdw 1.769 2.170 nonbonded pdb=" OP1 A 54378 " pdb="MG MG 55265 " model vdw 1.781 2.170 nonbonded pdb=" O2' C 5 485 " pdb=" O5' C 5 486 " model vdw 1.781 2.440 nonbonded pdb=" O2' G 9 751 " pdb=" O4' G 9 752 " model vdw 1.782 2.440 ... (remaining 1920310 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 5591 5.49 5 Mg 277 5.21 5 S 411 5.16 5 C 110996 2.51 5 N 39397 2.21 5 O 54512 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: 1.650 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: 0.170 Extract box with map and model: 22.670 Check model and map are aligned: 2.070 Convert atoms to be neutral: 1.180 Process input model: 787.990 Find NCS groups from input model: 5.180 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 824.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.208 226693 Z= 0.237 Angle : 0.562 15.679 332993 Z= 0.299 Chirality : 0.045 5.387 41452 Planarity : 0.006 0.276 21348 Dihedral : 16.153 179.910 103679 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.08), residues: 11145 helix: 0.54 (0.09), residues: 3740 sheet: -1.19 (0.12), residues: 1702 loop : -1.18 (0.08), residues: 5703 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1937 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1932 time to evaluate : 10.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 1932 average time/residue: 1.8158 time to fit residues: 6004.4914 Evaluate side-chains 1703 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1703 time to evaluate : 9.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 1395 optimal weight: 10.0000 chunk 1252 optimal weight: 10.0000 chunk 695 optimal weight: 6.9990 chunk 427 optimal weight: 6.9990 chunk 845 optimal weight: 0.2980 chunk 669 optimal weight: 9.9990 chunk 1295 optimal weight: 10.0000 chunk 501 optimal weight: 8.9990 chunk 787 optimal weight: 0.0980 chunk 964 optimal weight: 9.9990 chunk 1501 optimal weight: 30.0000 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 HIS L 19 GLN L 149 GLN N 109 HIS R 86 ASN U 27 HIS U 94 ASN X 105 ASN X 111 GLN X 125 ASN ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN e 52 GLN h 65 GLN o 21 HIS r 31 ASN AA 33 GLN FF 82 ASN GG 186 GLN II 7 ASN KK 28 HIS ** KK 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** PP 79 HIS QQ 11 GLN ** QQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** QQ 142 GLN TT 105 GLN ** YY 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** dd 16 GLN ee 88 GLN ** gg 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 226693 Z= 0.370 Angle : 0.687 24.499 332993 Z= 0.345 Chirality : 0.043 2.607 41452 Planarity : 0.006 0.106 21348 Dihedral : 15.582 179.935 79778 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.08), residues: 11145 helix: 0.44 (0.08), residues: 3724 sheet: -1.23 (0.12), residues: 1723 loop : -1.12 (0.08), residues: 5698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1884 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1731 time to evaluate : 9.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 118 residues processed: 1790 average time/residue: 1.8596 time to fit residues: 5696.3802 Evaluate side-chains 1760 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1642 time to evaluate : 10.626 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 0 residues processed: 118 average time/residue: 1.4844 time to fit residues: 348.5198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 834 optimal weight: 5.9990 chunk 465 optimal weight: 0.8980 chunk 1249 optimal weight: 30.0000 chunk 1022 optimal weight: 30.0000 chunk 414 optimal weight: 6.9990 chunk 1503 optimal weight: 20.0000 chunk 1624 optimal weight: 20.0000 chunk 1339 optimal weight: 10.0000 chunk 1491 optimal weight: 20.0000 chunk 512 optimal weight: 4.9990 chunk 1206 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 354 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS I 144 ASN L 19 GLN N 109 HIS R 86 ASN U 27 HIS U 94 ASN X 105 ASN X 111 GLN Z 132 GLN ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN CC 136 HIS CC 235 ASN CC 267 GLN ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** GG 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 7 ASN LL 141 ASN MM 55 ASN PP 79 HIS ** YY 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ee 88 GLN ** ee 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** gg 244 ASN ** gg 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.109 226693 Z= 0.408 Angle : 0.712 25.297 332993 Z= 0.357 Chirality : 0.044 2.468 41452 Planarity : 0.006 0.075 21348 Dihedral : 15.685 179.850 79778 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.08), residues: 11145 helix: 0.27 (0.08), residues: 3730 sheet: -1.25 (0.12), residues: 1706 loop : -1.16 (0.08), residues: 5709 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1848 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1710 time to evaluate : 10.