Starting phenix.real_space_refine (version: dev) on Sun Apr 24 12:15:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz5_0100/04_2022/6gz5_0100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz5_0100/04_2022/6gz5_0100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz5_0100/04_2022/6gz5_0100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz5_0100/04_2022/6gz5_0100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz5_0100/04_2022/6gz5_0100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz5_0100/04_2022/6gz5_0100_updated.pdb" } resolution = 3.5 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= 0.343 sd= 0.691 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 "BD TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP ARG 130": "NH1" <-> "NH2" Residue "BQ ARG 117": "NH1" <-> "NH2" Residue "Bd PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 99": "NH1" <-> "NH2" Residue "Ct ARG 10": "NH1" <-> "NH2" Residue "Ct ARG 50": "NH1" <-> "NH2" Residue "Ct ARG 144": "NH1" <-> "NH2" Residue "Ct PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ct ARG 249": "NH1" <-> "NH2" Residue "Ct ARG 264": "NH1" <-> "NH2" Residue "Ct PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ct ARG 342": "NH1" <-> "NH2" Residue "Ct TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ct PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ct ARG 415": "NH1" <-> "NH2" Residue "Ct ARG 428": "NH1" <-> "NH2" Residue "Ct ARG 449": "NH1" <-> "NH2" Residue "Ct ARG 456": "NH1" <-> "NH2" Residue "Ct ARG 495": "NH1" <-> "NH2" Residue "Ct ARG 506": "NH1" <-> "NH2" Residue "Ct ARG 526": "NH1" <-> "NH2" Residue "Ct ARG 601": "NH1" <-> "NH2" Residue "Ct TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ct ARG 607": "NH1" <-> "NH2" Residue "Ct ARG 625": "NH1" <-> "NH2" Residue "Ct ARG 631": "NH1" <-> "NH2" Residue "Ct ARG 716": "NH1" <-> "NH2" Residue "Ct ARG 727": "NH1" <-> "NH2" Residue "Ct TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ct ARG 765": "NH1" <-> "NH2" Residue "Ct ARG 801": "NH1" <-> "NH2" Residue "Ct ARG 841": "NH1" <-> "NH2" Residue "Ct PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 225601 Number of models: 1 Model: "" Number of chains: 105 Chain: "A2" Number of atoms: 77427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3612, 77427 Classifications: {'RNA': 3612} Modifications used: {'rna3p_pyr': 1417, 'rna2p_pur': 344, 'rna3p_pur': 1630, 'rna2p_pyr': 221} Link IDs: {'rna3p': 3046, 'rna2p': 565} Chain breaks: 11 Chain: "Bv" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1620 Classifications: {'RNA': 76} Modifications used: {'rna2p_pyr': 4, 'rna3p_pyr': 33, 'p5*END': 1, 'rna3p_pur': 32, 'rna2p_pur': 7} Link IDs: {'rna3p': 64, 'rna2p': 11} Chain: "Bx" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNA': 11} Modifications used: {'rna3p_pyr': 5, 'rna3p_pur': 6} Link IDs: {'rna3p': 10} Chain: "Bw" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1627 Classifications: {'RNA': 76} Modifications used: {'rna3p_pyr': 30, 'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 38, 'rna2p_pyr': 5} Link IDs: {'rna3p': 67, 'rna2p': 8} Chain: "B1" Number of atoms: 36456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1708, 36456 Classifications: {'RNA': 1708} Modifications used: {'rna3p_pyr': 686, 'p5*END': 1, 'rna2p_pur': 154, 'rna2p_pyr': 120, 'rna3p_pur': 748} Link IDs: {'rna3p': 1433, 'rna2p': 274} Chain breaks: 6 Chain: "BD" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1709 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "BF" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1502 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "BK" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 827 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "BM" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "BP" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 999 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "BQ" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "BR" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1011 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "BS" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "BT" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "BU" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "BZ" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "Bc" 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: "Bd" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "Bf" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 601 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "Bg" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "BA" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1704 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "BB" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1722 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "BC" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1724 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "BE" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2031 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain: "BG" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1884 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "BH" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1479 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "BI" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1696 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "BJ" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1495 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "BL" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1258 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 146} Chain: "BN" 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: "BO" 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: "BV" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 617 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "BW" 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': 3, 'TRANS': 125} Chain: "BX" 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: "BY" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "Ba" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 774 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "Bb" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 625 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "Be" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "A3" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3337 Classifications: {'RNA': 157} Modifications used: {'rna3p_pyr': 68, 'rna2p_pur': 15, 'rna3p_pur': 61, 'rna2p_pyr': 13} Link IDs: {'rna3p': 128, 'rna2p': 28} Chain: "A4" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2541 Classifications: {'RNA': 119} Modifications used: {'rna3p_pyr': 53, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 5} Link IDs: {'rna3p': 107, 'rna2p': 11} Chain: "AA" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1930 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain: "AB" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3178 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "AC" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2888 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "AD" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2392 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain: "AE" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1571 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "AF" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1950 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain: "AG" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1880 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 14, 'TRANS': 219} Chain: "AH" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "AI" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1692 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain breaks: 1 Chain: "AJ" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "AL" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1657 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "AM" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1138 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "AN" 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: "AO" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1606 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "AP" 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: "AQ" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "AR" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1517 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "AS" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1449 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "AT" 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: "AU" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 808 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "AV" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "AW" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 989 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "AX" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 958 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "AY" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1064 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "AZ" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1103 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Aa" 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: "Ab" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 559 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "Ac" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "Ad" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 879 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "Ae" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1064 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "Af" 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: "Ag" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Ah" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Ai" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 794 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Aj" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "Ak" 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: "Al" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Am" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 411 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "An" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 240 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "Ao" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 863 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "Ap" 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: "At" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "Au" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1744 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain: "Aq" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1140 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'CIS': 2, 'TRANS': 140, 'PCIS': 1} Chain: "AK" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1556 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'CIS': 4, 'TRANS': 188, 'PCIS': 1} Chain: "Ct" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6659 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 46, 'TRANS': 806} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DDE:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "A2" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 229 Unusual residues: {' MG': 229} Classifications: {'undetermined': 229} Link IDs: {None: 228} Chain: "Bx" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B1" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Unusual residues: {' MG': 73} Classifications: {'undetermined': 73} Link IDs: {None: 72} Chain: "BD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ba" 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: "A3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A4" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Aj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "An" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ao" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ap" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ct" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0N0M SG CYSBd 24 129.538 58.876 120.085 1.00 20.00 S ATOM A0N3Z SG CYSBd 39 127.046 58.279 117.532 1.00 20.00 S ATOM A15WH SG CYSBa 26 128.256 121.168 78.140 1.00 20.00 S ATOM A1674 SG CYSBa 74 130.562 118.971 76.505 1.00 20.00 S ATOM A167N SG CYSBa 77 127.663 117.277 75.142 1.00 20.00 S ATOM A2CE6 SG CYSAj 19 117.021 220.188 101.824 1.00 20.00 S ATOM A2CEY SG CYSAj 22 113.841 220.588 103.397 1.00 20.00 S ATOM A2CHH SG CYSAj 34 115.435 216.736 101.622 1.00 20.00 S ATOM A2CI0 SG CYSAj 37 112.774 218.791 100.268 1.00 20.00 S ATOM A2E66 SG CYSAo 12 45.790 157.077 119.472 1.00 20.00 S ATOM A2EJV SG CYSAo 72 46.120 154.658 115.540 1.00 20.00 S ATOM A2EKW SG CYSAo 77 44.752 158.296 115.014 1.00 20.00 S ATOM A2EZY SG CYSAp 39 153.116 177.072 63.489 1.00 20.00 S ATOM A2F0L SG CYSAp 42 156.312 178.646 62.892 1.00 20.00 S ATOM A2F3Z SG CYSAp 57 152.172 180.613 64.977 1.00 20.00 S Time building chain proxies: 86.16, per 1000 atoms: 0.38 Number of scatterers: 225601 At special positions: 0 Unit cell: (290.55, 294.45, 270.075, 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 5 29.99 S 475 16.00 P 5762 15.00 Mg 327 11.99 O 57703 8.00 N 41907 7.00 C 119422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYSBf 126 " - pdb=" SG CYSBf 144 " distance=2.03 Simple disulfide: pdb=" SG CYSBf 141 " - pdb=" SG CYSBf 144 " distance=2.04 Simple disulfide: pdb=" SG CYSAm 99 " - pdb=" SG CYSAm 110 " distance=2.03 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: 74.30 Conformation dependent library (CDL) restraints added in 10.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZNAj 101 " pdb="ZN ZNAj 101 " - pdb=" SG CYSAj 19 " pdb="ZN ZNAj 101 " - pdb=" SG CYSAj 37 " pdb="ZN ZNAj 101 " - pdb=" SG CYSAj 34 " pdb="ZN ZNAj 101 " - pdb=" SG CYSAj 22 " pdb=" ZNAo 201 " pdb="ZN ZNAo 201 " - pdb=" SG CYSAo 12 " pdb="ZN ZNAo 201 " - pdb=" SG CYSAo 77 " pdb="ZN ZNAo 201 " - pdb=" SG CYSAo 72 " pdb=" ZNAp 101 " pdb="ZN ZNAp 101 " - pdb=" SG CYSAp 57 " pdb="ZN ZNAp 101 " - pdb=" SG CYSAp 42 " pdb="ZN ZNAp 101 " - pdb=" SG CYSAp 39 " pdb=" ZNBa 102 " pdb="ZN ZNBa 102 " - pdb=" SG CYSBa 26 " pdb="ZN ZNBa 102 " - pdb=" SG CYSBa 77 " pdb="ZN ZNBa 102 " - pdb=" SG CYSBa 74 " pdb=" ZNBd 101 " pdb="ZN ZNBd 101 " - pdb=" SG CYSBd 39 " pdb="ZN ZNBd 101 " - pdb=" SG CYSBd 24 " Number of angles added : 6 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23632 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: 415 helices and 130 sheets defined 40.0% alpha, 15.3% beta 1664 base pairs and 3072 stacking pairs defined. Time for finding SS restraints: 87.57 Creating SS restraints... Processing helix chain 'BD' and resid 6 through 29 removed outlier: 3.767A pdb=" N PHEBD 11 " --> pdb=" O LYSBD 7 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VALBD 12 " --> pdb=" O LYSBD 8 " (cutoff:3.500A) Processing helix chain 'BD' and resid 54 through 60 removed outlier: 4.421A pdb=" N VALBD 58 " --> pdb=" O ARGBD 54 " (cutoff:3.500A) Processing helix chain 'BD' and resid 63 through 77 removed outlier: 4.892A pdb=" N ARGBD 67 " --> pdb=" O GLYBD 63 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARGBD 76 " --> pdb=" O VALBD 72 " (cutoff:3.500A) Processing helix chain 'BD' and resid 97 through 112 removed outlier: 3.827A pdb=" N TYRBD 107 " --> pdb=" O GLUBD 103 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLYBD 111 " --> pdb=" O TYRBD 107 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLYBD 112 " --> pdb=" O LYSBD 108 " (cutoff:3.500A) Processing helix chain 'BD' and resid 114 through 130 removed outlier: 4.069A pdb=" N GLYBD 130 " --> pdb=" O ILEBD 126 " (cutoff:3.500A) Processing helix chain 'BD' and resid 163 through 168 Processing helix chain 'BF' and resid 61 through 66 removed outlier: 5.656A pdb=" N GLNBF 65 " --> pdb=" O PHEBF 61 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYSBF 66 " --> pdb=" O ARGBF 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'BF' and resid 61 through 66' Processing helix chain 'BF' and resid 67 through 78 removed outlier: 5.399A pdb=" N METBF 78 " --> pdb=" O ASNBF 74 " (cutoff:3.500A) Processing helix chain 'BF' and resid 85 through 105 removed outlier: 4.794A pdb=" N THRBF 104 " --> pdb=" O ILEBF 100 " (cutoff:3.500A) Processing helix chain 'BF' and resid 107 through 119 Processing helix chain 'BF' and resid 142 through 163 Processing helix chain 'BF' and resid 168 through 183 removed outlier: 5.093A pdb=" N GLYBF 183 " --> pdb=" O ASNBF 179 " (cutoff:3.500A) Processing helix chain 'BF' and resid 187 through 204 removed outlier: 3.971A pdb=" N VALBF 199 " --> pdb=" O GLUBF 195 " (cutoff:3.500A) Processing helix chain 'BK' and resid 4 through 19 removed outlier: 4.606A pdb=" N TYRBK 12 " --> pdb=" O ARGBK 8 " (cutoff:3.500A) Processing helix chain 'BK' and resid 42 through 54 removed outlier: 4.153A pdb=" N SERBK 51 " --> pdb=" O LYSBK 47 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEUBK 52 " --> pdb=" O ALABK 48 " (cutoff:3.500A) Processing helix chain 'BK' and resid 72 through 81 removed outlier: 5.135A pdb=" N ASPBK 81 " --> pdb=" O GLNBK 77 " (cutoff:3.500A) Processing helix chain 'BK' and resid 82 through 87 Proline residue: BK 86 - end of helix No H-bonds generated for 'chain 'BK' and resid 82 through 87' Processing helix chain 'BM' and resid 11 through 29 removed outlier: 4.250A pdb=" N ASNBM 15 " --> pdb=" O VALBM 11 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEUBM 18 " --> pdb=" O VALBM 14 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASPBM 29 " --> pdb=" O ALABM 25 " (cutoff:3.500A) Processing helix chain 'BM' and resid 34 through 45 Processing helix chain 'BM' and resid 60 through 73 removed outlier: 4.413A pdb=" N LEUBM 64 " --> pdb=" O METBM 60 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VALBM 65 " --> pdb=" O TYRBM 61 " (cutoff:3.500A) Processing helix chain 'BM' and resid 81 through 90 removed outlier: 3.769A pdb=" N LEUBM 85 " --> pdb=" O ASPBM 81 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLUBM 87 " --> pdb=" O LYSBM 83 " (cutoff:3.500A) Processing helix chain 'BM' and resid 120 through 130 removed outlier: 3.618A pdb=" N CYSBM 130 " --> pdb=" O GLUBM 126 " (cutoff:3.500A) Processing helix chain 'BP' and resid 21 through 28 Processing helix chain 'BP' and resid 29 through 37 removed outlier: 5.005A pdb=" N GLNBP 35 " --> pdb=" O GLUBP 31 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEUBP 36 " --> pdb=" O GLNBP 32 " (cutoff:3.500A) Processing helix chain 'BP' and resid 38 through 48 removed outlier: 3.680A pdb=" N GLYBP 48 " --> pdb=" O ARGBP 44 " (cutoff:3.500A) Processing helix chain 'BP' and resid 50 through 68 removed outlier: 4.851A pdb=" N HISBP 54 " --> pdb=" O ARGBP 50 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEUBP 57 " --> pdb=" O GLNBP 53 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALABP 67 " --> pdb=" O ALABP 63 " (cutoff:3.500A) Proline residue: BP 68 - end of helix Processing helix chain 'BP' and resid 116 through 121 removed outlier: 4.364A pdb=" N SERBP 120 " --> pdb=" O LEUBP 116 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILEBP 121 " --> pdb=" O GLYBP 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 116 through 121' Processing helix chain 'BQ' and resid 47 through 53 removed outlier: 3.732A pdb=" N LEUBQ 51 " --> pdb=" O LEUBQ 47 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEUBQ 52 " --> pdb=" O GLNBQ 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLUBQ 