Starting phenix.real_space_refine (version: dev) on Sun Apr 24 04:44:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz4_0099/04_2022/6gz4_0099_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz4_0099/04_2022/6gz4_0099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz4_0099/04_2022/6gz4_0099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz4_0099/04_2022/6gz4_0099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz4_0099/04_2022/6gz4_0099_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gz4_0099/04_2022/6gz4_0099_updated.pdb" } resolution = 3.6 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= 0.345 sd= 0.672 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 "AC TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD ARG 143": "NH1" <-> "NH2" Residue "BD TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc ARG 66": "NH1" <-> "NH2" Residue "Bd PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac TYR 89": "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 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 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: 0.20s 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: 103 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: "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: "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: "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: "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: "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: "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': 345, 'rna3p_pur': 1629, 'rna2p_pyr': 221} Link IDs: {'rna3p': 3045, 'rna2p': 566} Chain breaks: 12 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': 32, 'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 38, 'rna2p_pyr': 3} Link IDs: {'rna3p': 69, 'rna2p': 6} Chain: "B1" Number of atoms: 36456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1708, 36456 Classifications: {'RNA': 1708} Modifications used: {'rna3p_pyr': 685, 'p5*END': 1, 'rna2p_pur': 154, 'rna2p_pyr': 121, 'rna3p_pur': 748} Link IDs: {'rna3p': 1432, 'rna2p': 275} 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: "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: "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: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A2" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 236 Unusual residues: {' MG': 236} Classifications: {'undetermined': 236} Link IDs: {None: 235} 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: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Unusual residues: {' MG': 67} Classifications: {'undetermined': 67} Link IDs: {None: 66} Chain: "BD" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BS" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bd" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 1, ' MG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "AL" 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 A0X54 SG CYSBd 21 114.999 55.564 116.091 1.00 20.00 S ATOM A0X5S SG CYSBd 24 118.078 59.509 117.531 1.00 20.00 S ATOM A0X95 SG CYSBd 39 116.077 58.659 114.628 1.00 20.00 S ATOM A1C20 SG CYSBa 23 126.806 115.463 73.986 1.00 20.00 S ATOM A1C2L SG CYSBa 26 126.951 115.831 77.971 1.00 20.00 S ATOM A1CD8 SG CYSBa 74 129.278 113.795 76.101 1.00 20.00 S ATOM A1CDR SG CYSBa 77 126.243 112.071 75.064 1.00 20.00 S ATOM A2CE6 SG CYSAj 19 115.933 214.380 101.719 1.00 20.00 S ATOM A2CEY SG CYSAj 22 112.851 214.660 103.479 1.00 20.00 S ATOM A2CHH SG CYSAj 34 114.307 210.910 101.746 1.00 20.00 S ATOM A2CI0 SG CYSAj 37 111.751 212.909 100.157 1.00 20.00 S ATOM A2E66 SG CYSAo 12 44.974 151.149 119.358 1.00 20.00 S ATOM A2EKW SG CYSAo 77 43.766 152.217 115.030 1.00 20.00 S ATOM A2EZY SG CYSAp 39 152.186 171.447 63.570 1.00 20.00 S ATOM A2F0L SG CYSAp 42 155.354 173.014 62.839 1.00 20.00 S ATOM A2F3Z SG CYSAp 57 151.134 175.119 65.152 1.00 20.00 S ATOM A2F4F SG CYSAp 60 152.713 175.934 61.654 1.00 20.00 S Time building chain proxies: 83.11, per 1000 atoms: 0.37 Number of scatterers: 225601 At special positions: 0 Unit cell: (288.6, 288.6, 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=2, symmetry=0 Simple disulfide: pdb=" SG CYSBf 126 " - pdb=" SG CYSBf 144 " distance=2.03 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: 71.17 Conformation dependent library (CDL) restraints added in 10.1 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 77 " pdb="ZN ZNAo 201 " - pdb=" SG CYSAo 12 " pdb=" ZNAp 101 " pdb="ZN ZNAp 101 " - pdb=" SG CYSAp 42 " pdb="ZN ZNAp 101 " - pdb=" SG CYSAp 39 " pdb="ZN ZNAp 101 " - pdb=" SG CYSAp 60 " pdb="ZN ZNAp 101 " - pdb=" SG CYSAp 57 " pdb=" ZNBa 102 " pdb="ZN ZNBa 102 " - pdb=" SG CYSBa 77 " pdb="ZN ZNBa 102 " - pdb=" SG CYSBa 26 " pdb="ZN ZNBa 102 " - pdb=" SG CYSBa 23 " pdb="ZN ZNBa 102 " - pdb=" SG CYSBa 74 " pdb=" ZNBd 103 " pdb="ZN ZNBd 103 " - pdb=" SG CYSBd 24 " pdb="ZN ZNBd 103 " - pdb=" SG CYSBd 39 " pdb="ZN ZNBd 103 " - pdb=" SG CYSBd 21 " Number of angles added : 18 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: 414 helices and 135 sheets defined 40.1% alpha, 15.7% beta 1672 base pairs and 3035 stacking pairs defined. Time for finding SS restraints: 86.52 Creating SS restraints... Processing helix chain 'AA' and resid 5 through 13 removed outlier: 3.884A pdb=" N ARGAA 9 " --> pdb=" O ILEAA 5 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYSAA 10 " --> pdb=" O ARGAA 6 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLYAA 11 " --> pdb=" O GLYAA 7 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALAAA 12 " --> pdb=" O GLNAA 8 " (cutoff:3.500A) removed outlier: 4.229A 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: 3.762A 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: 3.824A pdb=" N ALAAA 185 " --> pdb=" O LYSAA 181 " (cutoff:3.500A) Processing helix chain 'AA' and resid 200 through 205 removed outlier: 5.278A pdb=" N ASNAA 205 " --> pdb=" O GLYAA 201 " (cutoff:3.500A) Processing helix chain 'AA' and resid 173 through 178 removed outlier: 4.048A pdb=" N LYSAA 177 " --> pdb=" O ARGAA 174 " (cutoff:3.500A) Proline residue: AA 178 - end of helix Processing helix chain 'BA' and resid 11 through 22 Processing helix chain 'BA' and resid 34 through 39 removed outlier: 5.190A pdb=" N TYRBA 39 " --> pdb=" O GLUBA 35 " (cutoff:3.500A) Processing helix chain 'BA' and resid 50 through 68 removed outlier: 4.197A pdb=" N THRBA 54 " --> pdb=" O ASNBA 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILEBA 68 " --> pdb=" O ALABA 64 " (cutoff:3.500A) Processing helix chain 'BA' and resid 80 through 95 removed outlier: 4.040A pdb=" N ARGBA 85 " --> pdb=" O ASNBA 81 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALABA 86 " --> pdb=" O THRBA 82 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEUBA 88 " --> pdb=" O GLNBA 84 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYSBA 89 " --> pdb=" O ARGBA 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THRBA 94 " --> pdb=" O PHEBA 90 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLYBA 95 " --> pdb=" O ALABA 91 " (cutoff:3.500A) Processing helix chain 'BA' and resid 126 through 131 Processing helix chain 'BA' and resid 132 through 141 removed outlier: 4.503A pdb=" N SERBA 138 " --> pdb=" O LEUBA 134 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYRBA 139 " --> pdb=" O THRBA 135 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VALBA 140 " --> pdb=" O GLUBA 136 " (cutoff:3.500A) Processing helix chain 'BA' and resid 167 through 187 Processing helix chain 'BA' and resid 199 through 204 removed outlier: 4.110A pdb=" N PHEBA 203 " --> pdb=" O PROBA 