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 80 residues processed: 1799 average time/residue: 1.8032 time to fit residues: 5578.1448 Evaluate side-chains 1717 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1637 time to evaluate : 9.623 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 1.4069 time to fit residues: 223.2320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 1485 optimal weight: 10.0000 chunk 1130 optimal weight: 4.9990 chunk 780 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 717 optimal weight: 7.9990 chunk 1009 optimal weight: 6.9990 chunk 1509 optimal weight: 10.0000 chunk 1597 optimal weight: 20.0000 chunk 788 optimal weight: 0.9980 chunk 1430 optimal weight: 10.0000 chunk 430 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN M 131 GLN N 109 HIS R 86 ASN U 27 HIS U 94 ASN X 111 GLN ** X 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN ** AA 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** GG 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 7 ASN KK 39 ASN PP 79 HIS ** QQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TT 105 GLN VV 33 GLN ** YY 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.123 226693 Z= 0.251 Angle : 0.613 25.589 332993 Z= 0.312 Chirality : 0.039 2.429 41452 Planarity : 0.005 0.099 21348 Dihedral : 15.547 179.804 79778 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.08), residues: 11145 helix: 0.52 (0.08), residues: 3732 sheet: -1.16 (0.12), residues: 1697 loop : -1.04 (0.08), residues: 5716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1908 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1735 time to evaluate : 9.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 104 residues processed: 1831 average time/residue: 1.7279 time to fit residues: 5415.0983 Evaluate side-chains 1752 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1648 time to evaluate : 9.535 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 0 residues processed: 104 average time/residue: 1.3727 time to fit residues: 284.5664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 1330 optimal weight: 8.9990 chunk 906 optimal weight: 9.9990 chunk 23 optimal weight: 0.3980 chunk 1189 optimal weight: 8.9990 chunk 659 optimal weight: 1.9990 chunk 1363 optimal weight: 20.0000 chunk 1104 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 815 optimal weight: 8.9990 chunk 1434 optimal weight: 10.0000 chunk 403 optimal weight: 8.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN Q 8 ASN R 34 ASN R 86 ASN ** T 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 HIS U 94 ASN X 111 GLN ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 ASN g 112 GLN AA 24 HIS ** AA 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 136 HIS ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** II 7 ASN PP 79 HIS VV 33 GLN WW 91 ASN ** bb 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ee 88 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.152 226693 Z= 0.427 Angle : 0.729 25.964 332993 Z= 0.364 Chirality : 0.045 2.372 41452 Planarity : 0.006 0.085 21348 Dihedral : 15.696 179.936 79778 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.08), residues: 11145 helix: 0.25 (0.08), residues: 3746 sheet: -1.25 (0.12), residues: 1712 loop : -1.14 (0.08), residues: 5687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1872 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1671 time to evaluate : 9.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 201 outliers final: 126 residues processed: 1798 average time/residue: 1.7142 time to fit residues: 5281.7344 Evaluate side-chains 1758 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1632 time to evaluate : 9.604 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 0 residues processed: 126 average time/residue: 1.3684 time to fit residues: 336.3481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 537 optimal weight: 0.9990 chunk 1438 optimal weight: 8.9990 chunk 315 optimal weight: 7.9990 chunk 938 optimal weight: 0.0060 chunk 394 optimal weight: 0.4980 chunk 1599 optimal weight: 30.0000 chunk 1327 optimal weight: 8.9990 chunk 740 optimal weight: 0.0970 chunk 132 optimal weight: 4.9990 chunk 529 optimal weight: 2.9990 chunk 839 optimal weight: 10.0000 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN C 61 GLN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 HIS ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN R 86 ASN ** T 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 HIS U 94 ASN X 105 ASN X 111 GLN ** X 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 HIS r 31 ASN r 103 HIS CC 136 HIS ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** II 7 ASN PP 79 HIS ** QQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VV 33 GLN WW 91 ASN ** bb 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ee 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.364 226693 Z= 0.159 Angle : 0.561 25.146 332993 Z= 0.286 Chirality : 0.036 2.365 41452 Planarity : 0.004 0.079 21348 Dihedral : 15.405 179.939 79778 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.08), residues: 11145 helix: 0.77 (0.08), residues: 3735 sheet: -1.02 (0.12), residues: 1711 loop : -0.88 (0.08), residues: 5699 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1861 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1767 time to evaluate : 9.