53 " --> pdb=" O TYRBQ 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'BQ' and resid 47 through 53' Processing helix chain 'BQ' and resid 59 through 67 removed outlier: 4.387A pdb=" N PHEBQ 63 " --> pdb=" O GLYBQ 59 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASPBQ 67 " --> pdb=" O PHEBQ 63 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 76 through 99 removed outlier: 4.008A pdb=" N VALBQ 93 " --> pdb=" O SERBQ 89 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 101 through 116 removed outlier: 4.206A pdb=" N GLUBQ 107 " --> pdb=" O ALABQ 103 " (cutoff:3.500A) Processing helix chain 'BR' and resid 6 through 20 Processing helix chain 'BR' and resid 27 through 39 removed outlier: 3.965A pdb=" N ARGBR 33 " --> pdb=" O HISBR 29 " (cutoff:3.500A) Processing helix chain 'BR' and resid 43 through 64 removed outlier: 3.651A pdb=" N ARGBR 63 " --> pdb=" O LYSBR 59 " (cutoff:3.500A) Processing helix chain 'BR' and resid 71 through 84 Processing helix chain 'BR' and resid 99 through 109 Processing helix chain 'BS' and resid 25 through 34 removed outlier: 3.973A pdb=" N ALABS 29 " --> pdb=" O LYSBS 25 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALABS 32 " --> pdb=" O PHEBS 28 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILEBS 33 " --> pdb=" O ALABS 29 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYSBS 34 " --> pdb=" O ILEBS 30 " (cutoff:3.500A) Processing helix chain 'BS' and resid 37 through 49 removed outlier: 4.160A pdb=" N ALABS 41 " --> pdb=" O GLYBS 37 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HISBS 42 " --> pdb=" O ARGBS 38 " (cutoff:3.500A) Processing helix chain 'BS' and resid 60 through 74 Proline residue: BS 74 - end of helix Processing helix chain 'BS' and resid 99 through 118 removed outlier: 4.103A pdb=" N ASPBS 104 " --> pdb=" O ALABS 100 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASNBS 105 " --> pdb=" O ASNBS 101 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYSBS 116 " --> pdb=" O GLUBS 112 " (cutoff:3.500A) Processing helix chain 'BS' and resid 119 through 128 removed outlier: 4.532A pdb=" N GLYBS 128 " --> pdb=" O ARGBS 124 " (cutoff:3.500A) Processing helix chain 'BT' and resid 5 through 10 removed outlier: 3.840A pdb=" N VALBT 9 " --> pdb=" O THRBT 5 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASNBT 10 " --> pdb=" O VALBT 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'BT' and resid 5 through 10' Processing helix chain 'BT' and resid 11 through 26 removed outlier: 4.224A pdb=" N ARGBT 16 " --> pdb=" O GLNBT 12 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALABT 20 " --> pdb=" O ARGBT 16 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYSBT 23 " --> pdb=" O ALABT 19 " (cutoff:3.500A) Processing helix chain 'BT' and resid 31 through 37 removed outlier: 5.299A pdb=" N ASPBT 35 " --> pdb=" O PROBT 31 " (cutoff:3.500A) Processing helix chain 'BT' and resid 51 through 68 removed outlier: 4.232A pdb=" N GLYBT 68 " --> pdb=" O LEUBT 64 " (cutoff:3.500A) Processing helix chain 'BT' and resid 71 through 80 Processing helix chain 'BT' and resid 96 through 111 removed outlier: 3.766A pdb=" N ALABT 100 " --> pdb=" O SERBT 96 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEUBT 104 " --> pdb=" O ALABT 100 " (cutoff:3.500A) Processing helix chain 'BT' and resid 124 through 144 Processing helix chain 'BU' and resid 28 through 47 removed outlier: 4.647A pdb=" N GLUBU 45 " --> pdb=" O ARGBU 41 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYSBU 46 " --> pdb=" O GLYBU 42 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASNBU 47 " --> pdb=" O ALABU 43 " (cutoff:3.500A) Processing helix chain 'BU' and resid 94 through 103 removed outlier: 3.951A pdb=" N SERBU 103 " --> pdb=" O LYSBU 99 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 51 through 66 removed outlier: 3.542A pdb=" N TYRBZ 55 " --> pdb=" O ASPBZ 51 " (cutoff:3.500A) Proline residue: BZ 63 - end of helix removed outlier: 5.933A pdb=" N LYSBZ 66 " --> pdb=" O VALBZ 62 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 69 through 76 Processing helix chain 'BZ' and resid 80 through 95 Processing helix chain 'Bd' and resid 15 through 20 removed outlier: 4.305A pdb=" N ARGBd 19 " --> pdb=" O GLYBd 15 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SERBd 20 " --> pdb=" O GLNBd 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 15 through 20' Processing helix chain 'Bd' and resid 39 through 51 removed outlier: 6.127A pdb=" N PHEBd 43 " --> pdb=" O CYSBd 39 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARGBd 44 " --> pdb=" O ARGBd 40 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLNBd 45 " --> pdb=" O GLNBd 41 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYSBd 48 " --> pdb=" O ARGBd 44 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASPBd 49 " --> pdb=" O GLNBd 45 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 124 through 129 removed outlier: 5.826A pdb=" N GLYBf 127 " --> pdb=" O ASPBf 124 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALABf 128 " --> pdb=" O GLUBf 125 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLYBf 129 " --> pdb=" O CYSBf 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bf' and resid 124 through 129' Processing helix chain 'BA' and resid 11 through 22 Processing helix chain 'BA' and resid 34 through 39 removed outlier: 5.354A pdb=" N TYRBA 39 " --> pdb=" O GLUBA 35 " (cutoff:3.500A) Processing helix chain 'BA' and resid 50 through 68 removed outlier: 4.007A pdb=" N THRBA 54 " --> pdb=" O ASNBA 50 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYSBA 57 " --> pdb=" O ARGBA 53 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILEBA 68 " --> pdb=" O ALABA 64 " (cutoff:3.500A) Processing helix chain 'BA' and resid 81 through 94 removed outlier: 3.828A pdb=" N ARGBA 85 " --> pdb=" O ASNBA 81 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALABA 86 " --> pdb=" O THRBA 82 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEUBA 88 " --> pdb=" O GLNBA 84 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYSBA 89 " --> pdb=" O ARGBA 85 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALABA 92 " --> pdb=" O LEUBA 88 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALABA 93 " --> pdb=" O LYSBA 89 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THRBA 94 " --> pdb=" O PHEBA 90 " (cutoff:3.500A) Processing helix chain 'BA' and resid 126 through 131 Processing helix chain 'BA' and resid 132 through 141 removed outlier: 4.587A pdb=" N SERBA 138 " --> pdb=" O LEUBA 134 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYRBA 139 " --> pdb=" O THRBA 135 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VALBA 140 " --> pdb=" O GLUBA 136 " (cutoff:3.500A) Processing helix chain 'BA' and resid 167 through 187 removed outlier: 3.520A pdb=" N VALBA 171 " --> pdb=" O GLYBA 167 " (cutoff:3.500A) Processing helix chain 'BA' and resid 199 through 204 removed outlier: 3.897A pdb=" N PHEBA 203 " --> pdb=" O PROBA 199 " (cutoff:3.500A) Processing helix chain 'BA' and resid 207 through 219 removed outlier: 3.711A pdb=" N GLUBA 211 " --> pdb=" O PROBA 207 " (cutoff:3.500A) Processing helix chain 'BA' and resid 70 through 75 removed outlier: 3.624A pdb=" N VALBA 74 " --> pdb=" O PROBA 71 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SERBA 75 " --> pdb=" O ALABA 72 " (cutoff:3.500A) Processing helix chain 'BB' and resid 23 through 29 removed outlier: 3.809A pdb=" N LYSBB 27 " --> pdb=" O ASPBB 23 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASPBB 29 " --> pdb=" O PHEBB 25 " (cutoff:3.500A) Processing helix chain 'BB' and resid 57 through 65 removed outlier: 4.807A pdb=" N GLYBB 61 " --> pdb=" O ILEBB 57 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEUBB 62 " --> pdb=" O ALABB 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYSBB 63 " --> pdb=" O SERBB 59 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLYBB 64 " --> pdb=" O ASPBB 60 " (cutoff:3.500A) Processing helix chain 'BB' and resid 71 through 76 removed outlier: 6.667A pdb=" N GLNBB 75 " --> pdb=" O LEUBB 71 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASNBB 76 " --> pdb=" O ALABB 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 71 through 76' Processing helix chain 'BB' and resid 106 through 113 removed outlier: 4.722A pdb=" N METBB 113 " --> pdb=" O LYSBB 109 " (cutoff:3.500A) Processing helix chain 'BB' and resid 157 through 179 removed outlier: 6.166A pdb=" N VALBB 161 " --> pdb=" O GLNBB 157 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N METBB 172 " --> pdb=" O METBB 168 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THRBB 173 " --> pdb=" O METBB 169 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARGBB 174 " --> pdb=" O GLUBB 170 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THRBB 178 " --> pdb=" O ARGBB 174 " (cutoff:3.500A) removed outlier: 4.397A 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 202 removed outlier: 3.777A pdb=" N GLNBB 202 " --> pdb=" O GLUBB 198 " (cutoff:3.500A) Processing helix chain 'BB' and resid 224 through 233 Processing helix chain 'BC' and resid 64 through 73 removed outlier: 5.958A pdb=" N ARGBC 68 " --> pdb=" O THRBC 64 " (cutoff:3.500A) Processing helix chain 'BC' and resid 77 through 85 removed outlier: 3.808A pdb=" N ILEBC 81 " --> pdb=" O SERBC 77 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHEBC 84 " --> pdb=" O GLUBC 80 " (cutoff:3.500A) Processing helix chain 'BC' and resid 91 through 98 removed outlier: 3.748A pdb=" N ASPBC 95 " --> pdb=" O SERBC 91 " (cutoff:3.500A) Processing helix chain 'BC' and resid 146 through 162 Processing helix chain 'BC' and resid 207 through 218 Processing helix chain 'BC' and resid 232 through 250 removed outlier: 4.503A pdb=" N LYSBC 238 " --> pdb=" O GLYBC 234 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THRBC 247 " --> pdb=" O ALABC 243 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYRBC 248 " --> pdb=" O ILEBC 244 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SERBC 249 " --> pdb=" O SERBC 245 " (cutoff:3.500A) Processing helix chain 'BC' and resid 264 through 270 Processing helix chain 'BC' and resid 271 through 278 Processing helix chain 'BE' and resid 43 through 49 Processing helix chain 'BE' and resid 57 through 68 removed outlier: 3.834A pdb=" N VALBE 61 " --> pdb=" O THRBE 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N METBE 66 " --> pdb=" O LYSBE 62 " (cutoff:3.500A) Processing helix chain 'BE' and resid 115 through 122 removed outlier: 4.872A pdb=" N TYRBE 121 " --> pdb=" O GLUBE 117 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYSBE 122 " --> pdb=" O GLUBE 118 " (cutoff:3.500A) Processing helix chain 'BE' and resid 221 through 226 removed outlier: 3.898A pdb=" N ILEBE 225 " --> pdb=" O ARGBE 221 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHEBE 226 " --> pdb=" O LEUBE 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 221 through 226' Processing helix chain 'BE' and resid 247 through 258 Processing helix chain 'BG' and resid 20 through 28 removed outlier: 3.537A pdb=" N LEUBG 24 " --> pdb=" O ASPBG 20 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THRBG 26 " --> pdb=" O ARGBG 22 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHEBG 27 " --> pdb=" O LYSBG 23 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYRBG 28 " --> pdb=" O LEUBG 24 " (cutoff:3.500A) Processing helix chain 'BG' and resid 137 through 146 Processing helix chain 'BG' and resid 181 through 232 Processing helix chain 'BH' and resid 17 through 32 removed outlier: 4.014A pdb=" N GLYBH 22 " --> pdb=" O GLUBH 18 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N METBH 32 " --> pdb=" O LEUBH 28 " (cutoff:3.500A) Processing helix chain 'BH' and resid 36 through 43 removed outlier: 3.765A pdb=" N GLUBH 42 " --> pdb=" O ALABH 38 " (cutoff:3.500A) Processing helix chain 'BH' and resid 66 through 76 removed outlier: 4.530A pdb=" N LYSBH 70 " --> pdb=" O VALBH 66 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SERBH 71 " --> pdb=" O PROBH 67 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILEBH 75 " --> pdb=" O SERBH 71 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLNBH 76 " --> pdb=" O PHEBH 72 " (cutoff:3.500A) Processing helix chain 'BH' and resid 77 through 87 removed outlier: 3.574A pdb=" N ARGBH 81 " --> pdb=" O VALBH 77 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYSBH 86 " --> pdb=" O GLUBH 82 " (cutoff:3.500A) Processing helix chain 'BH' and resid 121 through 135 removed outlier: 3.725A pdb=" N ASPBH 127 " --> pdb=" O THRBH 123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLUBH 131 " --> pdb=" O ASPBH 127 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VALBH 134 " --> pdb=" O LEUBH 130 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHEBH 135 " --> pdb=" O GLUBH 131 " (cutoff:3.500A) Processing helix chain 'BH' and resid 163 through 181 removed outlier: 4.095A pdb=" N HISBH 168 " --> pdb=" O ASNBH 164 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYSBH 169 " --> pdb=" O ASNBH 165 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLUBH 171 " --> pdb=" O GLUBH 167 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THRBH 172 " --> pdb=" O HISBH 168 " (cutoff:3.500A) Processing helix chain 'BI' and resid 87 through 94 removed outlier: 4.121A pdb=" N VALBI 91 " --> pdb=" O ASNBI 87 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARGBI 92 " --> pdb=" O ASNBI 88 " (cutoff:3.500A) Processing helix chain 'BI' and resid 106 through 117 removed outlier: 3.844A pdb=" N ARGBI 110 " --> pdb=" O SERBI 106 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLNBI 111 " --> pdb=" O THRBI 107 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRPBI 112 " --> pdb=" O PROBI 108 " (cutoff:3.500A) Processing helix chain 'BI' and resid 141 through 152 removed outlier: 4.359A pdb=" N ILEBI 145 " --> pdb=" O ARGBI 141 " (cutoff:3.500A) Processing helix chain 'BI' and resid 159 through 169 removed outlier: 4.023A pdb=" N GLUBI 163 " --> pdb=" O SERBI 159 " (cutoff:3.500A) Processing helix chain 'BI' and resid 192 through 208 Processing helix chain 'BJ' and resid 21 through 36 Processing helix chain 'BJ' and resid 39 through 64 removed outlier: 3.834A pdb=" N VALBJ 43 " --> pdb=" O ASNBJ 39 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VALBJ 46 " --> pdb=" O GLUBJ 42 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEUBJ 63 " --> pdb=" O GLUBJ 59 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASPBJ 64 " --> pdb=" O LEUBJ 60 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 67 through 85 Processing helix chain 'BJ' and resid 93 through 100 removed outlier: 3.933A pdb=" N ILEBJ 97 " --> pdb=" O LYSBJ 93 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEUBJ 98 " --> pdb=" O LEUBJ 94 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 101 through 110 removed outlier: 5.059A pdb=" N PHEBJ 105 " --> pdb=" O LYSBJ 101 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEUBJ 106 " --> pdb=" O ILEBJ 102 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEUBJ 110 " --> pdb=" O LEUBJ 106 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 111 through 118 Processing helix chain 'BJ' and resid 122 through 133 removed outlier: 3.938A pdb=" N VALBJ 128 " --> pdb=" O HISBJ 124 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ARGBJ 133 " --> pdb=" O LEUBJ 129 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 171 through 180 removed outlier: 3.852A pdb=" N ARGBJ 175 " --> pdb=" O GLYBJ 171 " (cutoff:3.500A) Processing helix chain 'BL' and resid 47 through 53 removed outlier: 3.867A pdb=" N ILEBL 51 " --> pdb=" O PROBL 47 " (cutoff:3.500A) Processing helix chain 'BL' and resid 30 through 35 removed outlier: 5.029A pdb=" N LEUBL 33 " --> pdb=" O LYSBL 30 " (cutoff:3.500A) Proline residue: BL 34 - end of helix No H-bonds generated for 'chain 'BL' and resid 30 through 35' Processing helix chain 'BN' and resid 29 through 44 Processing helix chain 'BN' and resid 46 through 57 removed outlier: 3.714A pdb=" N VALBN 52 " --> pdb=" O SERBN 48 " (cutoff:3.500A) Processing helix chain 'BN' and resid 62 through 67 removed outlier: 3.557A pdb=" N VALBN 66 " --> pdb=" O GLNBN 62 " (cutoff:3.500A) Processing helix chain 'BN' and resid 70 through 79 removed outlier: 3.824A pdb=" N LYSBN 78 " --> pdb=" O ILEBN 74 " (cutoff:3.500A) Processing helix chain 'BN' and resid 85 through 106 removed outlier: 4.148A pdb=" N LEUBN 91 " --> pdb=" O ASPBN 87 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALABN 97 " --> pdb=" O LYSBN 93 " (cutoff:3.500A) Processing helix chain 'BN' and resid 108 through 133 Processing helix chain 'BN' and resid 142 through 149 removed outlier: 5.670A pdb=" N ALABN 146 " --> pdb=" O GLUBN 142 " (cutoff:3.500A) Processing helix chain 'BO' and resid 57 through 62 removed outlier: 4.005A pdb=" N LYSBO 61 " --> pdb=" O THRBO 57 " (cutoff:3.500A) Processing helix chain 'BO' and resid 64 through 69 removed outlier: 3.519A pdb=" N GLUBO 68 " --> pdb=" O ALABO 64 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SERBO 69 " --> pdb=" O ASPBO 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'BO' and resid 64 through 69' Processing helix chain 'BO' and resid 70 through 89 Processing helix chain 'BO' and resid 109 through 123 removed outlier: 4.619A pdb=" N GLNBO 113 " --> pdb=" O GLYBO 109 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SERBO 114 " --> pdb=" O PROBO 110 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARGBO 117 " --> pdb=" O GLNBO 113 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERBO 122 " --> pdb=" O ALABO 118 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLYBO 123 " --> pdb=" O LEUBO 119 " (cutoff:3.500A) Processing helix chain 'BV' and resid 56 through 63 Processing helix chain 'BV' and resid 64 through 77 removed outlier: 3.882A pdb=" N LEUBV 70 " --> pdb=" O ASPBV 66 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALABV 75 " --> pdb=" O ARGBV 71 " (cutoff:3.500A) Processing helix chain 'BW' and resid 5 through 21 removed outlier: 3.801A pdb=" N SERBW 13 " --> pdb=" O ASPBW 9 " (cutoff:3.500A) Processing helix chain 'BW' and resid 31 through 45 Processing helix chain 'BW' and resid 85 through 93 removed outlier: 4.129A pdb=" N TRPBW 89 " --> pdb=" O ASPBW 85 " (cutoff:3.500A) Processing helix chain 'BW' and resid 112 through 120 removed outlier: 3.929A pdb=" N ARGBW 117 " --> pdb=" O HISBW 113 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARGBW 118 " --> pdb=" O GLUBW 114 " (cutoff:3.500A) Processing helix chain 'BX' and resid 9 through 24 removed outlier: 4.504A pdb=" N TRPBX 22 " --> pdb=" O ARGBX 18 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N HISBX 23 " --> pdb=" O ASPBX 19 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASPBX 24 " --> pdb=" O GLNBX 20 " (cutoff:3.500A) Processing helix chain 'BX' and resid 25 through 32 Processing helix chain 'BX' and resid 33 through 38 Processing helix chain 'BX' and resid 89 through 95 removed outlier: 6.274A pdb=" N PHEBX 93 " --> pdb=" O GLYBX 89 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLUBX 95 " --> pdb=" O LEUBX 91 " (cutoff:3.500A) Processing helix chain 'BX' and resid 129 through 135 Processing helix chain 'BY' and resid 36 through 49 removed outlier: 3.661A pdb=" N ILEBY 40 " --> pdb=" O PROBY 36 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARGBY 41 " --> pdb=" O LYSBY 37 " (cutoff:3.500A) Processing helix chain 'BY' and resid 78 through 86 removed outlier: 3.688A pdb=" N GLUBY 86 " --> pdb=" O ALABY 82 " (cutoff:3.500A) Processing helix chain 'BY' and resid 87 through 95 removed outlier: 3.884A pdb=" N ARGBY 93 " --> pdb=" O HISBY 89 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HISBY 94 " --> pdb=" O ARGBY 90 " (cutoff:3.500A) Processing helix chain 'BY' and resid 105 through 118 removed outlier: 3.838A pdb=" N VALBY 117 " --> pdb=" O ARGBY 113 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARGBY 118 " --> pdb=" O METBY 114 " (cutoff:3.500A) Processing helix chain 'BY' and resid 119 through 126 Processing helix chain 'Ba' and resid 47 through 57 removed outlier: 4.654A pdb=" N ARGBa 51 " --> pdb=" O ALABa 47 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASPBa 52 " --> pdb=" O ALABa 48 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 74 through 82 removed outlier: 4.095A pdb=" N ILEBa 79 " --> pdb=" O VALBa 75 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HISBa 80 " --> pdb=" O SERBa 76 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 88 through 93 removed outlier: 4.809A pdb=" N LYSBa 93 " --> pdb=" O ARGBa 89 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 11 through 19 removed outlier: 5.604A pdb=" N HISBb 19 " --> pdb=" O GLUBb 15 " (cutoff:3.500A) Processing helix chain 'Be' and resid 10 through 16 Processing helix chain 'Be' and resid 29 through 41 Processing helix chain 'AA' and resid 5 through 13 removed outlier: 3.764A pdb=" N ARGAA 9 " --> pdb=" O ILEAA 5 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYSAA 10 " --> pdb=" O ARGAA 6 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLYAA 11 " --> pdb=" O GLYAA 7 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALAAA 12 " --> pdb=" O GLNAA 8 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLYAA 13 " --> pdb=" O ARGAA 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 5 through 13' Processing helix chain 'AA' and resid 33 through 38 Processing helix chain 'AA' and resid 103 through 108 removed outlier: 3.825A pdb=" N METAA 107 " --> pdb=" O PROAA 103 " (cutoff:3.500A) Proline residue: AA 108 - end of helix No H-bonds generated for 'chain 'AA' and resid 103 through 108' Processing helix chain 'AA' and resid 181 through 193 removed outlier: 3.796A pdb=" N ALAAA 185 " --> pdb=" O LYSAA 181 " (cutoff:3.500A) Processing helix chain 'AA' and resid 200 through 205 removed outlier: 5.227A pdb=" N ASNAA 205 " --> pdb=" O GLYAA 201 " (cutoff:3.500A) Processing helix chain 'AA' and resid 173 through 178 removed outlier: 4.043A pdb=" N LYSAA 177 " --> pdb=" O ARGAA 174 " (cutoff:3.500A) Proline residue: AA 178 - end of helix Processing helix chain 'AB' and resid 13 through 18 removed outlier: 4.023A pdb=" N LEUAB 17 " --> pdb=" O SERAB 13 " (cutoff:3.500A) Proline residue: AB 18 - end of helix No H-bonds generated for 'chain 'AB' and resid 13 through 18' Processing helix chain 'AB' and resid 111 through 120 removed outlier: 4.996A pdb=" N LYSAB 120 " --> pdb=" O ARGAB 116 " (cutoff:3.500A) Processing helix chain 'AB' and resid 121 through 126 removed outlier: 5.513A pdb=" N LYSAB 126 " --> pdb=" O TRPAB 122 " (cutoff:3.500A) Processing helix chain 'AB' and resid 130 through 140 removed outlier: 5.778A pdb=" N GLUAB 140 " --> pdb=" O LYSAB 136 " (cutoff:3.500A) Processing helix chain 'AB' and resid 141 through 157 removed outlier: 3.656A pdb=" N GLNAB 145 " --> pdb=" O ASPAB 141 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASPAB 149 " --> pdb=" O GLNAB 145 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHEAB 150 " --> pdb=" O LEUAB 146 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSAB 155 " --> pdb=" O SERAB 151 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYSAB 157 " --> pdb=" O METAB 153 " (cutoff:3.500A) Processing helix chain 'AB' and resid 167 through 172 removed outlier: 4.388A pdb=" N LEUAB 171 " --> pdb=" O GLNAB 167 " (cutoff:3.500A) Proline residue: AB 172 - end of helix No H-bonds generated for 'chain 'AB' and resid 167 through 172' Processing helix chain 'AB' and resid 189 through 201 Processing helix chain 'AB' and resid 206 through 211 removed outlier: 3.950A pdb=" N VALAB 210 " --> pdb=" O PROAB 206 " (cutoff:3.500A) Processing helix chain 'AB' and resid 230 through 235 Processing helix chain 'AB' and resid 381 through 390 Processing helix chain 'AC' and resid 25 through 30 removed outlier: 4.230A pdb=" N LYSAC 29 " --> pdb=" O PROAC 25 " (cutoff:3.500A) Processing helix chain 'AC' and resid 33 through 49 removed outlier: 4.275A pdb=" N ARGAC 49 " --> pdb=" O ARGAC 45 " (cutoff:3.500A) Processing helix chain 'AC' and resid 116 through 133 removed outlier: 3.794A pdb=" N ALAAC 132 " --> pdb=" O LEUAC 128 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEUAC 133 " --> pdb=" O ALAAC 129 " (cutoff:3.500A) Processing helix chain 'AC' and resid 134 through 141 Processing helix chain 'AC' and resid 155 through 161 removed outlier: 4.554A pdb=" N GLUAC 159 " --> pdb=" O GLUAC 155 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLYAC 160 " --> pdb=" O ASPAC 156 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYRAC 161 " --> pdb=" O LYSAC 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 155 through 161' Processing helix chain 'AC' and resid 163 through 175 removed outlier: 3.869A pdb=" N ALAAC 167 " --> pdb=" O LYSAC 163 " (cutoff:3.500A) Processing helix chain 'AC' and resid 176 through 187 removed outlier: 3.874A pdb=" N GLNAC 187 " --> pdb=" O VALAC 183 " (cutoff:3.500A) Processing helix chain 'AC' and resid 193 through 198 removed outlier: 4.559A pdb=" N ARGAC 197 " --> pdb=" O LYSAC 193 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASNAC 198 " --> pdb=" O GLYAC 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 193 through 198' Processing helix chain 'AC' and resid 216 through 222 Processing helix chain 'AC' and resid 236 through 241 Processing helix chain 'AC' and resid 253 through 265 removed outlier: 4.689A pdb=" N ASPAC 261 " --> pdb=" O PHEAC 257 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLUAC 262 " --> pdb=" O ARGAC 258 " (cutoff:3.500A) Processing helix chain 'AC' and resid 288 through 295 Processing helix chain 'AC' and resid 296 through 303 removed outlier: 4.158A pdb=" N ALAAC 301 " --> pdb=" O GLUAC 297 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEUAC 302 " --> pdb=" O ILEAC 298 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARGAC 303 " --> pdb=" O GLNAC 299 " (cutoff:3.500A) Processing helix chain 'AC' and resid 321 through 329 removed outlier: 4.793A pdb=" N METAC 325 " --> pdb=" O ASNAC 321 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEUAC 326 " --> pdb=" O LEUAC 322 " (cutoff:3.500A) Processing helix chain 'AC' and resid 330 through 365 removed outlier: 4.704A pdb=" N THRAC 334 " --> pdb=" O PROAC 330 " (cutoff:3.500A) Processing helix chain 'AC' and resid 58 through 63 removed outlier: 3.940A pdb=" N GLNAC 61 " --> pdb=" O ALAAC 58 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THRAC 62 " --> pdb=" O GLYAC 59 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SERAC 63 " --> pdb=" O HISAC 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 58 through 63' Processing helix chain 'AD' and resid 11 through 16 Processing helix chain 'AD' and resid 20 through 26 Processing helix chain 'AD' and resid 29 through 37 removed outlier: 6.212A pdb=" N ARGAD 33 " --> pdb=" O ASPAD 29 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARGAD 35 " --> pdb=" O TYRAD 31 " (cutoff:3.500A) Processing helix chain 'AD' and resid 82 through 87 Processing helix chain 'AD' and resid 94 through 114 Processing helix chain 'AD' and resid 157 through 170 removed outlier: 3.746A pdb=" N GLYAD 161 " --> pdb=" O ASNAD 157 " (cutoff:3.500A) Processing helix chain 'AD' and resid 191 through 201 removed outlier: 3.812A pdb=" N HISAD 195 " --> pdb=" O ASNAD 191 " (cutoff:3.500A) Processing helix chain 'AD' and resid 202 through 214 Processing helix chain 'AD' and resid 215 through 223 removed outlier: 3.588A pdb=" N TYRAD 219 " --> pdb=" O ASPAD 215 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHEAD 223 " --> pdb=" O TYRAD 219 " (cutoff:3.500A) Processing helix chain 'AD' and resid 224 through 230 Processing helix chain 'AD' and resid 232 through 251 removed outlier: 3.897A pdb=" N LYSAD 241 " --> pdb=" O GLUAD 237 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALAAD 245 " --> pdb=" O LYSAD 241 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASNAD 250 " --> pdb=" O ALAAD 246 " (cutoff:3.500A) Proline residue: AD 251 - end of helix Processing helix chain 'AD' and resid 272 through 297 removed outlier: 4.022A pdb=" N ALAAD 295 " --> pdb=" O GLNAD 291 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLUAD 296 " --> pdb=" O GLUAD 292 " (cutoff:3.500A) Processing helix chain 'AE' and resid 213 through 218 removed outlier: 3.870A pdb=" N LYSAE 218 " --> pdb=" O ASPAE 214 " (cutoff:3.500A) Processing helix chain 'AE' and resid 233 through 239 removed outlier: 6.858A pdb=" N LYSAE 237 " --> pdb=" O PHEAE 233 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLUAE 238 " --> pdb=" O ASPAE 234 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYSAE 239 " --> pdb=" O THRAE 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'AE' and resid 233 through 239' Processing helix chain 'AE' and resid 244 through 262 removed outlier: 4.159A pdb=" N ILEAE 248 " --> pdb=" O GLUAE 244 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASPAE 249 " --> pdb=" O GLNAE 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VALAE 253 " --> pdb=" O ASPAE 249 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLNAE 256 " --> pdb=" O ALAAE 252 " (cutoff:3.500A) Proline residue: AE 259 - end of helix Processing helix chain 'AE' and resid 266 through 274 removed outlier: 5.237A pdb=" N VALAE 274 " --> pdb=" O TYRAE 270 " (cutoff:3.500A) Processing helix chain 'AF' and resid 15 through 79 removed outlier: 4.069A pdb=" N GLUAF 68 " --> pdb=" O METAF 64 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILEAF 69 " --> pdb=" O TYRAF 65 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALAAF 75 " --> pdb=" O METAF 71 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARGAF 76 " --> pdb=" O ALAAF 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYSAF 77 " --> pdb=" O ARGAF 73 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALAAF 78 " --> pdb=" O METAF 74 " (cutoff:3.500A) Processing helix chain 'AF' and resid 102 through 113 removed outlier: 4.026A pdb=" N VALAF 108 " --> pdb=" O LYSAF 104 " (cutoff:3.500A) Processing helix chain 'AF' and resid 126 through 137 removed outlier: 3.995A pdb=" N ILEAF 135 " --> pdb=" O ASNAF 131 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VALAF 136 " --> pdb=" O METAF 132 " (cutoff:3.500A) Processing helix chain 'AF' and resid 146 through 156 removed outlier: 3.765A pdb=" N LEUAF 153 " --> pdb=" O SERAF 149 " (cutoff:3.500A) Processing helix chain 'AF' and resid 171 through 179 removed outlier: 4.288A pdb=" N ILEAF 175 " --> pdb=" O ASPAF 171 " (cutoff:3.500A) Processing helix chain 'AF' and resid 186 through 196 Processing helix chain 'AF' and resid 200 through 209 removed outlier: 3.815A pdb=" N ALAAF 204 " --> pdb=" O ARGAF 200 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TRPAF 209 " --> pdb=" O ASNAF 205 " (cutoff:3.500A) Processing helix chain 'AF' and resid 238 through 248 removed outlier: 4.100A pdb=" N ARGAF 242 " --> pdb=" O ASPAF 238 " (cutoff:3.500A) Processing helix chain 'AG' and resid 58 through 74 Processing helix chain 'AG' and resid 77 through 86 removed outlier: 4.769A pdb=" N GLNAG 82 " --> pdb=" O PROAG 78 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHEAG 83 " --> pdb=" O ALAAG 79 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N THRAG 84 " --> pdb=" O ILEAG 80 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLNAG 85 " --> pdb=" O ASNAG 81 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALAAG 86 " --> pdb=" O GLNAG 82 " (cutoff:3.500A) Processing helix chain 'AG' and resid 88 through 103 removed outlier: 4.715A pdb=" N LYSAG 101 " --> pdb=" O LYSAG 97 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYRAG 102 " --> pdb=" O LEUAG 98 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARGAG 103 " --> pdb=" O ALAAG 99 " (cutoff:3.500A) Processing helix chain 'AG' and resid 106 through 124 Processing helix chain 'AG' and resid 139 through 150 Processing helix chain 'AG' and resid 163 through 178 removed outlier: 4.654A pdb=" N VALAG 167 " --> pdb=" O PROAG 163 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHEAG 169 " --> pdb=" O GLUAG 165 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEUAG 170 " --> pdb=" O LEUAG 166 " (cutoff:3.500A) Proline residue: AG 171 - end of helix Processing helix chain 'AG' and resid 186 through 195 removed outlier: 3.757A pdb=" N LEUAG 190 " --> pdb=" O GLYAG 186 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEUAG 193 " --> pdb=" O ARGAG 189 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VALAG 194 " --> pdb=" O LEUAG 190 " (cutoff:3.500A) Processing helix chain 'AG' and resid 211 through 226 removed outlier: 3.600A pdb=" N ALAAG 221 " --> pdb=" O LYSAG 217 " (cutoff:3.500A) Processing helix chain 'AG' and resid 229 through 237 removed outlier: 3.853A pdb=" N ARGAG 235 " --> pdb=" O ASPAG 231 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HISAG 236 " --> pdb=" O GLUAG 232 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRPAG 237 " --> pdb=" O ILEAG 233 " (cutoff:3.500A) Processing helix chain 'AG' and resid 243 through 262 Processing helix chain 'AH' and resid 63 through 86 removed outlier: 4.265A pdb=" N ARGAH 71 " --> pdb=" O LEUAH 67 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THRAH 72 " --> pdb=" O ALAAH 68 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILEAH 73 " --> pdb=" O THRAH 69 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYSAH 74 " --> pdb=" O VALAH 70 " (cutoff:3.500A) Processing helix chain 'AH' and resid 150 through 166 removed outlier: 4.623A pdb=" N THRAH 166 " --> pdb=" O GLNAH 162 " (cutoff:3.500A) Processing helix chain 'AH' and resid 171 through 176 removed outlier: 4.538A pdb=" N PHEAH 175 " --> pdb=" O ASPAH 171 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEUAH 176 " --> pdb=" O ILEAH 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'AH' and resid 171 through 176' Processing helix chain 'AI' and resid 5 through 10 removed outlier: 3.877A pdb=" N TYRAI 9 " --> pdb=" O PROAI 5 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARGAI 10 " --> pdb=" O ALAAI 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'AI' and resid 5 through 10' Processing helix chain 'AI' and resid 42 through 47 removed outlier: 4.292A pdb=" N PHEAI 46 " --> pdb=" O LYSAI 42 " (cutoff:3.500A) Proline residue: AI 47 - end of helix No H-bonds generated for 'chain 'AI' and resid 42 through 47' Processing helix chain 'AI' and resid 61 through 80 Processing helix chain 'AI' and resid 144 through 160 removed outlier: 3.648A pdb=" N VALAI 148 " --> pdb=" O ASNAI 144 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILEAI 149 " --> pdb=" O LYSAI 145 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYSAI 158 " --> pdb=" O ARGAI 154 " (cutoff:3.500A) Proline residue: AI 160 - end of helix Processing helix chain 'AI' and resid 178 through 188 removed outlier: 4.315A pdb=" N GLUAI 182 " --> pdb=" O ALAAI 178 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASPAI 183 " --> pdb=" O ASPAI 179 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALAAI 186 " --> pdb=" O GLUAI 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLUAI 187 " --> pdb=" O ASPAI 183 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYSAI 188 " --> pdb=" O METAI 184 " (cutoff:3.500A) Processing helix chain 'AI' and resid 205 through 213 removed outlier: 3.996A pdb=" N TRPAI 209 " --> pdb=" O PROAI 205 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HISAI 213 " --> pdb=" O TRPAI 209 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 30 through 45 Processing helix chain 'AJ' and resid 76 through 91 Processing helix chain 'AJ' and resid 139 through 144 removed outlier: 4.299A pdb=" N ASPAJ 143 " --> pdb=" O PHEAJ 139 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 158 through 169 Processing helix chain 'AJ' and resid 95 through 100 removed outlier: 3.667A pdb=" N ASNAJ 98 " --> pdb=" O ARGAJ 95 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHEAJ 99 " --> pdb=" O LYSAJ 96 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SERAJ 100 " --> pdb=" O ASNAJ 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 95 through 100' Processing helix chain 'AJ' and resid 111 through 116 removed outlier: 3.638A pdb=" N LEUAJ 115 " --> pdb=" O HISAJ 112 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLYAJ 116 " --> pdb=" O ILEAJ 113 " (cutoff:3.500A) Processing helix chain 'AL' and resid 27 through 45 Processing helix chain 'AL' and resid 77 through 85 removed outlier: 3.860A pdb=" N LEUAL 81 " --> pdb=" O SERAL 77 " (cutoff:3.500A) Processing helix chain 'AL' and resid 87 through 95 Processing helix chain 'AL' and resid 106 through 124 Processing helix chain 'AL' and resid 139 through 147 removed outlier: 5.188A pdb=" N GLUAL 143 " --> pdb=" O SERAL 139 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEUAL 146 " --> pdb=" O GLUAL 142 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALAAL 147 " --> pdb=" O GLUAL 143 " (cutoff:3.500A) Processing helix chain 'AL' and resid 172 through 178 removed outlier: 5.310A pdb=" N ALAAL 178 " --> pdb=" O LYSAL 174 " (cutoff:3.500A) Processing helix chain 'AL' and resid 179 through 192 removed outlier: 3.730A pdb=" N ARGAL 183 " --> pdb=" O PHEAL 179 " (cutoff:3.500A) Processing helix chain 'AL' and resid 193 through 206 removed outlier: 3.597A pdb=" N ASPAL 206 " --> pdb=" O ALAAL 202 " (cutoff:3.500A) Processing helix chain 'AM' and resid 51 through 56 removed outlier: 4.605A pdb=" N GLNAM 56 " --> pdb=" O PHEAM 52 " (cutoff:3.500A) Processing helix chain 'AM' and resid 69 through 81 Processing helix chain 'AM' and resid 82 through 89 removed outlier: 4.054A pdb=" N THRAM 89 " --> pdb=" O LYSAM 85 " (cutoff:3.500A) Processing helix chain 'AM' and resid 90 through 104 Processing helix chain 'AM' and resid 105 through 140 Proline residue: AM 140 - end of helix Processing helix chain 'AN' and resid 3 through 14 removed outlier: 3.852A pdb=" N LYSAN 13 " --> pdb=" O GLUAN 9 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYSAN 14 " --> pdb=" O LEUAN 10 " (cutoff:3.500A) Processing helix chain 'AN' and resid 16 through 34 removed outlier: 3.698A pdb=" N PHEAN 21 " --> pdb=" O ASPAN 17 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEUAN 22 " --> pdb=" O VALAN 18 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SERAN 34 " --> pdb=" O TYRAN 30 " (cutoff:3.500A) Processing helix chain 'AN' and resid 44 through 52 Processing helix chain 'AN' and resid 83 through 88 removed outlier: 4.322A pdb=" N HISAN 87 " --> pdb=" O LYSAN 83 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLYAN 88 " --> pdb=" O PROAN 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 83 through 88' Processing helix chain 'AN' and resid 97 through 111 Processing helix chain 'AN' and resid 139 through 146 removed outlier: 4.598A pdb=" N ASNAN 145 " --> pdb=" O ALAAN 141 " (cutoff:3.500A) Proline residue: AN 146 - end of helix Processing helix chain 'AN' and resid 147 through 153 removed outlier: 6.968A pdb=" N ILEAN 151 " --> pdb=" O ASPAN 147 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THRAN 152 " --> pdb=" O THRAN 148 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYSAN 153 " --> pdb=" O GLNAN 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 147 through 153' Processing helix chain 'AN' and resid 158 through 163 removed outlier: 3.594A pdb=" N ARGAN 162 " --> pdb=" O HISAN 158 " (cutoff:3.500A) Processing helix chain 'AN' and resid 165 through 173 Processing helix chain 'AN' and resid 187 through 197 Processing helix