199 " (cutoff:3.500A) Processing helix chain 'BA' and resid 209 through 219 Processing helix chain 'BA' and resid 70 through 75 removed outlier: 3.580A pdb=" N ASPBA 73 " --> pdb=" O ASNBA 70 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SERBA 75 " --> pdb=" O ALABA 72 " (cutoff:3.500A) Processing helix chain 'AB' and resid 13 through 18 Proline residue: AB 18 - end of helix Processing helix chain 'AB' and resid 111 through 120 removed outlier: 4.987A pdb=" N LYSAB 120 " --> pdb=" O ARGAB 116 " (cutoff:3.500A) Processing helix chain 'AB' and resid 130 through 140 removed outlier: 5.691A pdb=" N GLUAB 140 " --> pdb=" O LYSAB 136 " (cutoff:3.500A) Processing helix chain 'AB' and resid 141 through 157 removed outlier: 3.780A pdb=" N GLNAB 145 " --> pdb=" O ASPAB 141 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASPAB 149 " --> pdb=" O GLNAB 145 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHEAB 150 " --> pdb=" O LEUAB 146 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYSAB 155 " --> pdb=" O SERAB 151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYSAB 157 " --> pdb=" O METAB 153 " (cutoff:3.500A) Processing helix chain 'AB' and resid 167 through 172 removed outlier: 4.652A 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: 4.351A 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 'BB' and resid 23 through 29 removed outlier: 3.832A pdb=" N LYSBB 27 " --> pdb=" O ASPBB 23 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASPBB 29 " --> pdb=" O PHEBB 25 " (cutoff:3.500A) Processing helix chain 'BB' and resid 57 through 65 removed outlier: 4.718A pdb=" N GLYBB 61 " --> pdb=" O ILEBB 57 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEUBB 62 " --> pdb=" O ALABB 58 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYSBB 63 " --> pdb=" O SERBB 59 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLYBB 64 " --> pdb=" O ASPBB 60 " (cutoff:3.500A) Processing helix chain 'BB' and resid 71 through 76 removed outlier: 6.764A pdb=" N GLNBB 75 " --> pdb=" O LEUBB 71 " (cutoff:3.500A) removed outlier: 6.169A 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 112 Processing helix chain 'BB' and resid 157 through 179 removed outlier: 6.139A pdb=" N VALBB 161 " --> pdb=" O GLNBB 157 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N METBB 172 " --> pdb=" O METBB 168 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THRBB 173 " --> pdb=" O METBB 169 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARGBB 174 " --> pdb=" O GLUBB 170 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THRBB 178 " --> pdb=" O ARGBB 174 " (cutoff:3.500A) removed outlier: 3.675A 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: 3.858A pdb=" N GLNBB 202 " --> pdb=" O GLUBB 198 " (cutoff:3.500A) Processing helix chain 'BB' and resid 224 through 233 Processing helix chain 'AC' and resid 25 through 30 removed outlier: 4.163A pdb=" N LYSAC 29 " --> pdb=" O PROAC 25 " (cutoff:3.500A) Processing helix chain 'AC' and resid 33 through 49 removed outlier: 4.412A pdb=" N ARGAC 49 " --> pdb=" O ARGAC 45 " (cutoff:3.500A) Processing helix chain 'AC' and resid 116 through 133 removed outlier: 3.789A pdb=" N ALAAC 132 " --> pdb=" O LEUAC 128 " (cutoff:3.500A) removed outlier: 4.071A 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: 4.651A pdb=" N GLUAC 159 " --> pdb=" O GLUAC 155 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLYAC 160 " --> pdb=" O ASPAC 156 " (cutoff:3.500A) removed outlier: 4.253A 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: 4.544A pdb=" N ALAAC 167 " --> pdb=" O LYSAC 163 " (cutoff:3.500A) Processing helix chain 'AC' and resid 176 through 187 removed outlier: 3.523A pdb=" N VALAC 183 " --> pdb=" O ASPAC 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLNAC 187 " --> pdb=" O VALAC 183 " (cutoff:3.500A) Processing helix chain 'AC' and resid 193 through 198 removed outlier: 4.774A pdb=" N ARGAC 197 " --> pdb=" O LYSAC 193 " (cutoff:3.500A) removed outlier: 4.588A 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: 4.760A 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 302 removed outlier: 4.070A pdb=" N ALAAC 301 " --> pdb=" O GLUAC 297 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEUAC 302 " --> pdb=" O ILEAC 298 " (cutoff:3.500A) Processing helix chain 'AC' and resid 321 through 329 removed outlier: 4.392A pdb=" N METAC 325 " --> pdb=" O ASNAC 321 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEUAC 326 " --> pdb=" O LEUAC 322 " (cutoff:3.500A) Processing helix chain 'AC' and resid 330 through 365 removed outlier: 4.872A pdb=" N THRAC 334 " --> pdb=" O PROAC 330 " (cutoff:3.500A) Processing helix chain 'AC' and resid 58 through 63 removed outlier: 4.070A pdb=" N GLNAC 61 " --> pdb=" O ALAAC 58 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THRAC 62 " --> pdb=" O GLYAC 59 " (cutoff:3.500A) removed outlier: 5.190A 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 'BC' and resid 64 through 73 removed outlier: 6.213A pdb=" N ARGBC 68 " --> pdb=" O THRBC 64 " (cutoff:3.500A) Processing helix chain 'BC' and resid 77 through 85 removed outlier: 3.813A pdb=" N ILEBC 81 " --> pdb=" O SERBC 77 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHEBC 84 " --> pdb=" O GLUBC 80 " (cutoff:3.500A) Processing helix chain 'BC' and resid 91 through 98 removed outlier: 4.052A 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: 4.580A pdb=" N LYSBC 238 " --> pdb=" O GLYBC 234 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THRBC 247 " --> pdb=" O ALABC 243 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYRBC 248 " --> pdb=" O ILEBC 244 " (cutoff:3.500A) removed outlier: 4.298A 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 'BD' and resid 6 through 29 removed outlier: 3.707A pdb=" N PHEBD 11 " --> pdb=" O LYSBD 7 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VALBD 12 " --> pdb=" O LYSBD 8 " (cutoff:3.500A) Processing helix chain 'BD' and resid 54 through 60 removed outlier: 4.446A pdb=" N VALBD 58 " --> pdb=" O ARGBD 54 " (cutoff:3.500A) Processing helix chain 'BD' and resid 63 through 77 removed outlier: 4.551A pdb=" N ARGBD 67 " --> pdb=" O GLYBD 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARGBD 76 " --> pdb=" O VALBD 72 " (cutoff:3.500A) Processing helix chain 'BD' and resid 97 through 112 removed outlier: 3.603A pdb=" N TYRBD 107 " --> pdb=" O GLUBD 103 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLYBD 111 " --> pdb=" O TYRBD 107 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLYBD 112 " --> pdb=" O LYSBD 108 " (cutoff:3.500A) Processing helix chain 'BD' and resid 114 through 130 removed outlier: 4.050A 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: 4.864A pdb=" N GLNBF 65 " --> pdb=" O PHEBF 61 " (cutoff:3.500A) removed outlier: 4.230A 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: 5.357A pdb=" N METBF 78 " --> pdb=" O ASNBF 74 " (cutoff:3.500A) Processing helix chain 'BF' and resid 85 through 105 removed outlier: 3.547A pdb=" N GLUBF 98 " --> pdb=" O LYSBF 94 " (cutoff:3.500A) removed outlier: 4.589A 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: 5.107A pdb=" N GLYBF 183 " --> pdb=" O ASNBF 179 " (cutoff:3.500A) Processing helix chain 'BF' and resid 187 through 204 removed outlier: 3.906A pdb=" N VALBF 199 " --> pdb=" O GLUBF 195 " (cutoff:3.500A) Processing helix chain 'BK' and resid 4 through 19 removed outlier: 3.941A pdb=" N ARGBK 8 " --> pdb=" O PROBK 4 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILEBK 9 " --> pdb=" O LYSBK 5 " (cutoff:3.500A) Processing helix chain 'BK' and resid 41 through 56 removed outlier: 5.825A pdb=" N VALBK 45 " --> pdb=" O PROBK 41 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SERBK 51 " --> pdb=" O LYSBK 47 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEUBK 52 " --> pdb=" O ALABK 48 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLYBK 56 " --> pdb=" O LEUBK 52 " (cutoff:3.500A) Processing helix chain 'BK' and resid 72 through 84 removed outlier: 4.692A pdb=" N ASPBK 81 " --> pdb=" O GLNBK 77 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYRBK 82 " --> pdb=" O TYRBK 78 " (cutoff:3.500A) Processing helix chain 'BM' and resid 11 through 29 removed outlier: 4.494A pdb=" N ASNBM 15 " --> pdb=" O VALBM 11 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEUBM 18 " --> pdb=" O VALBM 14 " (cutoff:3.500A) removed outlier: 4.542A 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: 4.578A pdb=" N LEUBM 64 " --> pdb=" O METBM 60 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VALBM 65 " --> pdb=" O TYRBM 61 " (cutoff:3.500A) Processing helix chain 'BM' and resid 81 through 90 removed outlier: 3.652A pdb=" N LEUBM 85 " --> pdb=" O ASPBM 81 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLUBM 87 " --> pdb=" O LYSBM 83 " (cutoff:3.500A) Processing helix chain 'BM' and resid 120 through 130 Processing helix chain 'BP' and resid 21 through 28 Processing helix chain 'BP' and resid 29 through 38 removed outlier: 4.868A pdb=" N GLNBP 35 " --> pdb=" O GLUBP 31 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEUBP 36 " --> pdb=" O GLNBP 32 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SERBP 38 " --> pdb=" O METBP 34 " (cutoff:3.500A) Processing helix chain 'BP' and resid 39 through 48 removed outlier: 3.668A pdb=" N GLYBP 48 " --> pdb=" O ARGBP 44 " (cutoff:3.500A) Processing helix chain 'BP' and resid 51 through 68 removed outlier: 3.769A pdb=" N LEUBP 57 " --> pdb=" O GLNBP 53 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALABP 67 " --> pdb=" O ALABP 63 " (cutoff:3.500A) Proline residue: BP 68 - end of helix Processing helix chain 'BP' and resid 115 through 121 removed outlier: 6.937A pdb=" N PHEBP 119 " --> pdb=" O TYRBP 115 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SERBP 120 " --> pdb=" O LEUBP 116 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILEBP 121 " --> pdb=" O GLYBP 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 115 through 121' Processing helix chain 'BQ' and resid 47 through 53 removed outlier: 3.903A pdb=" N LEUBQ 51 " --> pdb=" O LEUBQ 47 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEUBQ 52 " --> pdb=" O GLNBQ 48 " (cutoff:3.500A) removed outlier: 3.707A 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: 4.470A pdb=" N PHEBQ 63 " --> pdb=" O GLYBQ 59 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASPBQ 67 " --> pdb=" O PHEBQ 63 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 76 through 99 removed outlier: 4.012A pdb=" N VALBQ 93 " --> pdb=" O SERBQ 89 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 101 through 116 removed outlier: 4.128A 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: 4.203A pdb=" N ARGBR 33 " --> pdb=" O HISBR 29 " (cutoff:3.500A) Processing helix chain 'BR' and resid 43 through 64 removed outlier: 3.565A pdb=" N ARGBR 63 " --> pdb=" O LYSBR 59 " (cutoff:3.500A) Processing helix chain 'BR' and resid 71 through 83 removed outlier: 4.187A pdb=" N ASPBR 82 " --> pdb=" O ARGBR 78 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASNBR 83 " --> pdb=" O GLUBR 79 " (cutoff:3.500A) Processing helix chain 'BR' and resid 99 through 110 removed outlier: 4.518A pdb=" N ASPBR 110 " --> pdb=" O LEUBR 106 " (cutoff:3.500A) Processing helix chain 'BS' and resid 25 through 33 removed outlier: 4.182A pdb=" N THRBS 31 " --> pdb=" O ALABS 27 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALABS 32 " --> pdb=" O PHEBS 28 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILEBS 33 " --> pdb=" O ALABS 29 " (cutoff:3.500A) Processing helix chain 'BS' and resid 37 through 49 removed outlier: 4.452A pdb=" N ALABS 41 " --> pdb=" O GLYBS 37 " (cutoff:3.500A) removed outlier: 4.298A 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: 4.138A pdb=" N ASPBS 104 " --> pdb=" O ALABS 100 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASNBS 105 " --> pdb=" O ASNBS 101 " (cutoff:3.500A) Processing helix chain 'BS' and resid 119 through 128 removed outlier: 4.497A pdb=" N GLYBS 128 " --> pdb=" O ARGBS 124 " (cutoff:3.500A) Processing helix chain 'BT' and resid 5 through 10 removed outlier: 5.221A pdb=" N ASNBT 10 " --> pdb=" O VALBT 6 " (cutoff:3.500A) Processing helix chain 'BT' and resid 11 through 26 removed outlier: 4.265A pdb=" N ARGBT 16 " --> pdb=" O GLNBT 12 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALABT 17 " --> pdb=" O GLUBT 13 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALABT 20 " --> pdb=" O ARGBT 16 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SERBT 25 " --> pdb=" O PHEBT 21 " (cutoff:3.500A) Processing helix chain 'BT' and resid 31 through 37 removed outlier: 5.263A pdb=" N ASPBT 35 " --> pdb=" O PROBT 31 " (cutoff:3.500A) Processing helix chain 'BT' and resid 51 through 68 removed outlier: 4.228A 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: 3.869A pdb=" N ALABT 100 " --> pdb=" O SERBT 96 " (cutoff:3.500A) Processing helix chain 'BT' and resid 124 through 144 Processing helix chain 'BU' and resid 28 through 47 removed outlier: 4.713A pdb=" N GLUBU 45 " --> pdb=" O ARGBU 41 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYSBU 46 " --> pdb=" O GLYBU 42 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASNBU 47 " --> pdb=" O ALABU 43 " (cutoff:3.500A) Processing helix chain 'BU' and resid 94 through 103 removed outlier: 3.865A pdb=" N SERBU 103 " --> pdb=" O LYSBU 99 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 51 through 62 removed outlier: 3.790A pdb=" N TYRBZ 55 " --> pdb=" O ASPBZ 51 " (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: 3.911A pdb=" N ARGBd 19 " --> pdb=" O GLYBd 15 " (cutoff:3.500A) removed outlier: 5.426A 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: 6.582A pdb=" N PHEBd 43 " --> pdb=" O CYSBd 39 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARGBd 44 " --> pdb=" O ARGBd 40 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLNBd 45 " --> pdb=" O GLNBd 41 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYSBd 48 " --> pdb=" O ARGBd 44 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASPBd 49 " --> pdb=" O GLNBd 45 " (cutoff:3.500A) Processing helix chain 'BE' and resid 43 through 49 Processing helix chain 'BE' and resid 57 through 68 removed outlier: 4.108A pdb=" N VALBE 61 " --> pdb=" O THRBE 57 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N METBE 66 " --> pdb=" O LYSBE 62 " (cutoff:3.500A) Processing helix chain 'BE' and resid 115 through 122 removed outlier: 4.803A pdb=" N TYRBE 121 " --> pdb=" O GLUBE 117 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYSBE 122 " --> pdb=" O GLUBE 118 " (cutoff:3.500A) Processing helix chain 'BE' and resid 221 through 226 removed outlier: 3.701A pdb=" N ILEBE 225 " --> pdb=" O ARGBE 221 " (cutoff:3.500A) removed outlier: 6.367A 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 29 removed outlier: 3.672A pdb=" N LEUBG 24 " --> pdb=" O ASPBG 20 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THRBG 26 " --> pdb=" O ARGBG 22 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHEBG 27 " --> pdb=" O LYSBG 23 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYRBG 28 " --> pdb=" O LEUBG 24 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLUBG 29 " --> pdb=" O ARGBG 25 " (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 