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 47 residues processed: 1816 average time/residue: 1.7789 time to fit residues: 5506.0850 Evaluate side-chains 1707 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1660 time to evaluate : 10.575 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 1.3528 time to fit residues: 133.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 1541 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 911 optimal weight: 0.7980 chunk 1167 optimal weight: 10.0000 chunk 904 optimal weight: 9.9990 chunk 1346 optimal weight: 10.0000 chunk 893 optimal weight: 9.9990 chunk 1593 optimal weight: 20.0000 chunk 997 optimal weight: 0.9990 chunk 971 optimal weight: 0.9990 chunk 735 optimal weight: 0.1980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 GLN N 87 HIS N 91 GLN P 34 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN R 34 ASN ** T 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 HIS U 94 ASN X 111 GLN ** X 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 100 HIS ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN l 33 ASN ** m 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN CC 136 HIS EE 67 GLN ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 7 ASN VV 33 GLN WW 91 ASN cc 29 GLN ee 88 GLN ee 129 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.288 226693 Z= 0.186 Angle : 0.557 25.259 332993 Z= 0.284 Chirality : 0.036 2.285 41452 Planarity : 0.004 0.088 21348 Dihedral : 15.278 179.975 79778 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.08), residues: 11145 helix: 0.90 (0.09), residues: 3737 sheet: -0.93 (0.12), residues: 1703 loop : -0.80 (0.08), residues: 5705 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1785 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1703 time to evaluate : 10.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 44 residues processed: 1741 average time/residue: 1.7565 time to fit residues: 5223.7359 Evaluate side-chains 1684 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1640 time to evaluate : 10.615 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 1.5373 time to fit residues: 139.6888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 985 optimal weight: 0.6980 chunk 636 optimal weight: 0.9980 chunk 951 optimal weight: 7.9990 chunk 479 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 308 optimal weight: 0.6980 chunk 1012 optimal weight: 7.9990 chunk 1085 optimal weight: 20.0000 chunk 787 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 1252 optimal weight: 10.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN P 10 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN R 34 ASN ** T 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 HIS U 94 ASN X 111 GLN ** X 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** m 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 136 HIS ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HH 165 ASN II 7 ASN OO 83 GLN TT 105 GLN WW 91 ASN ** bb 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** cc 24 GLN ee 88 GLN ee 129 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.572 226693 Z= 0.285 Angle : 0.615 73.900 332993 Z= 0.307 Chirality : 0.038 2.265 41452 Planarity : 0.005 0.125 21348 Dihedral : 15.282 179.751 79778 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.08), residues: 11145 helix: 0.85 (0.08), residues: 3731 sheet: -0.91 (0.12), residues: 1719 loop : -0.82 (0.08), residues: 5695 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1762 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1662 time to evaluate : 9.