chain 'AO' and resid 15 through 30 removed outlier: 3.965A pdb=" N LEUAO 28 " --> pdb=" O ALAAO 24 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEUAO 29 " --> pdb=" O LYSAO 25 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLYAO 30 " --> pdb=" O GLNAO 26 " (cutoff:3.500A) Processing helix chain 'AO' and resid 46 through 61 removed outlier: 5.378A pdb=" N ARGAO 61 " --> pdb=" O PHEAO 57 " (cutoff:3.500A) Processing helix chain 'AO' and resid 65 through 70 removed outlier: 4.495A pdb=" N GLYAO 69 " --> pdb=" O ASNAO 65 " (cutoff:3.500A) Proline residue: AO 70 - end of helix No H-bonds generated for 'chain 'AO' and resid 65 through 70' Processing helix chain 'AO' and resid 75 through 89 removed outlier: 3.692A pdb=" N METAO 87 " --> pdb=" O THRAO 83 " (cutoff:3.500A) Proline residue: AO 89 - end of helix Processing helix chain 'AO' and resid 92 through 103 removed outlier: 5.131A pdb=" N ALAAO 97 " --> pdb=" O LYSAO 93 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYSAO 103 " --> pdb=" O LEUAO 99 " (cutoff:3.500A) Processing helix chain 'AO' and resid 109 through 116 removed outlier: 3.678A pdb=" N LYSAO 114 " --> pdb=" O PROAO 110 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYSAO 116 " --> pdb=" O TYRAO 112 " (cutoff:3.500A) Processing helix chain 'AO' and resid 124 through 129 Processing helix chain 'AO' and resid 137 through 146 removed outlier: 3.694A pdb=" N GLYAO 146 " --> pdb=" O ALAAO 142 " (cutoff:3.500A) Processing helix chain 'AO' and resid 151 through 185 removed outlier: 3.535A pdb=" N THRAO 155 " --> pdb=" O ALAAO 151 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYSAO 170 " --> pdb=" O ILEAO 166 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VALAO 185 " --> pdb=" O ALAAO 181 " (cutoff:3.500A) Processing helix chain 'AO' and resid 189 through 198 removed outlier: 4.004A pdb=" N THRAO 193 " --> pdb=" O ILEAO 189 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEUAO 196 " --> pdb=" O TYRAO 192 " (cutoff:3.500A) Processing helix chain 'AP' and resid 25 through 37 Processing helix chain 'AP' and resid 40 through 54 Processing helix chain 'AP' and resid 84 through 106 Processing helix chain 'AP' and resid 70 through 76 removed outlier: 3.763A pdb=" N ALAAP 73 " --> pdb=" O CYSAP 70 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYSAP 74 " --> pdb=" O ALAAP 71 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLNAP 75 " --> pdb=" O GLNAP 72 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 22 through 39 Processing helix chain 'AQ' and resid 41 through 54 removed outlier: 5.292A pdb=" N SERAQ 54 " --> pdb=" O ARGAQ 50 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 62 through 72 removed outlier: 3.938A pdb=" N METAQ 70 " --> pdb=" O METAQ 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEUAQ 72 " --> pdb=" O ARGAQ 68 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 106 through 117 Processing helix chain 'AQ' and resid 122 through 130 Processing helix chain 'AQ' and resid 146 through 153 removed outlier: 3.583A pdb=" N ARGAQ 150 " --> pdb=" O ARGAQ 146 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HISAQ 151 " --> pdb=" O GLUAQ 147 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHEAQ 152 " --> pdb=" O VALAQ 148 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLYAQ 153 " --> pdb=" O TYRAQ 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'AQ' and resid 146 through 153' Processing helix chain 'AR' and resid 4 through 16 removed outlier: 4.105A pdb=" N SERAR 12 " --> pdb=" O LYSAR 8 " (cutoff:3.500A) Processing helix chain 'AR' and resid 28 through 36 removed outlier: 4.296A pdb=" N ILEAR 32 " --> pdb=" O GLUAR 28 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALAAR 35 " --> pdb=" O GLUAR 31 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASNAR 36 " --> pdb=" O ILEAR 32 " (cutoff:3.500A) Processing helix chain 'AR' and resid 37 through 48 removed outlier: 3.598A pdb=" N LYSAR 46 " --> pdb=" O ARGAR 42 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASPAR 47 " --> pdb=" O LYSAR 43 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLYAR 48 " --> pdb=" O LEUAR 44 " (cutoff:3.500A) Processing helix chain 'AR' and resid 60 through 73 Processing helix chain 'AR' and resid 84 through 113 Proline residue: AR 90 - end of helix removed outlier: 6.561A pdb=" N VALAR 93 " --> pdb=" O METAR 89 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEUAR 106 " --> pdb=" O LEUAR 102 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARGAR 107 " --> pdb=" O ARGAR 103 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SERAR 112 " --> pdb=" O ARGAR 108 " (cutoff:3.500A) Processing helix chain 'AR' and resid 116 through 130 removed outlier: 3.660A pdb=" N TYRAR 120 " --> pdb=" O ASPAR 116 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HISAR 121 " --> pdb=" O ARGAR 117 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SERAR 122 " --> pdb=" O HISAR 118 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASNAR 130 " --> pdb=" O LYSAR 126 " (cutoff:3.500A) Processing helix chain 'AR' and resid 134 through 182 removed outlier: 3.511A pdb=" N ARGAR 151 " --> pdb=" O ALAAR 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALAAR 156 " --> pdb=" O LYSAR 152 " (cutoff:3.500A) Processing helix chain 'AS' and resid 36 through 52 Processing helix chain 'AS' and resid 101 through 117 Processing helix chain 'AS' and resid 120 through 125 removed outlier: 3.617A pdb=" N ILEAS 124 " --> pdb=" O ARGAS 120 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLNAS 125 " --> pdb=" O ALAAS 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'AS' and resid 120 through 125' Processing helix chain 'AS' and resid 139 through 147 removed outlier: 5.094A pdb=" N ASPAS 147 " --> pdb=" O LYSAS 143 " (cutoff:3.500A) Processing helix chain 'AT' and resid 11 through 16 removed outlier: 4.186A pdb=" N PHEAT 15 " --> pdb=" O THRAT 11 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SERAT 16 " --> pdb=" O ARGAT 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'AT' and resid 11 through 16' Processing helix chain 'AT' and resid 26 through 32 removed outlier: 4.357A pdb=" N TYRAT 30 " --> pdb=" O PROAT 26 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARGAT 32 " --> pdb=" O ALAAT 28 " (cutoff:3.500A) Processing helix chain 'AT' and resid 92 through 97 removed outlier: 4.372A pdb=" N ILEAT 96 " --> pdb=" O ARGAT 92 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYSAT 97 " --> pdb=" O ILEAT 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'AT' and resid 92 through 97' Processing helix chain 'AT' and resid 99 through 123 removed outlier: 4.162A pdb=" N ASPAT 103 " --> pdb=" O SERAT 99 " (cutoff:3.500A) Processing helix chain 'AU' and resid 25 through 32 removed outlier: 3.972A pdb=" N VALAU 29 " --> pdb=" O CYSAU 25 " (cutoff:3.500A) Processing helix chain 'AU' and resid 35 through 47 Processing helix chain 'AU' and resid 79 through 95 removed outlier: 4.041A pdb=" N LEUAU 83 " --> pdb=" O SERAU 79 " (cutoff:3.500A) Processing helix chain 'AV' and resid 69 through 74 removed outlier: 3.571A pdb=" N ARGAV 73 " --> pdb=" O LYSAV 69 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYSAV 74 " --> pdb=" O PROAV 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'AV' and resid 69 through 74' Processing helix chain 'AV' and resid 122 through 129 Processing helix chain 'AV' and resid 130 through 136 removed outlier: 3.785A pdb=" N ASNAV 135 " --> pdb=" O ARGAV 131 " (cutoff:3.500A) Processing helix chain 'AW' and resid 33 through 43 removed outlier: 4.130A pdb=" N LYSAW 43 " --> pdb=" O ALAAW 39 " (cutoff:3.500A) Processing helix chain 'AW' and resid 45 through 50 removed outlier: 5.925A pdb=" N ASNAW 50 " --> pdb=" O PROAW 46 " (cutoff:3.500A) Processing helix chain 'AW' and resid 52 through 59 removed outlier: 3.783A pdb=" N LYSAW 58 " --> pdb=" O LEUAW 54 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N HISAW 59 " --> pdb=" O TYRAW 55 " (cutoff:3.500A) Processing helix chain 'AW' and resid 61 through 68 removed outlier: 3.909A pdb=" N GLUAW 66 " --> pdb=" O GLYAW 62 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILEAW 67 " --> pdb=" O GLNAW 63 " (cutoff:3.500A) Processing helix chain 'AW' and resid 86 through 96 removed outlier: 4.176A pdb=" N LYSAW 93 " --> pdb=" O ASPAW 89 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARGAW 94 " --> pdb=" O ILEAW 90 " (cutoff:3.500A) Processing helix chain 'AW' and resid 97 through 122 removed outlier: 4.189A pdb=" N GLUAW 114 " --> pdb=" O ARGAW 110 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALAAW 115 " --> pdb=" O ALAAW 111 " (cutoff:3.500A) Processing helix chain 'AX' and resid 72 through 78 removed outlier: 3.871A pdb=" N ILEAX 77 " --> pdb=" O HISAX 73 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYSAX 78 " --> pdb=" O TYRAX 74 " (cutoff:3.500A) Processing helix chain 'AX' and resid 83 through 93 removed outlier: 3.820A pdb=" N LYSAX 89 " --> pdb=" O SERAX 85 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILEAX 90 " --> pdb=" O ALAAX 86 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLUAX 91 " --> pdb=" O METAX 87 " (cutoff:3.500A) Processing helix chain 'AX' and resid 105 through 117 Processing helix chain 'AX' and resid 145 through 154 Processing helix chain 'AY' and resid 10 through 21 Processing helix chain 'AY' and resid 22 through 31 removed outlier: 3.972A pdb=" N LYSAY 28 " --> pdb=" O HISAY 24 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SERAY 31 " --> pdb=" O ARGAY 27 " (cutoff:3.500A) Processing helix chain 'AY' and resid 35 through 43 Processing helix chain 'AY' and resid 100 through 105 removed outlier: 4.277A pdb=" N VALAY 104 " --> pdb=" O HISAY 100 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VALAY 105 " --> pdb=" O PROAY 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'AY' and resid 100 through 105' Processing helix chain 'AY' and resid 112 through 127 Processing helix chain 'AZ' and resid 59 through 67 Processing helix chain 'AZ' and resid 76 through 81 removed outlier: 3.579A pdb=" N LEUAZ 80 " --> pdb=" O ASNAZ 76 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N METAZ 81 " --> pdb=" O TYRAZ 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'AZ' and resid 76 through 81' Processing helix chain 'AZ' and resid 92 through 97 removed outlier: 4.325A pdb=" N VALAZ 96 " --> pdb=" O ASPAZ 92 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASNAZ 97 " --> pdb=" O LYSAZ 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'AZ' and resid 92 through 97' Processing helix chain 'AZ' and resid 103 through 125 removed outlier: 5.087A pdb=" N THRAZ 124 " --> pdb=" O GLUAZ 120 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLYAZ 125 " --> pdb=" O ARGAZ 121 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 127 through 133 removed outlier: 4.008A pdb=" N PHEAZ 131 " --> pdb=" O ASNAZ 127 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLNAZ 132 " --> pdb=" O LYSAZ 128 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYSAZ 133 " --> pdb=" O TRPAZ 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'AZ' and resid 127 through 133' Processing helix chain 'Aa' and resid 2 through 7 removed outlier: 3.617A pdb=" N ARGAa 6 " --> pdb=" O PROAa 2 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYSAa 7 " --> pdb=" O SERAa 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 2 through 7' Processing helix chain 'Aa' and resid 41 through 46 Processing helix chain 'Aa' and resid 64 through 69 removed outlier: 4.826A pdb=" N SERAa 68 " --> pdb=" O LYSAa 64 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHEAa 69 " --> pdb=" O ARGAa 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 64 through 69' Processing helix chain 'Aa' and resid 74 through 83 removed outlier: 4.483A pdb=" N TRPAa 79 " --> pdb=" O LEUAa 75 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THRAa 80 " --> pdb=" O ASPAa 76 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEUAa 81 " --> pdb=" O LYSAa 77 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VALAa 82 " --> pdb=" O LEUAa 78 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SERAa 83 " --> pdb=" O TRPAa 79 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 84 through 92 Processing helix chain 'Aa' and resid 102 through 107 removed outlier: 3.841A pdb=" N SERAa 106 " --> pdb=" O ASPAa 102 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 130 through 141 Processing helix chain 'Ab' and resid 11 through 20 removed outlier: 4.630A pdb=" N LYSAb 15 " --> pdb=" O ASNAb 11 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASNAb 19 " --> pdb=" O LYSAb 15 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLYAb 20 " --> pdb=" O TRPAb 16 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 36 through 53 removed outlier: 4.255A pdb=" N PHEAb 45 " --> pdb=" O ARGAb 41 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 55 through 69 Processing helix chain 'Ac' and resid 7 through 24 removed outlier: 3.915A pdb=" N LYSAc 23 " --> pdb=" O GLNAc 19 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 30 through 41 removed outlier: 4.324A pdb=" N LYSAc 36 " --> pdb=" O LYSAc 32 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N METAc 37 " --> pdb=" O GLNAc 33 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 53 through 68 Processing helix chain 'Ac' and resid 77 through 86 Processing helix chain 'Ac' and resid 103 through 108 Processing helix chain 'Ad' and resid 28 through 34 removed outlier: 4.947A pdb=" N HISAd 34 " --> pdb=" O HISAd 30 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 40 through 58 removed outlier: 3.555A pdb=" N ALAAd 45 " --> pdb=" O ARGAd 41 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEUAd 46 " --> pdb=" O ALAAd 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYSAd 47 " --> pdb=" O PROAd 43 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 65 through 74 Processing helix chain 'Ae' and resid 24 through 29 removed outlier: 3.640A pdb=" N TYRAe 28 " --> pdb=" O GLNAe 24 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VALAe 29 " --> pdb=" O SERAe 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ae' and resid 24 through 29' Processing helix chain 'Ae' and resid 43 through 48 Processing helix chain 'Ae' and resid 81 through 90 removed outlier: 4.554A pdb=" N LEUAe 88 " --> pdb=" O GLUAe 84 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEUAe 89 " --> pdb=" O LEUAe 85 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N METAe 90 " --> pdb=" O GLUAe 86 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 104 through 119 removed outlier: 3.983A pdb=" N ALAAe 110 " --> pdb=" O LYSAe 106 " (cutoff:3.500A) Processing helix chain 'Af' and resid 35 through 40 removed outlier: 4.434A pdb=" N GLUAf 40 " --> pdb=" O ARGAf 36 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 60 through 68 removed outlier: 3.992A pdb=" N METAg 65 " --> pdb=" O PROAg 61 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ARGAg 66 " --> pdb=" O LYSAg 62 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEUAg 67 " --> pdb=" O VALAg 63 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SERAg 68 " --> pdb=" O LEUAg 64 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 83 through 115 removed outlier: 6.133A pdb=" N VALAg 87 " --> pdb=" O CYSAg 83 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYSAg 92 " --> pdb=" O ARGAg 88 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 5 through 13 removed outlier: 3.932A pdb=" N GLYAh 11 " --> pdb=" O ARGAh 7 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYSAh 12 " --> pdb=" O ASPAh 8 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYSAh 13 " --> pdb=" O LEUAh 9 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 14 through 38 removed outlier: 3.795A pdb=" N LYSAh 19 " --> pdb=" O GLUAh 15 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLYAh 38 " --> pdb=" O ALAAh 34 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 42 through 74 removed outlier: 5.205A pdb=" N LYSAh 46 " --> pdb=" O SERAh 42 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHEAh 72 " --> pdb=" O ASNAh 68 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 88 through 94 Processing helix chain 'Ah' and resid 96 through 102 Processing helix chain 'Ah' and resid 104 through 114 Processing helix chain 'Ai' and resid 25 through 30 removed outlier: 4.144A pdb=" N ARGAi 29 " --> pdb=" O ARGAi 25 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARGAi 30 " --> pdb=" O HISAi 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ai' and resid 25 through 30' Processing helix chain 'Ai' and resid 34 through 49 removed outlier: 4.352A pdb=" N GLUAi 46 " --> pdb=" O ASPAi 42 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 51 through 63 removed outlier: 3.778A pdb=" N GLUAi 59 " --> pdb=" O ARGAi 55 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 65 through 77 Processing helix chain 'Ai' and resid 79 through 98 Processing helix chain 'Aj' and resid 4 through 11 removed outlier: 3.932A pdb=" N GLYAj 9 " --> pdb=" O THRAj 5 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYSAj 10 " --> pdb=" O SERAj 6 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARGAj 11 " --> pdb=" O SERAj 7 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 50 through 58 removed outlier: 3.759A pdb=" N LYSAj 54 " --> pdb=" O SERAj 50 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 64 through 77 removed outlier: 4.229A pdb=" N ILEAj 69 " --> pdb=" O ARGAj 65 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HISAj 76 " --> pdb=" O ARGAj 72 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 7 through 18 removed outlier: 5.224A pdb=" N LYSAk 18 " --> pdb=" O THRAk 14 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 49 through 60 Processing helix chain 'Al' and resid 6 through 21 removed outlier: 3.569A pdb=" N LYSAl 10 " --> pdb=" O THRAl 6 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ARGAl 21 " --> pdb=" O GLNAl 17 " (cutoff:3.500A) Processing helix chain 'Al' and resid 24 through 31 removed outlier: 4.343A pdb=" N ARGAl 28 " --> pdb=" O PROAl 24 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N METAl 29 " --> pdb=" O GLNAl 25 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THRAl 31 " --> pdb=" O ILEAl 27 " (cutoff:3.500A) Processing helix chain 'Am' and resid 79 through 91 Processing helix chain 'An' and resid 2 through 25 Processing helix chain 'Ao' and resid 35 through 47 removed outlier: 5.654A pdb=" N GLYAo 47 " --> pdb=" O ARGAo 43 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 19 through 35 removed outlier: 4.002A pdb=" N LYSAp 28 " --> pdb=" O LYSAp 24 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILEAp 29 " --> pdb=" O METAp 25 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 73 through 91 removed outlier: 5.976A pdb=" N LYSAp 90 " --> pdb=" O LEUAp 86 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASPAp 91 " --> pdb=" O LYSAp 87 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 9 through 14 removed outlier: 3.681A pdb=" N GLYAp 12 " --> pdb=" O GLYAp 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYSAp 13 " --> pdb=" O ILEAp 10 " (cutoff:3.500A) Processing helix chain 'At' and resid 2 through 13 removed outlier: 5.216A pdb=" N ASNAt 12 " --> pdb=" O METAt 8 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N CYSAt 13 " --> pdb=" O VALAt 9 " (cutoff:3.500A) Processing helix chain 'At' and resid 85 through 99 removed outlier: 5.884A pdb=" N THRAt 89 " --> pdb=" O ASNAt 85 " (cutoff:3.500A) Processing helix chain 'At' and resid 106 through 123 removed outlier: 3.694A pdb=" N LYSAt 122 " --> pdb=" O LEUAt 118 " (cutoff:3.500A) Proline residue: At 123 - end of helix Processing helix chain 'Au' and resid 6 through 20 