34 removed outlier: 4.006A pdb=" N GLYBH 22 " --> pdb=" O GLUBH 18 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N METBH 32 " --> pdb=" O LEUBH 28 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASNBH 33 " --> pdb=" O GLUBH 29 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SERBH 34 " --> pdb=" O LEUBH 30 " (cutoff:3.500A) Processing helix chain 'BH' and resid 37 through 43 Processing helix chain 'BH' and resid 66 through 76 removed outlier: 4.636A pdb=" N LYSBH 70 " --> pdb=" O VALBH 66 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SERBH 71 " --> pdb=" O PROBH 67 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILEBH 75 " --> pdb=" O SERBH 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLNBH 76 " --> pdb=" O PHEBH 72 " (cutoff:3.500A) Processing helix chain 'BH' and resid 77 through 87 removed outlier: 3.779A pdb=" N ARGBH 81 " --> pdb=" O VALBH 77 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSBH 86 " --> pdb=" O GLUBH 82 " (cutoff:3.500A) Processing helix chain 'BH' and resid 121 through 135 removed outlier: 4.331A pdb=" N VALBH 134 " --> pdb=" O LEUBH 130 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHEBH 135 " --> pdb=" O GLUBH 131 " (cutoff:3.500A) Processing helix chain 'BH' and resid 162 through 181 removed outlier: 4.856A pdb=" N VALBH 166 " --> pdb=" O GLNBH 162 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HISBH 168 " --> pdb=" O ASNBH 164 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYSBH 169 " --> pdb=" O ASNBH 165 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLUBH 171 " --> pdb=" O GLUBH 167 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THRBH 172 " --> pdb=" O HISBH 168 " (cutoff:3.500A) Processing helix chain 'BI' and resid 87 through 94 removed outlier: 3.794A pdb=" N VALBI 91 " --> pdb=" O ASNBI 87 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARGBI 92 " --> pdb=" O ASNBI 88 " (cutoff:3.500A) Processing helix chain 'BI' and resid 106 through 117 removed outlier: 3.777A pdb=" N ARGBI 110 " --> pdb=" O SERBI 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLNBI 111 " --> pdb=" O THRBI 107 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRPBI 112 " --> pdb=" O PROBI 108 " (cutoff:3.500A) Processing helix chain 'BI' and resid 141 through 152 removed outlier: 4.505A pdb=" N ILEBI 145 " --> pdb=" O ARGBI 141 " (cutoff:3.500A) Processing helix chain 'BI' and resid 159 through 169 removed outlier: 4.006A 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: 3.875A pdb=" N VALBJ 43 " --> pdb=" O ASNBJ 39 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VALBJ 46 " --> pdb=" O GLUBJ 42 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEUBJ 63 " --> pdb=" O GLUBJ 59 " (cutoff:3.500A) removed outlier: 5.259A 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: 3.938A pdb=" N ILEBJ 97 " --> pdb=" O LYSBJ 93 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEUBJ 98 " --> pdb=" O LEUBJ 94 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEUBJ 100 " --> pdb=" O TYRBJ 96 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 101 through 110 removed outlier: 4.867A pdb=" N PHEBJ 105 " --> pdb=" O LYSBJ 101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEUBJ 106 " --> pdb=" O ILEBJ 102 " (cutoff:3.500A) removed outlier: 5.648A 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: 4.088A pdb=" N VALBJ 128 " --> pdb=" O HISBJ 124 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARGBJ 133 " --> pdb=" O LEUBJ 129 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 171 through 180 removed outlier: 3.784A pdb=" N ARGBJ 175 " --> pdb=" O GLYBJ 171 " (cutoff:3.500A) Processing helix chain 'BL' and resid 47 through 53 removed outlier: 3.814A pdb=" N ILEBL 51 " --> pdb=" O PROBL 47 " (cutoff:3.500A) Processing helix chain 'BL' and resid 30 through 35 removed outlier: 5.384A 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: 3.656A pdb=" N VALBN 52 " --> pdb=" O SERBN 48 " (cutoff:3.500A) Processing helix chain 'BN' and resid 62 through 67 Processing helix chain 'BN' and resid 70 through 79 removed outlier: 3.778A pdb=" N LYSBN 78 " --> pdb=" O ILEBN 74 " (cutoff:3.500A) Processing helix chain 'BN' and resid 85 through 106 removed outlier: 4.097A pdb=" N LEUBN 91 " --> pdb=" O ASPBN 87 " (cutoff:3.500A) removed outlier: 3.506A 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: 5.543A pdb=" N ALABN 146 " --> pdb=" O GLUBN 142 " (cutoff:3.500A) Processing helix chain 'BO' and resid 57 through 62 removed outlier: 4.023A pdb=" N LYSBO 61 " --> pdb=" O THRBO 57 " (cutoff:3.500A) Processing helix chain 'BO' and resid 64 through 69 removed outlier: 5.069A pdb=" N SERBO 69 " --> pdb=" O ASPBO 65 " (cutoff:3.500A) Processing helix chain 'BO' and resid 70 through 89 Processing helix chain 'BO' and resid 109 through 123 removed outlier: 4.732A pdb=" N GLNBO 113 " --> pdb=" O GLYBO 109 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SERBO 114 " --> pdb=" O PROBO 110 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARGBO 117 " --> pdb=" O GLNBO 113 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SERBO 122 " --> pdb=" O ALABO 118 " (cutoff:3.500A) removed outlier: 4.575A 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: 3.905A pdb=" N LEUBV 70 " --> pdb=" O ASPBV 66 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALABV 75 " --> pdb=" O ARGBV 71 " (cutoff:3.500A) Processing helix chain 'BW' and resid 5 through 21 removed outlier: 3.774A 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: 4.237A pdb=" N TRPBW 89 " --> pdb=" O ASPBW 85 " (cutoff:3.500A) Processing helix chain 'BW' and resid 112 through 120 removed outlier: 3.799A pdb=" N ARGBW 117 " --> pdb=" O HISBW 113 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARGBW 118 " --> pdb=" O GLUBW 114 " (cutoff:3.500A) Processing helix chain 'BX' and resid 9 through 24 removed outlier: 4.556A pdb=" N TRPBX 22 " --> pdb=" O ARGBX 18 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HISBX 23 " --> pdb=" O ASPBX 19 " (cutoff:3.500A) removed outlier: 4.613A 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 39 removed outlier: 4.594A pdb=" N ASNBX 39 " --> pdb=" O ALABX 35 " (cutoff:3.500A) Processing helix chain 'BX' and resid 89 through 95 removed outlier: 6.318A pdb=" N PHEBX 93 " --> pdb=" O GLYBX 89 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLUBX 95 " --> pdb=" O LEUBX 91 " (cutoff:3.500A) Processing helix chain 'BX' and resid 129 through 136 removed outlier: 4.083A pdb=" N GLYBX 136 " --> pdb=" O ALABX 132 " (cutoff:3.500A) Processing helix chain 'BY' and resid 36 through 49 Processing helix chain 'BY' and resid 78 through 86 removed outlier: 3.687A pdb=" N GLUBY 86 " --> pdb=" O ALABY 82 " (cutoff:3.500A) Processing helix chain 'BY' and resid 87 through 95 removed outlier: 3.700A pdb=" N ARGBY 93 " --> pdb=" O HISBY 89 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HISBY 94 " --> pdb=" O ARGBY 90 " (cutoff:3.500A) Processing helix chain 'BY' and resid 105 through 118 removed outlier: 3.826A pdb=" N VALBY 117 " --> pdb=" O ARGBY 113 " (cutoff:3.500A) removed outlier: 5.089A 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: 4.348A pdb=" N ARGBa 51 " --> pdb=" O ALABa 47 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASPBa 52 " --> pdb=" O ALABa 48 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 74 through 82 removed outlier: 4.451A pdb=" N ILEBa 79 " --> pdb=" O VALBa 75 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HISBa 80 " --> pdb=" O SERBa 76 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 88 through 93 removed outlier: 4.830A pdb=" N LYSBa 93 " --> pdb=" O