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 64 residues processed: 1703 average time/residue: 1.7639 time to fit residues: 5128.3237 Evaluate side-chains 1688 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1624 time to evaluate : 9.542 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 1.3806 time to fit residues: 176.5864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 1449 optimal weight: 10.0000 chunk 1526 optimal weight: 10.0000 chunk 1392 optimal weight: 8.9990 chunk 1484 optimal weight: 10.0000 chunk 1525 optimal weight: 10.0000 chunk 893 optimal weight: 9.9990 chunk 646 optimal weight: 9.9990 chunk 1165 optimal weight: 10.0000 chunk 455 optimal weight: 0.6980 chunk 1341 optimal weight: 10.0000 chunk 1404 optimal weight: 6.9990 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN R 34 ASN ** T 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 HIS U 94 ASN X 111 GLN ** X 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** m 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN CC 136 HIS DD 207 HIS ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 7 ASN ** QQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** RR 83 ASN WW 91 ASN bb 29 ASN ** cc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ee 129 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.032 226693 Z= 0.589 Angle : 0.796 106.097 332993 Z= 0.383 Chirality : 0.047 2.207 41452 Planarity : 0.006 0.116 21348 Dihedral : 15.320 179.631 79778 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.08), residues: 11145 helix: 0.55 (0.08), residues: 3748 sheet: -1.00 (0.12), residues: 1738 loop : -0.94 (0.08), residues: 5659 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1757 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1660 time to evaluate : 10.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 76 residues processed: 1701 average time/residue: 1.7310 time to fit residues: 5019.8907 Evaluate side-chains 1715 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1639 time to evaluate : 9.618 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 1.3943 time to fit residues: 209.1129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 1479 optimal weight: 10.0000 chunk 974 optimal weight: 0.7980 chunk 1569 optimal weight: 10.0000 chunk 958 optimal weight: 4.9990 chunk 744 optimal weight: 0.9990 chunk 1091 optimal weight: 10.0000 chunk 1646 optimal weight: 10.0000 chunk 1515 optimal weight: 10.0000 chunk 1311 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 1012 optimal weight: 10.0000 overall best weight: 3.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN J 168 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN ** T 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 HIS U 94 ASN X 111 GLN ** X 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** m 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 7 ASN WW 91 ASN bb 29 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.141 226693 Z= 0.629 Angle : 0.807 106.097 332993 Z= 0.393 Chirality : 0.047 2.207 41452 Planarity : 0.006 0.186 21348 Dihedral : 15.320 179.631 79778 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.08), residues: 11145 helix: 0.55 (0.08), residues: 3748 sheet: -1.00 (0.12), residues: 1738 loop : -0.94 (0.08), residues: 5659 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22290 Ramachandran restraints generated. 11145 Oldfield, 0 Emsley, 11145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1647 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1646 time to evaluate : 10.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1646 average time/residue: 1.7673 time to fit residues: 4943.6762 Evaluate side-chains 1640 residues out of total 9731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1640 time to evaluate : 9.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.3002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1653 random chunks: chunk 804 optimal weight: 0.9980 chunk 1041 optimal weight: 20.0000 chunk 1396 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 1209 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 364 optimal weight: 0.9980 chunk 1313 optimal weight: 2.9990 chunk 549 optimal weight: 2.9990 chunk 1348 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN ** T 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 HIS U 94 ASN X 111 GLN ** X 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** m 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN ** AA 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 7 ASN WW 91 ASN bb 29 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.143938 restraints weight = 281132.563| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.50 r_work: 0.3482 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work: 0.3330 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.104 226693 Z= 0.625 Angle : 0.806 106.063 332993 Z= 0.392 Chirality : 0.047 2.207 41452 Planarity : 0.006 0.184 21348 Dihedral : 15.320 179.630 79778 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.08), residues: 11145 helix: 0.55 (0.08), residues: 3748 sheet: -1.00 (0.12), residues: 1738 loop : -0.94 (0.08), residues: 5659 =============================================================================== Job complete usr+sys time: 65457.32 seconds wall clock time: 1133 minutes 42.24 seconds (68022.24 seconds total)