Processing helix chain 'Au' and resid 71 through 81 Processing helix chain 'Au' and resid 86 through 97 removed outlier: 3.930A pdb=" N LYSAu 95 " --> pdb=" O LYSAu 91 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASNAu 96 " --> pdb=" O LYSAu 92 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYSAu 97 " --> pdb=" O LEUAu 93 " (cutoff:3.500A) Processing helix chain 'Au' and resid 98 through 107 removed outlier: 3.623A pdb=" N LEUAu 103 " --> pdb=" O LEUAu 99 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYSAu 106 " --> pdb=" O LYSAu 102 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYRAu 107 " --> pdb=" O LEUAu 103 " (cutoff:3.500A) Processing helix chain 'Au' and resid 116 through 124 Proline residue: Au 121 - end of helix Processing helix chain 'Au' and resid 127 through 132 Processing helix chain 'Au' and resid 143 through 154 removed outlier: 4.348A pdb=" N LYSAu 147 " --> pdb=" O ASNAu 143 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SERAu 153 " --> pdb=" O ASPAu 149 " (cutoff:3.500A) Processing helix chain 'Au' and resid 175 through 195 removed outlier: 3.698A pdb=" N PHEAu 189 " --> pdb=" O LEUAu 185 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEUAu 190 " --> pdb=" O ALAAu 186 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYSAu 195 " --> pdb=" O VALAu 191 " (cutoff:3.500A) Processing helix chain 'Au' and resid 197 through 202 removed outlier: 4.592A pdb=" N ASNAu 200 " --> pdb=" O ASNAu 197 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARGAu 202 " --> pdb=" O GLNAu 199 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 30 through 37 Proline residue: Aq 34 - end of helix Processing helix chain 'Aq' and resid 40 through 52 removed outlier: 5.701A pdb=" N ASPAq 44 " --> pdb=" O LYSAq 40 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 77 through 86 removed outlier: 3.828A pdb=" N LYSAq 86 " --> pdb=" O ILEAq 82 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 106 through 118 removed outlier: 3.901A pdb=" N VALAq 110 " --> pdb=" O PHEAq 106 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASNAq 111 " --> pdb=" O ASPAq 107 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N HISAq 118 " --> pdb=" O ARGAq 114 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 128 through 137 removed outlier: 5.190A pdb=" N GLNAq 137 " --> pdb=" O LEUAq 133 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 147 through 154 removed outlier: 3.631A pdb=" N ASPAq 153 " --> pdb=" O HISAq 149 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 157 through 162 removed outlier: 6.929A pdb=" N GLUAq 161 " --> pdb=" O SERAq 157 " (cutoff:3.500A) Processing helix chain 'AK' and resid 5 through 24 removed outlier: 6.222A pdb=" N TRPAK 9 " --> pdb=" O ASPAK 5 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYSAK 10 " --> pdb=" O ARGAK 6 " (cutoff:3.500A) Processing helix chain 'AK' and resid 36 through 48 Processing helix chain 'AK' and resid 57 through 70 removed outlier: 4.420A pdb=" N METAK 61 " --> pdb=" O LYSAK 57 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARGAK 62 " --> pdb=" O ASNAK 58 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYSAK 63 " --> pdb=" O THRAK 59 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALAAK 64 " --> pdb=" O METAK 60 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILEAK 65 " --> pdb=" O METAK 61 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLUAK 70 " --> pdb=" O ARGAK 66 " (cutoff:3.500A) Processing helix chain 'AK' and resid 76 through 82 Proline residue: AK 80 - end of helix No H-bonds generated for 'chain 'AK' and resid 76 through 82' Processing helix chain 'AK' and resid 99 through 104 removed outlier: 5.926A pdb=" N ARGAK 103 " --> pdb=" O ARGAK 99 " (cutoff:3.500A) Processing helix chain 'AK' and resid 135 through 142 Processing helix chain 'AK' and resid 168 through 179 Processing helix chain 'Ct' and resid 5 through 14 removed outlier: 3.731A pdb=" N ILECt 12 " --> pdb=" O GLNCt 8 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N METCt 13 " --> pdb=" O ILECt 9 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASPCt 14 " --> pdb=" O ARGCt 10 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 31 through 44 removed outlier: 4.248A pdb=" N LEUCt 35 " --> pdb=" O GLYCt 31 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALACt 43 " --> pdb=" O LEUCt 39 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 60 through 66 Processing helix chain 'Ct' and resid 111 through 122 removed outlier: 3.777A pdb=" N VALCt 115 " --> pdb=" O PHECt 111 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 136 through 150 Processing helix chain 'Ct' and resid 159 through 166 removed outlier: 3.926A pdb=" N ALACt 163 " --> pdb=" O LYSCt 159 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUCt 164 " --> pdb=" O METCt 160 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 170 through 191 Processing helix chain 'Ct' and resid 224 through 235 removed outlier: 4.272A pdb=" N PHECt 228 " --> pdb=" O THRCt 224 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N METCt 231 " --> pdb=" O GLNCt 227 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALACt 234 " --> pdb=" O GLUCt 230 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 245 through 263 removed outlier: 3.516A pdb=" N ARGCt 249 " --> pdb=" O GLYCt 245 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYSCt 251 " --> pdb=" O ALACt 247 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRPCt 261 " --> pdb=" O METCt 257 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLYCt 262 " --> pdb=" O LYSCt 258 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASPCt 263 " --> pdb=" O LYSCt 259 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 287 through 293 removed outlier: 4.355A pdb=" N GLNCt 291 " --> pdb=" O ARGCt 287 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEUCt 292 " --> pdb=" O THRCt 288 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 294 through 307 Processing helix chain 'Ct' and resid 308 through 319 removed outlier: 4.416A pdb=" N GLUCt 317 " --> pdb=" O ALACt 313 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYSCt 318 " --> pdb=" O LYSCt 314 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 325 through 330 removed outlier: 4.411A pdb=" N ASPCt 329 " --> pdb=" O SERCt 325 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYSCt 330 " --> pdb=" O GLUCt 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ct' and resid 325 through 330' Processing helix chain 'Ct' and resid 333 through 344 removed outlier: 5.701A pdb=" N LYSCt 337 " --> pdb=" O LYSCt 333 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEUCt 344 " --> pdb=" O METCt 340 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 345 through 358 removed outlier: 4.201A pdb=" N ALACt 349 " --> pdb=" O PROCt 345 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEUCt 350 " --> pdb=" O ALACt 346 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N HISCt 357 " --> pdb=" O METCt 353 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEUCt 358 " --> pdb=" O ILECt 354 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 360 through 369 Processing helix chain 'Ct' and resid 379 through 388 removed outlier: 6.774A pdb=" N METCt 383 " --> pdb=" O ASPCt 379 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLYCt 384 " --> pdb=" O GLUCt 380 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 474 through 480 removed outlier: 4.494A pdb=" N PHECt 478 " --> pdb=" O GLYCt 474 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VALCt 480 " --> pdb=" O ASPCt 476 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 516 through 532 removed outlier: 4.055A pdb=" N LEUCt 520 " --> pdb=" O ASPCt 516 " (cutoff:3.500A) Proline residue: Ct 532 - end of helix Processing helix chain 'Ct' and resid 550 through 563 Processing helix chain 'Ct' and resid 612 through 620 removed outlier: 3.689A pdb=" N ASPCt 618 " --> pdb=" O ALACt 614 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 627 through 638 Processing helix chain 'Ct' and resid 642 through 649 Processing helix chain 'Ct' and resid 673 through 690 removed outlier: 4.499A pdb=" N ASPCt 677 " --> pdb=" O ASNCt 673 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SERCt 678 " --> pdb=" O GLUCt 674 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLYCt 690 " --> pdb=" O ALACt 686 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 712 through 717 removed outlier: 7.208A pdb=" N ARGCt 716 " --> pdb=" O ASPCt 712 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLYCt 717 " --> pdb=" O ALACt 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ct' and resid 712 through 717' Processing helix chain 'Ct' and resid 719 through 737 Proline residue: Ct 723 - end of helix removed outlier: 3.953A pdb=" N ALACt 736 " --> pdb=" O SERCt 732 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLNCt 737 " --> pdb=" O VALCt 733 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 752 through 767 removed outlier: 3.773A pdb=" N VALCt 756 " --> pdb=" O PROCt 752 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLYCt 757 " --> pdb=" O GLUCt 753 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLYCt 758 " --> pdb=" O GLNCt 754 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLYCt 761 " --> pdb=" O GLYCt 757 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VALCt 762 " --> pdb=" O GLYCt 758 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEUCt 763 " --> pdb=" O ILECt 759 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 789 through 794 removed outlier: 4.455A pdb=" N PHECt 794 " --> pdb=" O VALCt 790 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 795 through 805 Processing helix chain 'Ct' and resid 829 through 843 removed outlier: 4.219A pdb=" N ARGCt 841 " --> pdb=" O GLUCt 837 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYSCt 842 " --> pdb=" O THRCt 838 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 849 through 854 removed outlier: 5.384A pdb=" N PHECt 853 " --> pdb=" O ALACt 849 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEUCt 854 " --> pdb=" O LEUCt 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ct' and resid 849 through 854' Processing sheet with id= 1, first strand: chain 'BD' and resid 35 through 40 removed outlier: 3.651A pdb=" N GLUBD 47 " --> pdb=" O ARGBD 40 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'BD' and resid 149 through 155 removed outlier: 4.189A pdb=" N GLYBD 133 " --> pdb=" O METBD 189 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'BK' and resid 21 through 24 removed outlier: 3.836A pdb=" N METBK 21 " --> pdb=" O TRPBK 69 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'BM' and resid 30 through 33 removed outlier: 7.728A pdb=" N GLYBM 30 " --> pdb=" O LYSBM 112 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SERBM 107 " --> pdb=" O ALABM 53 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASNBM 75 " --> pdb=" O HISBM 48 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'BP' and resid 75 through 78 removed outlier: 4.529A pdb=" N SERBP 92 " --> pdb=" O ILEBP 107 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'BQ' and resid 8 through 14 removed outlier: 4.582A pdb=" N THRBQ 20 " --> pdb=" O LYSBQ 73 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'BT' and resid 81 through 84 Processing sheet with id= 8, first strand: chain 'BT' and resid 113 through 116 removed outlier: 4.646A pdb=" N GLYBT 120 " --> pdb=" O ASPBT 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'BU' and resid 56 through 66 removed outlier: 5.662A pdb=" N LYSBU 86 " --> pdb=" O PROBU 57 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEUBU 61 " --> pdb=" O METBU 82 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N METBU 82 " --> pdb=" O LEUBU 61 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THRBU 65 " --> pdb=" O ASPBU 78 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILEBU 20 " --> pdb=" O LEUBU 91 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLYBU 109 " --> pdb=" O ARGBU 27 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'BZ' and resid 97 through 100 removed outlier: 7.515A pdb=" N ILEBZ 108 " --> pdb=" O VALBZ 100 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'Bc' and resid 9 through 13 Processing sheet with id= 12, first strand: chain 'Bc' and resid 18 through 22 removed outlier: 3.752A pdb=" N GLYBc 19 " --> pdb=" O GLNBc 29 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Bf' and resid 138 through 141 removed outlier: 6.580A pdb=" N HISBf 139 " --> pdb=" O THRBf 147 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THRBf 147 " --> pdb=" O HISBf 139 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N CYSBf 141 " --> pdb=" O CYSBf 145 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'Bg' and resid 3 through 11 removed outlier: 6.906A pdb=" N VALBg 309 " --> pdb=" O ARGBg 8 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THRBg 10 " --> pdb=" O VALBg 307 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VALBg 307 " --> pdb=" O THRBg 10 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLNBg 296 " --> pdb=" O VALBg 312 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THRBg 297 " --> pdb=" O SERBg 292 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SERBg 288 " --> pdb=" O GLYBg 301 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'Bg' and resid 19 through 23 removed outlier: 3.547A pdb=" N GLNBg 20 " --> pdb=" O ALABg 34 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASPBg 29 " --> pdb=" O LEUBg 45 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N METBg 42 " --> pdb=" O GLNBg 56 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYRBg 52 " --> pdb=" O THRBg 46 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'Bg' and resid 67 through 72 removed outlier: 4.231A pdb=" N ASPBg 68 " --> pdb=" O GLYBg 81 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N PHEBg 77 " --> pdb=" O SERBg 72 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THRBg 86 " --> pdb=" O SERBg 82 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARGBg 99 " --> pdb=" O LEUBg 89 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Bg' and resid 109 through 114 removed outlier: 5.582A pdb=" N GLNBg 119 " --> pdb=" O SERBg 114 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THRBg 128 " --> pdb=" O SERBg 124 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'Bg' and resid 153 through 158 removed outlier: 5.392A pdb=" N CYSBg 153 " --> pdb=" O CYSBg 168 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILEBg 164 " --> pdb=" O SERBg 157 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VALBg 176 " --> pdb=" O LYSBg 185 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Bg' and resid 197 through 201 removed outlier: 5.846A pdb=" N LEUBg 206 " --> pdb=" O SERBg 201 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SERBg 205 " --> pdb=" O LEUBg 221 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLYBg 214 " --> pdb=" O GLYBg 232 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYRBg 228 " --> pdb=" O LEUBg 218 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Bg' and resid 238 through 242 removed outlier: 3.561A pdb=" N ALABg 238 " --> pdb=" O ALABg 251 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TRPBg 247 " --> pdb=" O SERBg 242 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N TYRBg 246 " --> pdb=" O LEUBg 261 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SERBg 255 " --> pdb=" O THRBg 252 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASPBg 268 " --> pdb=" O ILEBg 258 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Bg' and resid 39 through 42 removed outlier: 3.811A pdb=" N ARGBg 57 " --> pdb=" O METBg 42 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Bg' and resid 173 through 176 removed outlier: 3.768A pdb=" N THRBg 186 " --> pdb=" O VALBg 176 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'BA' and resid 24 through 28 removed outlier: 5.041A pdb=" N HISBA 24 " --> pdb=" O ILEBA 49 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYRBA 47 " --> pdb=" O GLYBA 26 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THRBA 28 " --> pdb=" O GLYBA 45 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLYBA 45 " --> pdb=" O THRBA 28 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'BA' and resid 76 through 79 removed outlier: 3.724A pdb=" N SERBA 78 " --> pdb=" O ILEBA 99 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLYBA 101 " --> pdb=" O SERBA 78 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'BA' and resid 121 through 125 Processing sheet with id= 26, first strand: chain 'BB' and resid 45 through 48 removed outlier: 4.223A pdb=" N GLYBB 45 " --> pdb=" O VALBB 33 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BB' and resid 66 through 70 removed outlier: 7.650A pdb=" N HISBB 101 " --> pdb=" O METBB 217 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEUBB 105 " --> pdb=" O ARGBB 213 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ARGBB 213 " --> pdb=" O LEUBB 105 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYSBB 214 " --> pdb=" O PHEBB 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYSBB 216 " --> pdb=" O ARGBB 136 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THRBB 119 " --> pdb=" O THRBB 143 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BC' and resid 103 through 107 removed outlier: 4.464A pdb=" N LYSBC 103 " --> pdb=" O GLYBC 131 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHEBC 127 " --> pdb=" O LEUBC 107 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'BC' and resid 183 through 187 removed outlier: 4.282A pdb=" N ALABC 198 " --> pdb=" O ASPBC 221 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASPBC 221 " --> pdb=" O ALABC 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VALBC 205 " --> pdb=" O CYSBC 222 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THRBC 224 " --> pdb=" O VALBC 205 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BC' and resid 124 through 131 Processing sheet with id= 31, first strand: chain 'BE' and resid 87 through 91 removed outlier: 4.693A pdb=" N ASPBE 88 " --> pdb=" O LEUBE 101 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'BE' and resid 123 through 126 removed outlier: 4.600A pdb=" N ASPBE 158 " --> pdb=" O VALBE 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYSBE 168 " --> pdb=" O ASPBE 163 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'BE' and resid 128 through 132 removed outlier: 4.053A pdb=" N ILEBE 136 " --> pdb=" O GLYBE 132 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARGBE 145 " --> pdb=" O THRBE 141 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'BE' and resid 181 through 184 removed outlier: 3.944A pdb=" N ARGBE 191 " --> pdb=" O VALBE 183 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BE' and resid 197 through 200 removed outlier: 3.984A pdb=" N ASNBE 216 " --> pdb=" O ASPBE 212 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BE' and resid 158 through 161 removed outlier: 3.693A pdb=" N GLNBE 161 " --> pdb=" O ASNBE 171 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASNBE 171 " --> pdb=" O GLNBE 161 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BG' and resid 11 through 18 removed outlier: 3.614A pdb=" N CYSBG 12 " --> pdb=" O PHEBG 7 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASNBG 110 " --> pdb=" O SERBG 53 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VALBG 49 " --> pdb=" O VALBG 114 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYRBG 48 " --> pdb=" O ALABG 38 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILEBG 52 " --> pdb=" O THRBG 34 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THRBG 34 " --> pdb=" O ILEBG 52 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'BG' and resid 74 through 77 Processing sheet with id= 39, first strand: chain 'BG' and resid 159 through 164 removed outlier: 6.815A pdb=" N LYSBG 168 " --> pdb=" O LYSBG 164 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BG' and resid 54 through 57 removed outlier: 3.513A pdb=" N GLYBG 54 " --> pdb=" O ASNBG 110 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BH' and resid 47 through 53 removed outlier: 5.235A pdb=" N ALABH 47 " --> pdb=" O PHEBH 63 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARGBH 57 " --> pdb=" O VALBH 53 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HISBH 91 " --> pdb=" O LYSBH 58 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BH' and resid 141 through 146 removed outlier: 4.062A pdb=" N GLYBH 141 " --> pdb=" O HISBH 157 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASPBH 184 " --> pdb=" O ARGBH 152 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'BI' and resid 42 through 48 removed outlier: 6.950A pdb=" N ARGBI 42 " --> pdb=" O LEUBI 58 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'BI' and resid 72 through 78 removed outlier: 5.096A pdb=" N ALABI 185 " --> pdb=" O VALBI 62 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASNBI 64 " --> pdb=" O ALABI 185 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYSBI 100 " --> pdb=" O ILEBI 175 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'BL' and resid 71 through 76 removed outlier: 5.458A pdb=" N ARGBL 71 " --> pdb=" O GLUBL 130 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THRBL 127 " --> pdb=" O LEUBL 143 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BL' and resid 85 through 89 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'BO' and resid 39 through 46 removed outlier: 3.851A pdb=" N ASPBO 39 " --> pdb=" O SERBO 36 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILEBO 95 " --> pdb=" O GLYBO 127 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BO' and resid 94 through 98 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'BV' and resid 15 through 18 removed outlier: 4.639A pdb=" N ARGBV 15 " --> pdb=" O ILEBV 24 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARGBV 22 " --> pdb=" O CYSBV 17 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BV' and resid 32 through 38 removed outlier: 6.054A pdb=" N GLNBV 49 " --> pdb=" O GLUBV 38 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BW' and resid 23 through 28 removed outlier: 6.579A pdb=" N ARGBW 23 " --> pdb=" O LEUBW 65 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VALBW 63 " --> pdb=" O VALBW 25 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALABW 58 " --> pdb=" O ASPBW 55 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASPBW 55 " --> pdb=" O ALABW 58 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLUBW 49 " --> pdb=" O ASNBW 64 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THRBW 66 " --> pdb=" O ILEBW 47 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ILEBW 47 " --> pdb=" O THRBW 66 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BW' and resid 71 through 74 removed outlier: 3.771A pdb=" N GLYBW 127 " --> pdb=" O VALBW 103 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VALBW 103 " --> pdb=" O LEUBW 126 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYSBW 124 " --> pdb=" O THRBW 105 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'BX' and resid 46 through 51 removed outlier: 3.762A pdb=" N VALBX 51 " --> pdb=" O ASPBX 98 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASPBX 98 " --> pdb=" O VALBX 51 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEUBX 101 " --> pdb=" O VALBX 123 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BX' and resid 52 through 59 removed outlier: 3.580A pdb=" N GLUBX 53 " --> pdb=" O ARGBX 71 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALABX 65 " --> pdb=" O ALABX 59 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYSBX 68 " --> pdb=" O VALBX 85 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LYSBX 79 " --> pdb=" O LEUBX 74 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BY' and resid 6 through 10 removed outlier: 4.186A pdb=" N THRBY 6 " --> pdb=" O LEUBY 28 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VALBY 24 " --> pdb=" O ARGBY 10 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYSBY 11 " --> pdb=" O VALBY 24 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BY' and resid 54 through 61 removed outlier: 6.213A pdb=" N VALBY 54 " --> pdb=" O TYRBY 76 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYRBY 76 " --> pdb=" O VALBY 54 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHEBY 60 " --> pdb=" O THRBY 70 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THRBY 70 " --> pdb=" O PHEBY 60 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'BY' and resid 20 through 29 Processing sheet with id= 58, first strand: chain 'Ba' and resid 36 through 43 Processing sheet with id= 59, first strand: chain 'Bb' and resid 32 through 37 removed outlier: 4.199A pdb=" N LYSBb 42 " --> pdb=" O CYSBb 37 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Bb' and resid 64 through 67 removed outlier: 3.748A pdb=" N ARGBb 72 " --> pdb=" O GLNBb 65 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N THRBb 67 " --> pdb=" O LYSBb 70 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYSBb 70 " --> pdb=" O THRBb 67 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'AA' and resid 47 through 50 removed outlier: 3.812A pdb=" N ASPAA 47 " --> pdb=" O LYSAA 60 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYSAA 60 " --> pdb=" O LYSAA 46 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'AA' and resid 110 through 114 removed outlier: 3.808A pdb=" N THRAA 111 " --> pdb=" O VALAA 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VALAA 136 " --> pdb=" O THRAA 111 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SERAA 154 " --> pdb=" O LEUAA 150 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'AA' and resid 58 through 65 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 'AB' and resid 45 through 50 removed outlier: 3.667A pdb=" N PHEAB 46 " --> pdb=" O LEUAB 347 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEUAB 347 " --> pdb=" O PHEAB 46 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYSAB 50 " --> pdb=" O ARGAB 343 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARGAB 343 " --> pdb=" O LYSAB 50 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VALAB 344 " --> pdb=" O VALAB 222 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VALAB 222 " --> pdb=" O VALAB 344 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N HISAB 275 " --> pdb=" O THRAB 223 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'AB' and resid 52 through 59 removed outlier: 3.813A pdb=" N LYSAB 286 " --> pdb=" O METAB 332 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'AB' and resid 98 through 102 removed outlier: 7.123A pdb=" N GLYAB 91 " --> pdb=" O PHEAB 102 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VALAB 87 " --> pdb=" O ALAAB 107 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'AB' and resid 180 through 184 Processing sheet with id= 68, first strand: chain 'AB' and resid 84 through 88 removed outlier: 6.225A pdb=" N ILEAB 163 " --> pdb=" O VALAB 87 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'AB' and resid 84 through 87 removed outlier: 4.246A pdb=" N GLNAB 203 " --> pdb=" O VALAB 86 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'AB' and resid 215 through 218 removed outlier: 4.346A pdb=" N GLUAB 215 " --> pdb=" O ILEAB 284 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILEAB 284 " --> pdb=" O GLUAB 215 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYSAB 282 " --> pdb=" O ILEAB 217 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'AC' and resid 207 through 210 Processing sheet with id= 72, first strand: chain 'AD' and resid 76 through 80 removed outlier: 6.356A pdb=" N ILEAD 60 " --> pdb=" O ALAAD 80 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASPAD 59 " --> pdb=" O THRAD 56 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'AE' and resid 186 through 190 removed outlier: 4.681A pdb=" N ARGAE 187 " --> pdb=" O VALAE 175 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VALAE 175 " --> pdb=" O ARGAE 187 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEUAE 174 " --> pdb=" O LEUAE 165 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYSAE 160 " --> pdb=" O ILEAE 152 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THRAE 148 " --> pdb=" O PHEAE 164 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILEAE 149 " --> pdb=" O THRAE 197 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'AF' and resid 139 through 144 removed outlier: 7.873A pdb=" N TYRAF 139 " --> pdb=" O ILEAF 95 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASNAF 119 " --> pdb=" O ARGAF 94 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHEAF 118 " --> pdb=" O LEUAF 213 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'AF' and resid 158 through 161 removed outlier: 8.867A pdb=" N GLYAF 158 " --> pdb=" O LEUAF 169 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'AG' and resid 180 through 185 Processing sheet with id= 77, first strand: chain 'AH' and resid 5 through 12 removed outlier: 5.068A pdb=" N LYSAH 53 " --> pdb=" O ILEAH 12 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'AH' and resid 17 through 20 Processing sheet with id= 79, first strand: chain 'AH' and resid 102 through 106 removed outlier: 6.317A pdb=" N LEUAH 111 " --> pdb=" O GLNAH 106 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N SERAH 110 " --> pdb=" O METAH 128 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'AH' and resid 132 through 137 removed outlier: 5.509A pdb=" N GLUAH 143 " --> pdb=" O SERAH 137 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASPAH 142 " --> pdb=" O SERAH 94 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'AI' and resid 85 through 90 removed outlier: 7.021A pdb=" N ILEAI 135 " --> pdb=" O ARGAI 90 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N METAI 136 " --> pdb=" O METAI 52 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'AI' and resid 189 through 192 removed outlier: 6.092A pdb=" N ARGAI 189 " --> pdb=" O ILEAI 200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILEAI 200 " --> pdb=" O ARGAI 189 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'AJ' and resid 19 through 26 removed outlier: 5.332A pdb=" N ILEAJ 68 " --> pdb=" O VALAJ 26 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALAAJ 69 " --> pdb=" O SERAJ 51 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'AJ' and resid 104 through 110 removed outlier: 5.687A pdb=" N PHEAJ 130 " --> pdb=" O PHEAJ 107 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'AL' and resid 57 through 60 Processing sheet with id= 86, first strand: chain 'AM' and resid 10 through 15 removed outlier: 3.935A pdb=" N ARGAM 11 " --> pdb=" O ILEAM 27 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VALAM 15 " --> pdb=" O LYSAM 23 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYSAM 23 " --> pdb=" O VALAM 15 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEUAM 37 " --> pdb=" O VALAM 28 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'AN' and resid 35 through 39 removed outlier: 6.383A pdb=" N ALAAN 35 " --> pdb=" O ARGAN 65 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILEAN 61 " --> pdb=" O ALAAN 39 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLYAN 58 " --> pdb=" O ASPAN 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASPAN 136 " --> pdb=" O GLYAN 58 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILEAN 133 " --> pdb=" O LEUAN 116 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'AN' and resid 117 through 122 removed outlier: 3.713A pdb=" N ASNAN 117 " --> pdb=" O ILEAN 133 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHEAN 129 " --> pdb=" O VALAN 121 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'AO' and resid 5 through 10 Processing sheet with id= 90, first strand: chain 'AP' and resid 13 through 20 removed outlier: 8.179A pdb=" N LYSAP 13 " --> pdb=" O GLUAP 152 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'AP' and resid 124 through 130 removed outlier: 5.168A pdb=" N METAP 125 " --> pdb=" O SERAP 141 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASNAP 137 " --> pdb=" O THRAP 129 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'AQ' and resid 118 through 121 removed outlier: 3.671A pdb=" N LYSAQ 119 " --> pdb=" O LEUAQ 98 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALAAQ 102 " --> pdb=" O LEUAQ 121 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYSAQ 99 " --> pdb=" O LYSAQ 78 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'AS' and resid 27 through 34 removed outlier: 6.801A pdb=" N VALAS 13 " --> pdb=" O VALAS 62 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'AS' and resid 91 through 99 removed outlier: 4.195A pdb=" N ASNAS 77 " --> pdb=" O ILEAS 132 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYSAS 128 " --> pdb=" O TRPAS 81 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'AS' and resid 9 through 13 removed outlier: 4.839A pdb=" N GLUAS 9 " --> pdb=" O VALAS 67 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'AT' and resid 39 through 43 removed outlier: 3.965A pdb=" N LYSAT 60 " --> pdb=" O ILEAT 42 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VALAT 80 " --> pdb=" O LYSAT 83 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYSAT 83 " --> pdb=" O VALAT 80 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'AU' and resid 61 through 65 removed outlier: 6.341A pdb=" N GLUAU 108 " --> pdb=" O LYSAU 20 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VALAU 103 " --> pdb=" O GLUAU 111 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARGAU 113 " --> pdb=" O ARGAU 101 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'AV' and resid 76 through 80 removed outlier: 6.821A pdb=" N METAV 62 " --> pdb=" O ILEAV 40 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYSAV 35 " --> pdb=" O CYSAV 28 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALAAV 24 " --> pdb=" O ILEAV 39 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASNAV 101 " --> pdb=" O VALAV 25 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASPAV 100 " --> pdb=" O ARGAV 85 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARGAV 85 " --> pdb=" O ASPAV 100 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'AW' and resid 18 through 22 Processing sheet with id=100, first strand: chain 'AX' and resid 95 through 101 removed outlier: 3.665A pdb=" N GLUAX 133 " --> pdb=" O ARGAX 129 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'AY' and resid 72 through 75 removed outlier: 3.730A pdb=" N GLNAY 72 " --> pdb=" O TYRAY 81 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'AY' and resid 86 through 89 removed outlier: 5.008A pdb=" N THRAY 93 " --> pdb=" O LYSAY 89 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'AZ' and resid 9 through 12 removed outlier: 4.403A pdb=" N LYSAZ 9 " --> pdb=" O ILEAZ 25 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEUAZ 42 " --> pdb=" O VALAZ 26 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'Ac' and resid 69 through 74 removed outlier: 3.817A pdb=" N GLYAc 70 " --> pdb=" O LYSAc 44 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEUAc 45 " --> pdb=" O ILEAc 96 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'Ad' and resid 61 through 64 removed outlier: 4.731A pdb=" N ASPAd 61 " --> pdb=" O LEUAd 102 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VALAd 21 " --> pdb=" O ARGAd 90 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THRAd 22 " --> pdb=" O VALAd 122 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VALAd 120 " --> pdb=" O GLUAd 24 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'Ae' and resid 74 through 80 Processing sheet with id=107, first strand: chain 'Af' and resid 66 through 74 removed outlier: 3.777A pdb=" N ARGAf 46 " --> pdb=" O METAf 104 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VALAf 50 " --> pdb=" O ARGAf 100 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARGAf 100 " --> pdb=" O VALAf 50 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LYSAf 8 " --> pdb=" O GLUAf 31 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEUAf 27 " --> pdb=" O ALAAf 12 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILEAf 30 " --> pdb=" O GLYAf 82 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLYAf 82 " --> pdb=" O ILEAf 30 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARGAf 76 " --> pdb=" O ARGAf 85 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'Ag' and resid 19 through 24 removed outlier: 4.965A pdb=" N LYSAg 19 " --> pdb=" O THRAg 35 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'Ak' and resid 2 through 5 removed outlier: 4.862A pdb=" N VALAk 46 " --> pdb=" O ILEAk 5 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SERAk 22 " --> pdb=" O ARGAk 37 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYSAk 27 " --> pdb=" O LEUAk 69 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'Am' and resid 93 through 96 removed outlier: 5.884A pdb=" N LYSAm 93 " --> pdb=" O LYSAm 124 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'Ao' and resid 20 through 25 removed outlier: 4.325A pdb=" N ILEAo 66 " --> pdb=" O ILEAo 85 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILEAo 85 " --> pdb=" O ILEAo 66 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N SERAo 79 " --> pdb=" O CYSAo 72 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'Ap' and resid 53 through 56 removed outlier: 4.848A pdb=" N GLYAp 53 " --> pdb=" O GLYAp 66 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'At' and resid 46 through 53 removed outlier: 8.276A pdb=" N ARGAt 46 " --> pdb=" O ARGAt 67 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARGAt 67 " --> pdb=" O ARGAt 46 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THRAt 48 " --> pdb=" O LYSAt 65 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SERAt 76 " --> pdb=" O ARGAt 66 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'Au' and resid 50 through 53 Processing sheet with id=115, first strand: chain 'Au' and resid 64 through 69 Processing sheet with id=116, first strand: chain 'Au' and resid 163 through 169 removed outlier: 6.104A pdb=" N LEUAu 163 " --> pdb=" O LEUAu 38 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VALAu 32 " --> pdb=" O VALAu 169 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEUAu 204 " --> pdb=" O LEUAu 216 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'Aq' and resid 13 through 18 removed outlier: 3.985A pdb=" N THRAq 59 " --> pdb=" O THRAq 18 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VALAq 60 " --> pdb=" O PROAq 75 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'AK' and resid 51 through 55 removed outlier: 3.778A pdb=" N LYSAK 26 " --> pdb=" O THRAK 91 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILEAK 29 " --> pdb=" O GLNAK 190 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'AK' and resid 144 through 147 removed outlier: 7.823A pdb=" N THRAK 144 " --> pdb=" O LEUAK 155 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'AK' and resid 26 through 29 removed outlier: 3.593A pdb=" N GLNAK 191 " --> pdb=" O ILEAK 29 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'Ct' and resid 72 through 80 removed outlier: 3.765A pdb=" N SERCt 105 " --> pdb=" O VALCt 24 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALACt 26 " --> pdb=" O SERCt 105 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYSCt 152 " --> pdb=" O ASPCt 123 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N THRCt 211 " --> pdb=" O PROCt 153 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEUCt 155 " --> pdb=" O THRCt 211 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N METCt 157 " --> pdb=" O GLYCt 213 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'Ct' and resid 395 through 399 Processing sheet with id=123, first strand: chain 'Ct' and resid 411 through 415 Processing sheet with id=124, first strand: chain 'Ct' and resid 504 through 509 removed outlier: 4.640A pdb=" N HISCt 544 " --> pdb=" O VALCt 509 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'Ct' and resid 579 through 583 removed outlier: 6.745A pdb=" N LYSCt 785 " --> pdb=" O PHECt 771 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'Ct' and resid 590 through 595 removed outlier: 5.662A pdb=" N ASNCt 600 " --> pdb=" O SERCt 595 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYRCt 603 " --> pdb=" O HISCt 705 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VALCt 704 " --> pdb=" O THRCt 663 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'Ct' and resid 599 through 603 removed outlier: 9.053A pdb=" N HISCt 599 " --> pdb=" O HISCt 710 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HISCt 710 " --> pdb=" O HISCt 599 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASPCt 706 " --> pdb=" O TYRCt 603 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 'Ct' and resid 745 through 751 removed outlier: 6.376A pdb=" N GLUCt 748 " --> pdb=" O GLNCt 811 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHECt 809 " --> pdb=" O GLNCt 750 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'Ct' and resid 741 through 745 No H-bonds generated for sheet with id=129 Processing sheet with id=130, first strand: chain 'Ct' and resid 772 through 775 removed outlier: 3.536A pdb=" N GLUCt 772 " --> pdb=" O LYSCt 785 " (cutoff:3.500A) 3845 hydrogen bonds defined for protein. 11415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4279 hydrogen bonds 7194 hydrogen bond angles 0 basepair planarities 1664 basepair parallelities 3072 stacking parallelities Total time for adding SS restraints: 484.67 Time building geometry restraints manager: 81.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 42145 1.33 - 1.46: 89030 1.46 - 1.58: 98255 1.58 - 1.70: 11497 1.70 - 1.82: 747 Bond restraints: 241674 Sorted by residual: bond pdb=" N3B GNPCt 901 " pdb=" PG GNPCt 901 " ideal model delta sigma weight residual 1.801 1.705 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O5' GNPCt 901 " pdb=" PA GNPCt 901 " ideal model delta sigma weight residual 1.660 1.573 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C LYSCt 333 " pdb=" N PROCt 334 " ideal model delta sigma weight residual 1.332 1.358 -0.025 8.20e-03 1.49e+04 9.62e+00 bond pdb=" C PROBP 68 " pdb=" N PROBP 69 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.72e+00 bond pdb=" C PROBg 283 " pdb=" N PROBg 284 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.99e+00 ... (remaining 241669 not shown) Histogram of bond angle deviations from ideal: 97.37 - 105.24: 28152 105.24 - 113.10: 142185 113.10 - 120.96: 115649 120.96 - 128.82: 62876 128.82 - 136.69: 5215 Bond angle restraints: 354077 Sorted by residual: angle pdb=" CA PROAK 108 " pdb=" C PROAK 108 " pdb=" N ALAAK 109 " ideal model delta sigma weight residual 115.71 123.19 -7.48 1.19e+00 7.06e-01 3.95e+01 angle pdb=" C ASNCt 158 " pdb=" N LYSCt 159 " pdb=" CA LYSCt 159 " ideal model delta sigma weight residual 121.54 133.44 -11.90 1.91e+00 2.74e-01 3.88e+01 angle pdb=" N ILECt 12 " pdb=" CA ILECt 12 " pdb=" C ILECt 12 " ideal model delta sigma weight residual 111.77 105.41 6.36 1.04e+00 9.25e-01 3.74e+01 angle pdb=" C GLUBI 132 " pdb=" N GLUBI 133 " pdb=" CA GLUBI 133 " ideal model delta sigma weight residual 121.54 132.99 -11.45 1.91e+00 2.74e-01 3.60e+01 angle pdb=" C ASPCt 463 " pdb=" N VALCt 464 " pdb=" CA VALCt 464 " ideal model delta sigma weight residual 122.13 132.89 -10.76 1.85e+00 2.92e-01 3.38e+01 ... (remaining 354072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 129460 35.98 - 71.96: 3804 71.96 - 107.94: 288 107.94 - 143.92: 17 143.92 - 179.90: 54 Dihedral angle restraints: 133623 sinusoidal: 96984 harmonic: 36639 Sorted by residual: dihedral pdb=" CA TYRAf 106 " pdb=" C TYRAf 106 " pdb=" N PROAf 107 " pdb=" CA PROAf 107 " ideal model delta harmonic sigma weight residual 180.00 -111.08 -68.92 0 5.00e+00 4.00e-02 1.90e+02 dihedral pdb=" CA LEUAC 150 " pdb=" C LEUAC 150 " pdb=" N PROAC 151 " pdb=" CA PROAC 151 " ideal model delta harmonic sigma weight residual 180.00 -111.16 -68.84 0 5.00e+00 4.00e-02 1.90e+02 dihedral pdb=" CA VALBJ 137 " pdb=" C VALBJ 137 " pdb=" N ARGBJ 138 " pdb=" CA ARGBJ 138 " ideal model delta harmonic sigma weight residual 180.00 -129.00 -51.00 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 133620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 40752 0.074 - 0.148: 2946 0.148 - 0.222: 237 0.222 - 0.296: 24 0.296 - 0.370: 8 Chirality restraints: 43967 Sorted by residual: chirality pdb=" CB ILECt 649 " pdb=" CA ILECt 649 " pdb=" CG1 ILECt 649 " pdb=" CG2 ILECt 649 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB ILEAX 77 " pdb=" CA ILEAX 77 " pdb=" CG1 ILEAX 77 " pdb=" CG2 ILEAX 77 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C3' UA2 901 " pdb=" C4' UA2 901 " pdb=" O3' UA2 901 " pdb=" C2' UA2 901 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 43964 not shown) Planarity restraints: 23440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALAAt 86 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ALAAt 86 " 0.075 2.00e-02 2.50e+03 pdb=" O ALAAt 86 " -0.028 2.00e-02 2.50e+03 pdb=" N ARGAt 87 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYRAf 106 " -0.064 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PROAf 107 " 0.169 5.00e-02 4.00e+02 pdb=" CA PROAf 107 " -0.054 5.00e-02 4.00e+02 pdb=" CD PROAf 107 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLUBI 132 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C GLUBI 132 " -0.066 2.00e-02 2.50e+03 pdb=" O GLUBI 132 " 0.025 2.00e-02 2.50e+03 pdb=" N GLUBI 133 " 0.023 2.00e-02 2.50e+03 ... (remaining 23437 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 1 2.08 - 2.78: 46915 2.78 - 3.49: 284508 3.49 - 4.19: 663070 4.19 - 4.90: 938415 Nonbonded interactions: 1932909 Sorted by model distance: nonbonded pdb="MG MGB11914 " pdb="MG MGB11966 " model vdw 1.375 1.300 nonbonded pdb=" OP1 UA21618 " pdb="MG MGA25195 " model vdw 2.093 2.170 nonbonded pdb=" OP2 GA22493 " pdb="MG MGA25172 " model vdw 2.095 2.170 nonbonded pdb=" OP1 CA2 345 " pdb="MG MGA25297 " model vdw 2.104 2.170 nonbonded pdb=" O6 GA22495 " pdb="MG MGA25172 " model vdw 2.106 2.170 ... (remaining 1932904 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 5 6.06 5 P 5762 5.49 5 Mg 327 5.21 5 S 475 5.16 5 C 119422 2.51 5 N 41907 2.21 5 O 57703 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 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: 0.230 Extract box with map and model: 27.970 Check model and map are aligned: 2.700 Convert atoms to be neutral: 1.320 Process input model: 913.780 Find NCS groups from input model: 6.370 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:1.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 958.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 241674 Z= 0.206 Angle : 0.786 14.934 354077 Z= 0.395 Chirality : 0.040 0.370 43967 Planarity : 0.006 0.098 23440 Dihedral : 13.931 179.898 109982 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.63 % Favored : 91.18 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.06), residues: 12536 helix: -2.39 (0.06), residues: 4220 sheet: -1.48 (0.12), residues: 1766 loop : -2.95 (0.06), residues: 6550 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5123 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 5107 time to evaluate : 11.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 5117 average time/residue: 2.1538 time to fit residues: 18264.7959 Evaluate side-chains 3129 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3128 time to evaluate : 11.113 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.4761 time to fit residues: 15.9619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 1525 optimal weight: 10.0000 chunk 1368 optimal weight: 10.0000 chunk 759 optimal weight: 20.0000 chunk 467 optimal weight: 10.0000 chunk 923 optimal weight: 5.9990 chunk 731 optimal weight: 20.0000 chunk 1415 optimal weight: 9.9990 chunk 547 optimal weight: 5.9990 chunk 860 optimal weight: 9.9990 chunk 1053 optimal weight: 10.0000 chunk 1640 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 74 GLN BM 55 ASN BP 46 ASN BP 103 ASN BQ 11 GLN ** BQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 80 GLN BR 48 ASN BR 62 GLN BS 17 ASN BS 19 ASN BS 42 HIS BS 72 GLN BS 125 HIS BT 137 GLN BZ 106 GLN BZ 112 ASN Bc 26 GLN Bd 10 HIS Bd 16 GLN Bg 4 GLN Bg 20 GLN Bg 56 GLN Bg 133 ASN Bg 143 GLN BA 111 GLN BA 131 HIS BA 169 HIS ** BB 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 53 GLN BB 75 GLN ** BB 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 235 ASN BE 8 HIS BE 17 HIS BE 112 HIS ** BE 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 4 ASN ** BG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 81 HIS BG 227 GLN BH 91 HIS BH 193 GLN BI 116 HIS BI 168 GLN BI 181 GLN BJ 124 HIS BJ 134 HIS BJ 140 GLN BJ 156 HIS BL 11 GLN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BO 43 HIS BO 79 GLN ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 2 GLN BV 29 HIS ** BV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 16 ASN BX 61 GLN BX 77 ASN BX 127 ASN BY 29 HIS BY 85 ASN Be 44 ASN AA 83 HIS ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 209 HIS AA 216 HIS AB 302 ASN AB 322 HIS AB 380 GLN AC 38 ASN AC 41 HIS AC 50 GLN AC 198 ASN AC 215 ASN AC 347 HIS ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 244 HIS AE 191 GLN AE 279 ASN ** AF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 146 ASN AF 163 ASN AG 66 GLN AG 82 GLN AG 108 GLN AH 42 ASN AH 106 GLN ** AH 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 163 GLN ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 86 HIS AI 133 GLN AI 147 HIS AI 213 HIS AJ 10 ASN AJ 112 HIS AL 67 HIS AL 149 GLN AL 175 ASN AM 48 GLN AM 66 HIS AN 32 GLN ** AN 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 109 HIS AN 145 ASN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 14 HIS AO 65 ASN ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 97 ASN AP 101 ASN AP 118 GLN AQ 57 ASN AR 39 GLN ** AR 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 37 HIS AS 117 HIS AS 125 GLN ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 38 ASN AU 55 ASN AV 77 HIS AV 101 ASN AW 45 ASN AW 48 GLN AW 95 ASN AX 69 ASN AY 24 HIS AY 61 HIS AZ 40 HIS AZ 127 ASN Aa 60 HIS Aa 74 ASN ** Ab 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Ac 33 GLN ** Ad 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 52 GLN Af 21 GLN Af 99 HIS Ag 73 HIS Ah 62 ASN Ah 63 GLN ** Ah 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 20 ASN Ai 36 HIS ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 48 ASN Al 20 ASN Al 25 GLN Al 43 HIS Am 90 ASN ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 120 ASN Ao 3 ASN Ao 19 GLN Ao 90 HIS Ap 56 HIS At 4 HIS ** At 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 21 ASN Au 84 HIS Au 140 HIS Au 143 ASN Au 171 HIS Au 184 HIS Au 188 ASN Au 197 ASN ** Au 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 18 ASN Ct 101 ASN Ct 138 GLN Ct 219 HIS Ct 352 GLN Ct 493 ASN Ct 588 ASN Ct 600 ASN Ct 630 GLN Ct 705 HIS Ct 710 HIS Ct 803 ASN Ct 833 GLN Total number of N/Q/H flips: 160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.166 241674 Z= 0.468 Angle : 0.788 14.392 354077 Z= 0.398 Chirality : 0.042 0.429 43967 Planarity : 0.007 0.153 23440 Dihedral : 14.941 179.814 83293 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.89 % Favored : 90.91 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.07), residues: 12536 helix: -0.53 (0.07), residues: 4247 sheet: -1.30 (0.11), residues: 1905 loop : -2.53 (0.07), residues: 6384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4002 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 575 poor density : 3427 time to evaluate : 12.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 575 outliers final: 333 residues processed: 3704 average time/residue: 1.7710 time to fit residues: 11299.4221 Evaluate side-chains 3325 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 2992 time to evaluate : 12.866 Switching outliers to nearest non-outliers outliers start: 333 outliers final: 0 residues processed: 333 average time/residue: 1.4290 time to fit residues: 915.3310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 911 optimal weight: 2.9990 chunk 508 optimal weight: 20.0000 chunk 1364 optimal weight: 4.9990 chunk 1116 optimal weight: 5.9990 chunk 452 optimal weight: 50.0000 chunk 1643 optimal weight: 0.7980 chunk 1774 optimal weight: 5.9990 chunk 1463 optimal weight: 6.9990 chunk 1629 optimal weight: 0.8980 chunk 560 optimal weight: 8.9990 chunk 1318 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 159 HIS ** BF 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 29 GLN Bd 16 GLN Bg 4 GLN Bg 20 GLN ** Bg 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 84 GLN BA 131 HIS ** BB 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 75 GLN ** BB 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 202 GLN BE 17 HIS BE 50 ASN ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 56 ASN BG 65 GLN BI 22 HIS ** BI 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 88 ASN BI 168 GLN BL 108 ASN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 32 HIS BO 79 GLN ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 2 GLN BV 29 HIS ** BW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 39 ASN BX 63 ASN ** BX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 85 ASN Bb 26 GLN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 162 ASN ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 186 ASN AB 204 GLN AB 301 ASN AB 380 GLN AC 50 GLN ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN ** AE 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 151 ASN AF 226 HIS AG 112 GLN ** AG 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 78 GLN AH 106 GLN AH 140 GLN AH 163 GLN ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 100 ASN AI 133 GLN AI 213 HIS AJ 10 ASN AJ 98 ASN AJ 167 GLN AL 104 ASN AL 111 GLN AL 159 ASN AM 33 GLN AM 83 ASN AM 120 ASN AN 8 GLN ** AN 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 145 ASN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AP 28 ASN AP 72 GLN ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 125 GLN AR 178 GLN ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 69 ASN AX 108 GLN AY 24 HIS Aa 25 HIS Aa 120 GLN Ab 12 GLN Ac 19 GLN ** Ad 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 23 HIS Af 24 HIS Ah 63 GLN Ah 107 GLN ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 66 HIS ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 25 GLN Ao 90 HIS Ao 102 GLN ** At 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 58 ASN AK 71 ASN ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 18 ASN Ct 477 GLN Ct 565 HIS Ct 803 ASN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.101 241674 Z= 0.204 Angle : 0.612 13.863 354077 Z= 0.310 Chirality : 0.035 0.312 43967 Planarity : 0.005 0.164 23440 Dihedral : 14.770 179.960 83293 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.27 % Favored : 91.59 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.07), residues: 12536 helix: 0.20 (0.08), residues: 4222 sheet: -1.08 (0.12), residues: 1885 loop : -2.32 (0.07), residues: 6429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3456 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 3147 time to evaluate : 11.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 309 outliers final: 142 residues processed: 3268 average time/residue: 1.7942 time to fit residues: 10170.6866 Evaluate side-chains 3040 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 2898 time to evaluate : 11.159 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 0 residues processed: 142 average time/residue: 1.4754 time to fit residues: 401.9293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 1623 optimal weight: 4.9990 chunk 1235 optimal weight: 0.9990 chunk 852 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 784 optimal weight: 0.0010 chunk 1103 optimal weight: 9.9990 chunk 1648 optimal weight: 4.9990 chunk 1745 optimal weight: 8.9990 chunk 861 optimal weight: 8.9990 chunk 1562 optimal weight: 7.9990 chunk 470 optimal weight: 10.0000 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 159 HIS ** BF 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BR 62 GLN ** BS 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 16 GLN Bg 4 GLN BA 84 GLN BA 131 HIS BB 202 GLN BE 112 HIS ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 56 ASN BG 186 GLN BI 7 ASN BI 22 HIS BI 168 GLN BL 108 ASN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 15 ASN BW 24 GLN ** BW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 85 ASN AA 95 GLN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 301 ASN AB 380 GLN AC 50 GLN ** AC 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 39 GLN AD 63 GLN ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 106 GLN ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 133 GLN AL 149 GLN ** AN 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AP 28 ASN AP 72 GLN ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 44 ASN AR 27 ASN ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 144 ASN ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 69 ASN AY 72 GLN Ab 49 HIS Ac 15 ASN Ah 63 GLN ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 25 GLN Am 90 ASN ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 25 GLN Ao 90 HIS ** At 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 72 ASN AK 176 ASN Ct 18 ASN ** Ct 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 803 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.200 241674 Z= 0.238 Angle : 0.608 15.493 354077 Z= 0.309 Chirality : 0.035 0.461 43967 Planarity : 0.005 0.133 23440 Dihedral : 14.737 179.894 83293 Min Nonbonded Distance : 1.196 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.90 % Favored : 90.98 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.07), residues: 12536 helix: 0.53 (0.08), residues: 4221 sheet: -0.91 (0.12), residues: 1841 loop : -2.19 (0.07), residues: 6474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3319 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 2969 time to evaluate : 12.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 350 outliers final: 198 residues processed: 3107 average time/residue: 1.7675 time to fit residues: 9545.7238 Evaluate side-chains 3025 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 2827 time to evaluate : 11.117 Switching outliers to nearest non-outliers outliers start: 198 outliers final: 0 residues processed: 198 average time/residue: 1.4851 time to fit residues: 567.1066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 1453 optimal weight: 4.9990 chunk 990 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 1299 optimal weight: 6.9990 chunk 720 optimal weight: 30.0000 chunk 1489 optimal weight: 0.6980 chunk 1206 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 891 optimal weight: 7.9990 chunk 1566 optimal weight: 9.9990 chunk 440 optimal weight: 40.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BD 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 159 HIS ** BF 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 16 GLN BA 84 GLN BA 131 HIS ** BB 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 53 GLN BC 272 HIS BE 17 HIS BE 112 HIS ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 186 GLN BI 7 ASN BI 22 HIS BI 168 GLN BL 108 ASN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BO 79 GLN ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 2 GLN ** BW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 85 ASN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 302 ASN ** AB 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 GLN ** AE 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 110 GLN AG 195 HIS AH 106 GLN ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 133 GLN AL 111 GLN AL 149 GLN AM 33 GLN ** AM 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 50 ASN AO 72 HIS AP 28 ASN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 72 GLN ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 27 ASN ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 38 ASN ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY 72 GLN Ab 10 HIS Af 55 ASN ** Ag 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 63 GLN ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 25 GLN ** Ao 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 90 HIS Ap 34 HIS ** Au 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 630 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.214 241674 Z= 0.350 Angle : 0.677 14.582 354077 Z= 0.344 Chirality : 0.039 0.384 43967 Planarity : 0.006 0.117 23440 Dihedral : 14.890 179.761 83293 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.54 % Favored : 90.30 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.15 % 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: -1.45 (0.07), residues: 12536 helix: 0.61 (0.08), residues: 4224 sheet: -0.92 (0.12), residues: 1879 loop : -2.14 (0.07), residues: 6433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3322 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 2987 time to evaluate : 11.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 335 outliers final: 180 residues processed: 3139 average time/residue: 1.7937 time to fit residues: 9797.6503 Evaluate side-chains 3040 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 2860 time to evaluate : 11.207 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 180 outliers final: 1 residues processed: 180 average time/residue: 1.4921 time to fit residues: 514.1290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 587 optimal weight: 4.9990 chunk 1572 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 1024 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 1747 optimal weight: 5.9990 chunk 1450 optimal weight: 20.0000 chunk 809 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 578 optimal weight: 5.9990 chunk 917 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 74 GLN BD 159 HIS ** BF 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 46 ASN ** BT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 16 GLN Bg 133 ASN ** Bg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 84 GLN ** BB 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 186 GLN BI 7 ASN BI 22 HIS ** BI 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 168 GLN ** BJ 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 108 ASN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 47 ASN ** BW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 16 HIS ** BX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 63 HIS BY 85 ASN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AE 279 ASN ** AG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 106 GLN ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 100 ASN ** AJ 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 149 GLN ** AM 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 87 HIS AO 50 ASN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 72 GLN ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 34 ASN AR 40 GLN ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 48 GLN AY 24 HIS AY 72 GLN ** Aa 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 120 GLN ** Ag 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 28 ASN Ah 63 GLN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 26 HIS ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 25 GLN ** Au 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 41 GLN AK 127 ASN ** Ct 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 241674 Z= 0.296 Angle : 0.647 13.398 354077 Z= 0.329 Chirality : 0.037 0.318 43967 Planarity : 0.005 0.106 23440 Dihedral : 14.888 179.694 83293 Min Nonbonded Distance : 1.181 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.20 % Favored : 90.65 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.07), residues: 12536 helix: 0.70 (0.08), residues: 4214 sheet: -0.86 (0.12), residues: 1880 loop : -2.09 (0.07), residues: 6442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3239 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 2956 time to evaluate : 11.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 283 outliers final: 172 residues processed: 3071 average time/residue: 1.9897 time to fit residues: 10723.5157 Evaluate side-chains 2979 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 2807 time to evaluate : 11.252 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 2 residues processed: 172 average time/residue: 1.5163 time to fit residues: 508.1459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 1684 optimal weight: 0.0670 chunk 196 optimal weight: 10.0000 chunk 995 optimal weight: 2.9990 chunk 1276 optimal weight: 9.9990 chunk 988 optimal weight: 7.9990 chunk 1470 optimal weight: 8.9990 chunk 975 optimal weight: 10.0000 chunk 1740 optimal weight: 20.0000 chunk 1089 optimal weight: 9.9990 chunk 1061 optimal weight: 0.9990 chunk 803 optimal weight: 7.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 159 HIS ** BF 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 45 ASN Bd 16 GLN ** Bg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 84 GLN BB 40 ASN ** BE 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 216 ASN ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 186 GLN BI 146 GLN BI 168 GLN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 90 GLN ** BX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 110 HIS ** BY 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 29 ASN ** AA 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 97 ASN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 162 ASN ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 186 ASN AB 302 ASN AB 315 ASN ** AB 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 279 ASN ** AG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 112 GLN ** AG 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 106 GLN ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 111 GLN AL 149 GLN ** AM 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 50 ASN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 72 GLN ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 34 ASN AR 40 GLN AS 66 GLN ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 44 GLN ** AU 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 72 GLN AZ 78 ASN ** AZ 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 55 ASN ** Ag 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 63 GLN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 25 GLN Ao 90 HIS ** Au 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 111 ASN AK 58 ASN AK 127 ASN ** Ct 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 241674 Z= 0.249 Angle : 0.628 13.768 354077 Z= 0.319 Chirality : 0.036 0.364 43967 Planarity : 0.005 0.118 23440 Dihedral : 14.860 179.828 83293 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.14 % Favored : 90.71 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.11 % 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: -1.26 (0.07), residues: 12536 helix: 0.78 (0.08), residues: 4239 sheet: -0.78 (0.12), residues: 1866 loop : -2.05 (0.08), residues: 6431 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3086 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 2898 time to evaluate : 11.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 114 residues processed: 2979 average time/residue: 1.8379 time to fit residues: 9582.3550 Evaluate side-chains 2922 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 2808 time to evaluate : 11.323 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 1.4860 time to fit residues: 334.1356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 1076 optimal weight: 9.9990 chunk 695 optimal weight: 8.9990 chunk 1039 optimal weight: 10.0000 chunk 524 optimal weight: 20.0000 chunk 342 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 1106 optimal weight: 3.9990 chunk 1185 optimal weight: 8.9990 chunk 860 optimal weight: 0.0870 chunk 162 optimal weight: 10.0000 chunk 1368 optimal weight: 10.0000 overall best weight: 6.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 22 ASN BD 159 HIS BD 174 HIS ** BF 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 77 HIS ** BT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 45 ASN ** Bd 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 147 HIS BA 84 GLN BB 40 ASN ** BE 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 224 ASN BE 232 ASN ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 7 ASN BI 168 GLN BJ 143 ASN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 110 HIS ** BY 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 15 GLN ** AA 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 97 ASN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 162 ASN ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 187 GLN ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 112 GLN ** AG 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 106 GLN ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 100 ASN ** AJ 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 48 GLN AM 120 ASN AO 50 ASN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 72 GLN ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 50 GLN AS 125 GLN ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 131 GLN ** AU 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 72 GLN Aa 34 ASN ** Aa 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 120 GLN Af 55 ASN Ah 63 GLN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 30 GLN ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 352 GLN ** Ct 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.185 241674 Z= 0.363 Angle : 0.696 19.419 354077 Z= 0.353 Chirality : 0.039 0.344 43967 Planarity : 0.005 0.107 23440 Dihedral : 14.970 179.702 83293 Min Nonbonded Distance : 1.171 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.04 % Favored : 89.81 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.07), residues: 12536 helix: 0.67 (0.08), residues: 4252 sheet: -0.80 (0.12), residues: 1880 loop : -2.08 (0.08), residues: 6404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3140 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 2949 time to evaluate : 11.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 111 residues processed: 3009 average time/residue: 1.8725 time to fit residues: 9853.3106 Evaluate side-chains 2972 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 2861 time to evaluate : 11.368 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 0 residues processed: 111 average time/residue: 1.5614 time to fit residues: 340.2065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 1583 optimal weight: 8.9990 chunk 1667 optimal weight: 6.9990 chunk 1521 optimal weight: 5.9990 chunk 1622 optimal weight: 8.9990 chunk 976 optimal weight: 0.7980 chunk 706 optimal weight: 40.0000 chunk 1273 optimal weight: 4.9990 chunk 497 optimal weight: 10.0000 chunk 1465 optimal weight: 4.9990 chunk 1534 optimal weight: 5.9990 chunk 1616 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 22 ASN BD 159 HIS BD 174 HIS ** BF 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 10 GLN ** BS 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 45 ASN ** Bd 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 84 GLN BB 186 ASN ** BE 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 224 ASN ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 186 GLN BI 168 GLN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 61 GLN ** BX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 110 HIS ** BY 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 29 ASN ** AA 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 97 ASN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 162 ASN ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 315 ASN ** AB 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN ** AG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 51 HIS AI 100 ASN AJ 71 HIS ** AJ 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 111 GLN AL 149 GLN AM 48 GLN AO 50 ASN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 34 ASN AR 118 HIS ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AX 108 GLN AY 72 GLN AY 86 GLN ** Aa 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 58 GLN Ae 107 ASN Af 55 ASN ** Ag 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 63 GLN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 73 HIS ** Au 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 18 ASN Ct 352 GLN Ct 565 HIS ** Ct 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 241674 Z= 0.272 Angle : 0.656 18.576 354077 Z= 0.333 Chirality : 0.037 0.315 43967 Planarity : 0.005 0.147 23440 Dihedral : 14.932 179.638 83293 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.28 % Favored : 90.56 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.07), residues: 12536 helix: 0.72 (0.08), residues: 4243 sheet: -0.78 (0.12), residues: 1914 loop : -2.03 (0.08), residues: 6379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3017 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 2904 time to evaluate : 11.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 65 residues processed: 2951 average time/residue: 1.9284 time to fit residues: 9956.3895 Evaluate side-chains 2847 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 2782 time to evaluate : 12.470 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 1.7104 time to fit residues: 222.6873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 1065 optimal weight: 0.0010 chunk 1715 optimal weight: 9.9990 chunk 1046 optimal weight: 3.9990 chunk 813 optimal weight: 10.0000 chunk 1192 optimal weight: 6.9990 chunk 1799 optimal weight: 7.9990 chunk 1655 optimal weight: 0.0470 chunk 1432 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 1106 optimal weight: 7.9990 chunk 878 optimal weight: 3.9990 overall best weight: 3.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 22 ASN BD 159 HIS BD 174 HIS ** BF 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 10 GLN ** BT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 45 ASN Bg 196 ASN BA 84 GLN ** BB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 214 ASN ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 61 GLN ** BX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 110 HIS ** BY 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 29 ASN Be 44 ASN AA 95 GLN AA 97 ASN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 315 ASN AB 380 GLN ** AC 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AG 64 GLN AG 112 GLN ** AG 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 48 GLN AO 50 ASN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 44 GLN ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY 72 GLN AZ 78 ASN Aa 49 HIS Aa 74 ASN Ab 61 ASN Af 55 ASN Ah 63 GLN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 200 ASN ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.197 241674 Z= 0.215 Angle : 0.637 18.250 354077 Z= 0.323 Chirality : 0.036 0.306 43967 Planarity : 0.005 0.162 23440 Dihedral : 14.863 179.693 83293 Min Nonbonded Distance : 1.200 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.44 % Favored : 90.41 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.94 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.08), residues: 12536 helix: 0.77 (0.08), residues: 4228 sheet: -0.68 (0.12), residues: 1906 loop : -1.99 (0.08), residues: 6402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25072 Ramachandran restraints generated. 12536 Oldfield, 0 Emsley, 12536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2952 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 2877 time to evaluate : 11.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 36 residues processed: 2903 average time/residue: 1.8141 time to fit residues: 9168.3172 Evaluate side-chains 2835 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 2799 time to evaluate : 11.503 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 1.4933 time to fit residues: 114.3609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1806 random chunks: chunk 1138 optimal weight: 3.9990 chunk 1526 optimal weight: 2.9990 chunk 438 optimal weight: 10.0000 chunk 1321 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 398 optimal weight: 50.0000 chunk 1435 optimal weight: 0.9990 chunk 600 optimal weight: 8.9990 chunk 1473 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 264 optimal weight: 40.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 159 HIS BD 174 HIS BS 10 GLN ** BS 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 45 ASN Bd 28 HIS BA 84 GLN BB 202 GLN ** BE 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 186 GLN ** BI 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 181 GLN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BO 79 GLN ** BO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 110 HIS ** BY 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 29 ASN Be 15 GLN AA 95 GLN AA 97 ASN ** AA 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 282 HIS ** AD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 182 ASN ** AE 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 159 HIS ** AG 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 236 HIS AH 39 ASN AH 189 GLN ** AI 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 98 ASN ** AL 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 48 GLN AN 32 GLN AO 50 ASN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 40 GLN ** AS 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY 72 GLN ** Aa 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Af 55 ASN Ah 63 GLN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 48 ASN ** Am 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 565 HIS ** Ct 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078679 restraints weight = 486332.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081103 restraints weight = 154535.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.082524 restraints weight = 82827.126| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.426 241674 Z= 0.228 Angle : 0.638 20.019 354077 Z= 0.324 Chirality : 0.036 0.301 43967 Planarity : 0.006 0.171 23440 Dihedral : 14.831 179.947 83293 Min Nonbonded Distance : 1.200 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.34 % Favored : 90.52 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.08), residues: 12536 helix: 0.79 (0.08), residues: 4251 sheet: -0.63 (0.12), residues: 1873 loop : -1.97 (0.08), residues: 6412 =============================================================================== Job complete usr+sys time: 125732.26 seconds wall clock time: 2153 minutes 16.70 seconds (129196.70 seconds total)