ARGBa 89 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 11 through 19 removed outlier: 5.701A 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 30 through 42 removed outlier: 3.581A pdb=" N ARGBe 41 " --> pdb=" O GLNBe 37 " (cutoff:3.500A) 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: 6.195A pdb=" N ARGAD 33 " --> pdb=" O ASPAD 29 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARGAD 35 " --> pdb=" O TYRAD 31 " (cutoff:3.500A) Processing helix chain 'AD' and resid 79 through 87 removed outlier: 4.723A pdb=" N LEUAD 83 " --> pdb=" O TYRAD 79 " (cutoff:3.500A) Proline residue: AD 84 - end of helix Processing helix chain 'AD' and resid 94 through 114 Processing helix chain 'AD' and resid 157 through 170 removed outlier: 3.722A pdb=" N GLYAD 161 " --> pdb=" O ASNAD 157 " (cutoff:3.500A) Processing helix chain 'AD' and resid 191 through 201 Processing helix chain 'AD' and resid 202 through 215 Processing helix chain 'AD' and resid 216 through 223 removed outlier: 4.804A 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 250 removed outlier: 3.700A pdb=" N LYSAD 241 " --> pdb=" O GLUAD 237 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALAAD 245 " --> pdb=" O LYSAD 241 " (cutoff:3.500A) Processing helix chain 'AD' and resid 272 through 297 removed outlier: 3.922A pdb=" N ALAAD 295 " --> pdb=" O GLNAD 291 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLUAD 296 " --> pdb=" O GLUAD 292 " (cutoff:3.500A) Processing helix chain 'AE' and resid 213 through 218 removed outlier: 4.033A pdb=" N LYSAE 218 " --> pdb=" O ASPAE 214 " (cutoff:3.500A) Processing helix chain 'AE' and resid 233 through 239 removed outlier: 6.766A pdb=" N LYSAE 237 " --> pdb=" O PHEAE 233 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLUAE 238 " --> pdb=" O ASPAE 234 " (cutoff:3.500A) removed outlier: 4.887A 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: 4.351A pdb=" N ILEAE 248 " --> pdb=" O GLUAE 244 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASPAE 249 " --> pdb=" O GLNAE 245 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VALAE 253 " --> pdb=" O ASPAE 249 " (cutoff:3.500A) removed outlier: 4.512A 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: 5.308A pdb=" N VALAE 274 " --> pdb=" O TYRAE 270 " (cutoff:3.500A) Processing helix chain 'AF' and resid 15 through 79 removed outlier: 3.860A pdb=" N GLUAF 68 " --> pdb=" O METAF 64 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILEAF 69 " --> pdb=" O TYRAF 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALAAF 72 " --> pdb=" O GLUAF 68 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALAAF 75 " --> pdb=" O METAF 71 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARGAF 76 " --> pdb=" O ALAAF 72 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSAF 77 " --> pdb=" O ARGAF 73 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALAAF 78 " --> pdb=" O METAF 74 " (cutoff:3.500A) Processing helix chain 'AF' and resid 102 through 113 removed outlier: 4.023A pdb=" N VALAF 108 " --> pdb=" O LYSAF 104 " (cutoff:3.500A) Processing helix chain 'AF' and resid 126 through 137 removed outlier: 3.955A pdb=" N ILEAF 135 " --> pdb=" O ASNAF 131 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VALAF 136 " --> pdb=" O METAF 132 " (cutoff:3.500A) Processing helix chain 'AF' and resid 146 through 156 removed outlier: 3.745A pdb=" N LEUAF 153 " --> pdb=" O SERAF 149 " (cutoff:3.500A) Processing helix chain 'AF' and resid 171 through 179 removed outlier: 4.321A pdb=" N ILEAF 175 " --> pdb=" O ASPAF 171 " (cutoff:3.500A) Processing helix chain 'AF' and resid 186 through 197 removed outlier: 4.039A pdb=" N VALAF 197 " --> pdb=" O GLUAF 193 " (cutoff:3.500A) Processing helix chain 'AF' and resid 200 through 209 removed outlier: 3.645A pdb=" N ALAAF 204 " --> pdb=" O ARGAF 200 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TRPAF 209 " --> pdb=" O ASNAF 205 " (cutoff:3.500A) Processing helix chain 'AF' and resid 238 through 248 removed outlier: 4.203A pdb=" N ARGAF 242 " --> pdb=" O ASPAF 238 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARGAF 246 " --> pdb=" O ARGAF 242 " (cutoff:3.500A) Processing helix chain 'AG' and resid 58 through 74 Processing helix chain 'AG' and resid 77 through 86 removed outlier: 4.423A pdb=" N GLNAG 82 " --> pdb=" O PROAG 78 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHEAG 83 " --> pdb=" O ALAAG 79 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N THRAG 84 " --> pdb=" O ILEAG 80 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLNAG 85 " --> pdb=" O ASNAG 81 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALAAG 86 " --> pdb=" O GLNAG 82 " (cutoff:3.500A) Processing helix chain 'AG' and resid 88 through 103 removed outlier: 4.694A pdb=" N LYSAG 101 " --> pdb=" O LYSAG 97 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYRAG 102 " --> pdb=" O LEUAG 98 " (cutoff:3.500A) removed outlier: 3.876A 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 removed outlier: 3.607A pdb=" N THRAG 145 " --> pdb=" O ASNAG 141 " (cutoff:3.500A) Processing helix chain 'AG' and resid 163 through 178 removed outlier: 4.574A pdb=" N VALAG 167 " --> pdb=" O PROAG 163 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHEAG 169 " --> pdb=" O GLUAG 165 " (cutoff:3.500A) removed outlier: 5.908A 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: 3.799A pdb=" N LEUAG 190 " --> pdb=" O GLYAG 186 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEUAG 193 " --> pdb=" O ARGAG 189 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VALAG 194 " --> pdb=" O LEUAG 190 " (cutoff:3.500A) Processing helix chain 'AG' and resid 211 through 230 removed outlier: 3.671A pdb=" N ALAAG 221 " --> pdb=" O LYSAG 217 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASNAG 227 " --> pdb=" O ARGAG 223 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASPAG 228 " --> pdb=" O THRAG 224 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARGAG 229 " --> pdb=" O ASNAG 225 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYRAG 230 " --> pdb=" O TYRAG 226 " (cutoff:3.500A) Processing helix chain 'AG' and resid 231 through 237 removed outlier: 3.939A pdb=" N ARGAG 235 " --> pdb=" O ASPAG 231 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HISAG 236 " --> pdb=" O GLUAG 232 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPAG 237 " --> pdb=" O ILEAG 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'AG' and resid 231 through 237' Processing helix chain 'AG' and resid 243 through 262 Processing helix chain 'AH' and resid 63 through 86 removed outlier: 4.293A pdb=" N ARGAH 71 " --> pdb=" O LEUAH 67 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THRAH 72 " --> pdb=" O ALAAH 68 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILEAH 73 " --> pdb=" O THRAH 69 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYSAH 74 " --> pdb=" O VALAH 70 " (cutoff:3.500A) Processing helix chain 'AH' and resid 150 through 166 removed outlier: 4.756A pdb=" N THRAH 166 " --> pdb=" O GLNAH 162 " (cutoff:3.500A) Processing helix chain 'AH' and resid 171 through 176 removed outlier: 4.564A pdb=" N PHEAH 175 " --> pdb=" O ASPAH 171 " (cutoff:3.500A) removed outlier: 5.172A 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: 3.978A pdb=" N TYRAI 9 " --> pdb=" O PROAI 5 " (cutoff:3.500A) removed outlier: 4.382A 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: 4.254A 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: 3.608A pdb=" N VALAI 148 " --> pdb=" O ASNAI 144 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILEAI 149 " --> pdb=" O LYSAI 145 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHEAI 157 " --> pdb=" O ARGAI 153 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYSAI 158 " --> pdb=" O ARGAI 154 " (cutoff:3.500A) Proline residue: AI 160 - end of helix Processing helix chain 'AI' and resid 177 through 188 removed outlier: 4.186A pdb=" N GLUAI 182 " --> pdb=" O ALAAI 178 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASPAI 183 " --> pdb=" O ASPAI 179 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALAAI 186 " --> pdb=" O GLUAI 182 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLUAI 187 " --> pdb=" O ASPAI 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYSAI 188 " --> pdb=" O METAI 184 " (cutoff:3.500A) Processing helix chain 'AI' and resid 205 through 213 removed outlier: 4.048A pdb=" N TRPAI 209 " --> pdb=" O PROAI 205 " (cutoff:3.500A) removed outlier: 4.359A 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 111 through 116 removed outlier: 4.680A pdb=" N LEUAJ 115 " --> pdb=" O GLUAJ 111 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLYAJ 116 " --> pdb=" O HISAJ 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 111 through 116' Processing helix chain 'AJ' and resid 139 through 144 removed outlier: 4.403A pdb=" N ASPAJ 143 " --> pdb=" O PHEAJ 139 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 158 through 170 removed outlier: 5.016A pdb=" N TYRAJ 170 " --> pdb=" O PHEAJ 166 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 95 through 100 removed outlier: 3.708A pdb=" N PHEAJ 99 " --> pdb=" O LYSAJ 96 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SERAJ 100 " --> pdb=" O ASNAJ 97 " (cutoff:3.500A) Processing helix chain 'AL' and resid 17 through 22 removed outlier: 4.576A pdb=" N ARGAL 21 " --> pdb=" O ASPAL 17 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VALAL 22 " --> pdb=" O TRPAL 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'AL' and resid 17 through 22' Processing helix chain 'AL' and resid 27 through 45 Processing helix chain 'AL' and resid 77 through 85 removed outlier: 4.018A 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 140 through 145 Processing helix chain 'AL' and resid 171 through 177 removed outlier: 4.718A pdb=" N ASNAL 175 " --> pdb=" O GLUAL 171 " (cutoff:3.500A) Processing helix chain 'AL' and resid 179 through 192 removed outlier: 3.814A pdb=" N ARGAL 183 " --> pdb=" O PHEAL 179 " (cutoff:3.500A) Processing helix chain 'AL' and resid 193 through 206 removed outlier: 4.056A pdb=" N ASPAL 206 " --> pdb=" O ALAAL 202 " (cutoff:3.500A) Processing helix chain 'AM' and resid 51 through 56 removed outlier: 4.495A 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: 3.980A 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: 3.859A pdb=" N LYSAN 13 " --> pdb=" O GLUAN 9 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYSAN 14 " --> pdb=" O LEUAN 10 " (cutoff:3.500A) Processing helix chain 'AN' and resid 16 through 34 removed outlier: 3.580A pdb=" N PHEAN 21 " --> pdb=" O ASPAN 17 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEUAN 22 " --> pdb=" O VALAN 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEUAN 33 " --> pdb=" O GLNAN 29 " (cutoff:3.500A) removed outlier: 4.911A 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: 4.355A pdb=" N HISAN 87 " --> pdb=" O LYSAN 83 " (cutoff:3.500A) removed outlier: 6.138A 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: 4.732A 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: 6.886A pdb=" N ILEAN 151 " --> pdb=" O ASPAN 147 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THRAN 152 " --> pdb=" O THRAN 148 " (cutoff:3.500A) removed outlier: 3.869A 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: 3.599A 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: 3.810A pdb=" N LEUAO 28 " --> pdb=" O ALAAO 24 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEUAO 29 " --> pdb=" O LYSAO 25 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLYAO 30 " --> pdb=" O GLNAO 26 " (cutoff:3.500A) Processing helix chain 'AO' and resid 46 through 61 removed outlier: 5.318A pdb=" N ARGAO 61 " --> pdb=" O PHEAO 57 " (cutoff:3.500A) Processing helix chain 'AO' and resid 65 through 70 removed outlier: 4.537A 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: 3.673A 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: 5.072A pdb=" N ALAAO 97 " --> pdb=" O LYSAO 93 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYSAO 103 " --> pdb=" O LEUAO 99 " (cutoff:3.500A) Processing helix chain 'AO' and resid 109 through 116 removed outlier: 5.207A 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: 3.651A pdb=" N GLYAO 146 " --> pdb=" O ALAAO 142 " (cutoff:3.500A) Processing helix chain 'AO' and resid 151 through 185 removed outlier: 4.021A pdb=" N LYSAO 170 " --> pdb=" O ILEAO 166 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VALAO 185 " --> pdb=" O ALAAO 181 " (cutoff:3.500A) Processing helix chain 'AO' and resid 187 through 198 removed outlier: 3.605A pdb=" N LYSAO 191 " --> pdb=" O LYSAO 187 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THRAO 193 " --> pdb=" O ILEAO 189 " (cutoff:3.500A) Processing helix chain 'AP' and resid 10 through 15 removed outlier: 3.818A pdb=" N SERAP 14 " --> pdb=" O ASNAP 10 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYSAP 15 " --> pdb=" O PROAP 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP' and resid 10 through 15' Processing helix chain 'AP' and resid 25 through 37 removed outlier: 3.816A pdb=" N ALAAP 35 " --> pdb=" O GLUAP 31 " (cutoff:3.500A) 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: 3.969A pdb=" N ALAAP 73 " --> pdb=" O CYSAP 70 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAP 74 " --> pdb=" O ALAAP 71 " (cutoff:3.500A) removed outlier: 3.724A 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: 5.370A pdb=" N SERAQ 54 " --> pdb=" O ARGAQ 50 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 62 through 72 removed outlier: 3.913A pdb=" N METAQ 70 " --> pdb=" O METAQ 66 " (cutoff:3.500A) removed outlier: 3.823A 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: 3.754A pdb=" N ARGAQ 150 " --> pdb=" O ARGAQ 146 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HISAQ 151 " --> pdb=" O GLUAQ 147 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHEAQ 152 " --> pdb=" O VALAQ 148 " (cutoff:3.500A) removed outlier: 5.909A 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: 4.062A pdb=" N SERAR 12 " --> pdb=" O LYSAR 8 " (cutoff:3.500A) Processing helix chain 'AR' and resid 28 through 36 removed outlier: 3.741A pdb=" N ILEAR 32 " --> pdb=" O GLUAR 28 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALAAR 35 " --> pdb=" O GLUAR 31 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASNAR 36 " --> pdb=" O ILEAR 32 " (cutoff:3.500A) Processing helix chain 'AR' and resid 37 through 48 removed outlier: 3.611A pdb=" N LYSAR 46 " --> pdb=" O ARGAR 42 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASPAR 47 " --> pdb=" O LYSAR 43 " (cutoff:3.500A) removed outlier: 4.430A 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: 6.566A pdb=" N VALAR 93 " --> pdb=" O METAR 89 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEUAR 106 " --> pdb=" O LEUAR 102 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARGAR 107 " --> pdb=" O ARGAR 103 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SERAR 112 " --> pdb=" O ARGAR 108 " (cutoff:3.500A) Processing helix chain 'AR' and resid 116 through 130 removed outlier: 3.645A pdb=" N TYRAR 120 " --> pdb=" O ASPAR 116 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HISAR 121 " --> pdb=" O ARGAR 117 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SERAR 122 " --> pdb=" O HISAR 118 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASNAR 130 " --> pdb=" O LYSAR 126 " (cutoff:3.500A) Processing helix chain 'AR' and resid 134 through 182 Processing helix chain 'AS' and resid 36 through 52 Processing helix chain 'AS' and resid 101 through 117 removed outlier: 3.601A pdb=" N HISAS 117 " --> pdb=" O METAS 113 " (cutoff:3.500A) Processing helix chain 'AS' and resid 120 through 125 removed outlier: 3.895A pdb=" N ILEAS 124 " --> pdb=" O ARGAS 120 " (cutoff:3.500A) removed outlier: 6.109A 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: 5.240A pdb=" N ASPAS 147 " --> pdb=" O LYSAS 143 " (cutoff:3.500A) Processing helix chain 'AT' and resid 11 through 16 removed outlier: 4.150A pdb=" N PHEAT 15 " --> pdb=" O THRAT 11 " (cutoff:3.500A) removed outlier: 5.342A 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: 4.308A pdb=" N TYRAT 30 " --> pdb=" O PROAT 26 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARGAT 32 " --> pdb=" O ALAAT 28 " (cutoff:3.500A) Processing helix chain 'AT' and resid 92 through 97 removed outlier: 4.350A pdb=" N ILEAT 96 " --> pdb=" O ARGAT 92 " (cutoff:3.500A) removed outlier: 5.575A 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: 4.335A pdb=" N ASPAT 103 " --> pdb=" O SERAT 99 " (cutoff:3.500A) Processing helix chain 'AU' and resid 25 through 32 removed outlier: 4.469A pdb=" N VALAU 29 " --> pdb=" O CYSAU 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLUAU 30 " --> pdb=" O THRAU 26 " (cutoff:3.500A) Processing helix chain 'AU' and resid 35 through 47 Processing helix chain 'AU' and resid 79 through 95 removed outlier: 4.079A pdb=" N LEUAU 83 " --> pdb=" O SERAU 79 " (cutoff:3.500A) Processing helix chain 'AV' and resid 69 through 74 removed outlier: 5.533A pdb=" N LYSAV 74 " --> pdb=" O PROAV 70 " (cutoff:3.500A) Processing helix chain 'AV' and resid 122 through 129 removed outlier: 3.936A pdb=" N LEUAV 128 " --> pdb=" O GLUAV 124 " (cutoff:3.500A) Processing helix chain 'AV' and resid 130 through 136 Processing helix chain 'AW' and resid 33 through 43 removed outlier: 4.038A pdb=" N LYSAW 43 " --> pdb=" O ALAAW 39 " (cutoff:3.500A) Processing helix chain 'AW' and resid 45 through 50 removed outlier: 5.821A pdb=" N ASNAW 50 " --> pdb=" O PROAW 46 " (cutoff:3.500A) Processing helix chain 'AW' and resid 52 through 60 removed outlier: 4.014A pdb=" N HISAW 59 " --> pdb=" O TYRAW 55 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LYSAW 60 " --> pdb=" O ARGAW 56 " (cutoff:3.500A) Processing helix chain 'AW' and resid 61 through 68 removed outlier: 3.681A pdb=" N GLUAW 66 " --> pdb=" O GLYAW 62 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILEAW 67 " --> pdb=" O GLNAW 63 " (cutoff:3.500A) Processing helix chain 'AW' and resid 87 through 96 removed outlier: 3.908A pdb=" N GLNAW 96 " --> pdb=" O ALAAW 92 " (cutoff:3.500A) Processing helix chain 'AW' and resid 97 through 122 removed outlier: 4.287A pdb=" N GLUAW 114 " --> pdb=" O ARGAW 110 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALAAW 115 " --> pdb=" O ALAAW 111 " (cutoff:3.500A) Processing helix chain 'AX' and resid 72 through 78 removed outlier: 3.939A pdb=" N ILEAX 77 " --> pdb=" O HISAX 73 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYSAX 78 " --> pdb=" O TYRAX 74 " (cutoff:3.500A) Processing helix chain 'AX' and resid 83 through 92 removed outlier: 3.501A pdb=" N LYSAX 89 " --> pdb=" O SERAX 85 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILEAX 90 " --> pdb=" O ALAAX 86 " (cutoff:3.500A) removed outlier: 3.836A 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: 4.102A pdb=" N LYSAY 28 " --> pdb=" O HISAY 24 " (cutoff:3.500A) removed outlier: 3.932A 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: 4.326A pdb=" N VALAY 104 " --> pdb=" O HISAY 100 " (cutoff:3.500A) removed outlier: 5.778A 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: 3.563A pdb=" N LEUAZ 80 " --> pdb=" O ASNAZ 76 " (cutoff:3.500A) removed outlier: 5.123A 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: 4.364A pdb=" N VALAZ 96 " --> pdb=" O ASPAZ 92 " (cutoff:3.500A) removed outlier: 4.175A 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: 5.109A pdb=" N THRAZ 124 " --> pdb=" O GLUAZ 120 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLYAZ 125 " --> pdb=" O ARGAZ 121 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 127 through 133 removed outlier: 3.941A pdb=" N PHEAZ 131 " --> pdb=" O ASNAZ 127 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYSAZ 133 " --> pdb=" O TRPAZ 129 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 2 through 7 removed outlier: 5.522A pdb=" N LYSAa 7 " --> pdb=" O SERAa 3 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 41 through 46 Processing helix chain 'Aa' and resid 64 through 69 removed outlier: 4.975A pdb=" N SERAa 68 " --> pdb=" O LYSAa 64 " (cutoff:3.500A) removed outlier: 5.492A 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: 4.426A pdb=" N TRPAa 79 " --> pdb=" O LEUAa 75 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THRAa 80 " --> pdb=" O ASPAa 76 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEUAa 81 " --> pdb=" O LYSAa 77 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VALAa 82 " --> pdb=" O LEUAa 78 " (cutoff:3.500A) removed outlier: 5.001A 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: 3.658A 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: 4.623A pdb=" N LYSAb 15 " --> pdb=" O ASNAb 11 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASNAb 19 " --> pdb=" O LYSAb 15 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLYAb 20 " --> pdb=" O TRPAb 16 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 36 through 53 removed outlier: 4.130A 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: 3.637A pdb=" N LYSAc 23 " --> pdb=" O GLNAc 19 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 30 through 41 removed outlier: 4.290A pdb=" N LYSAc 36 " --> pdb=" O LYSAc 32 " (cutoff:3.500A) removed outlier: 3.699A 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 removed outlier: 3.547A pdb=" N METAc 108 " --> pdb=" O ILEAc 104 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 28 through 34 removed outlier: 4.849A pdb=" N HISAd 34 " --> pdb=" O HISAd 30 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 40 through 58 removed outlier: 4.279A pdb=" N ARGAd 44 " --> pdb=" O LYSAd 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUAd 46 " --> pdb=" O ALAAd 42 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 65 through 74 Processing helix chain 'Ae' and resid 24 through 29 removed outlier: 3.644A pdb=" N TYRAe 28 " --> pdb=" O GLNAe 24 " (cutoff:3.500A) removed outlier: 4.717A 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: 4.551A pdb=" N LEUAe 88 " --> pdb=" O GLUAe 84 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEUAe 89 " --> pdb=" O LEUAe 85 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N METAe 90 " --> pdb=" O GLUAe 86 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 105 through 119 removed outlier: 4.115A pdb=" N ALAAe 110 " --> pdb=" O LYSAe 106 " (cutoff:3.500A) Processing helix chain 'Af' and resid 35 through 40 removed outlier: 4.556A pdb=" N GLUAf 40 " --> pdb=" O ARGAf 36 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 60 through 68 removed outlier: 4.045A pdb=" N METAg 65 " --> pdb=" O PROAg 61 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARGAg 66 " --> pdb=" O LYSAg 62 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N SERAg 68 " --> pdb=" O LEUAg 64 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 83 through 115 removed outlier: 6.150A pdb=" N VALAg 87 " --> pdb=" O CYSAg 83 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYSAg 92 " --> pdb=" O ARGAg 88 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 5 through 13 removed outlier: 4.052A pdb=" N GLYAh 11 " --> pdb=" O ARGAh 7 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYSAh 12 " --> pdb=" O ASPAh 8 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYSAh 13 " --> pdb=" O LEUAh 9 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 14 through 38 removed outlier: 4.161A pdb=" N LYSAh 19 " --> pdb=" O GLUAh 15 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLYAh 38 " --> pdb=" O ALAAh 34 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 42 through 74 removed outlier: 5.137A pdb=" N LYSAh 46 " --> pdb=" O SERAh 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLUAh 67 " --> pdb=" O GLNAh 63 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHEAh 72 " --> pdb=" O ASNAh 68 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 80 through 85 Proline residue: Ah 85 - end of helix 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: 4.324A pdb=" N ARGAi 29 " --> pdb=" O ARGAi 25 " (cutoff:3.500A) removed outlier: 4.676A 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: 4.364A pdb=" N GLUAi 46 " --> pdb=" O ASPAi 42 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 51 through 63 removed outlier: 3.777A 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 97 Processing helix chain 'Aj' and resid 4 through 11 removed outlier: 3.954A pdb=" N GLYAj 9 " --> pdb=" O THRAj 5 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYSAj 10 " --> pdb=" O SERAj 6 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARGAj 11 " --> pdb=" O SERAj 7 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 50 through 58 removed outlier: 3.870A pdb=" N LYSAj 54 " --> pdb=" O SERAj 50 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 64 through 77 removed outlier: 4.486A pdb=" N ILEAj 69 " --> pdb=" O ARGAj 65 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HISAj 76 " --> pdb=" O ARGAj 72 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 7 through 18 removed outlier: 3.936A pdb=" N PHEAk 11 " --> pdb=" O GLUAk 7 " (cutoff:3.500A) removed outlier: 5.189A 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: 5.123A pdb=" N ARGAl 21 " --> pdb=" O GLNAl 17 " (cutoff:3.500A) Processing helix chain 'Al' and resid 24 through 31 removed outlier: 4.301A pdb=" N ARGAl 28 " --> pdb=" O PROAl 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N METAl 29 " --> pdb=" O GLNAl 25 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYSAl 30 " --> pdb=" O TRPAl 26 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N THRAl 31 " --> pdb=" O ILEAl 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Al' and resid 24 through 31' 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: 5.703A pdb=" N GLYAo 47 " --> pdb=" O ARGAo 43 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 19 through 35 removed outlier: 3.989A pdb=" N LYSAp 28 " --> pdb=" O LYSAp 24 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILEAp 29 " --> pdb=" O METAp 25 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 73 through 91 removed outlier: 5.823A pdb=" N LYSAp 90 " --> pdb=" O LEUAp 86 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASPAp 91 " --> pdb=" O LYSAp 87 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 9 through 14 removed outlier: 3.684A pdb=" N GLYAp 12 " --> pdb=" O GLYAp 9 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYSAp 13 " --> pdb=" O ILEAp 10 " (cutoff:3.500A) Processing helix chain 'At' and resid 2 through 11 Processing helix chain 'At' and resid 85 through 99 removed outlier: 5.836A pdb=" N THRAt 89 " --> pdb=" O ASNAt 85 " (cutoff:3.500A) Processing helix chain 'At' and resid 106 through 123 removed outlier: 3.690A 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: 3.971A pdb=" N LYSAu 95 " --> pdb=" O LYSAu 91 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASNAu 96 " --> pdb=" O LYSAu 92 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYSAu 97 " --> pdb=" O LEUAu 93 " (cutoff:3.500A) Processing helix chain 'Au' and resid 98 through 107 removed outlier: 3.746A pdb=" N LEUAu 103 " --> pdb=" O LEUAu 99 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALAAu 104 " --> pdb=" O VALAu 100 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYSAu 106 " --> pdb=" O LYSAu 102 " (cutoff:3.500A) removed outlier: 3.582A 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: 4.304A pdb=" N LYSAu 147 " --> pdb=" O ASNAu 143 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SERAu 153 " --> pdb=" O ASPAu 149 " (cutoff:3.500A) Processing helix chain 'Au' and resid 175 through 195 removed outlier: 4.419A pdb=" N PHEAu 189 " --> pdb=" O LEUAu 185 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEUAu 190 " --> pdb=" O ALAAu 186 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYSAu 195 " --> pdb=" O VALAu 191 " (cutoff:3.500A) Processing helix chain 'Au' and resid 197 through 202 removed outlier: 4.912A pdb=" N ASNAu 200 " --> pdb=" O ASNAu 197 " (cutoff:3.500A) removed outlier: 3.993A 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: 5.811A pdb=" N ASPAq 44 " --> pdb=" O LYSAq 40 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 77 through 87 removed outlier: 4.073A pdb=" N LYSAq 86 " --> pdb=" O ILEAq 82 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLUAq 87 " --> pdb=" O LYSAq 83 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 106 through 118 removed outlier: 3.894A pdb=" N VALAq 110 " --> pdb=" O PHEAq 106 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASNAq 111 " --> pdb=" O ASPAq 107 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N HISAq 118 " --> pdb=" O ARGAq 114 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 128 through 137 removed outlier: 4.379A pdb=" N GLNAq 137 " --> pdb=" O LEUAq 133 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 147 through 154 removed outlier: 3.790A pdb=" N ILEAq 151 " --> pdb=" O HISAq 147 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASPAq 153 " --> pdb=" O HISAq 149 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 157 through 162 removed outlier: 6.812A pdb=" N GLUAq 161 " --> pdb=" O SERAq 157 " (cutoff:3.500A) Processing helix chain 'AK' and resid 5 through 24 removed outlier: 6.365A pdb=" N TRPAK 9 " --> pdb=" O ASPAK 5 " (cutoff:3.500A) removed outlier: 4.414A 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: 4.441A pdb=" N METAK 61 " --> pdb=" O LYSAK 57 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARGAK 62 " --> pdb=" O ASNAK 58 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYSAK 63 " --> pdb=" O THRAK 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALAAK 64 " --> pdb=" O METAK 60 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ILEAK 65 " --> pdb=" O METAK 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLUAK 70 " --> pdb=" O ARGAK 66 " (cutoff:3.500A) Processing helix chain 'AK' and resid 99 through 104 removed outlier: 5.864A pdb=" N ARGAK 103 " --> pdb=" O ARGAK 99 " (cutoff:3.500A) Processing helix chain 'AK' and resid 134 through 142 removed outlier: 5.639A pdb=" N PHEAK 138 " --> pdb=" O LYSAK 134 " (cutoff:3.500A) Processing helix chain 'AK' and resid 168 through 179 Processing helix chain 'AK' and resid 74 through 81 removed outlier: 4.187A pdb=" N LYSAK 77 " --> pdb=" O ALAAK 74 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEUAK 78 " --> pdb=" O LEUAK 75 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUAK 79 " --> pdb=" O GLUAK 76 " (cutoff:3.500A) Proline residue: AK 80 - end of helix No H-bonds generated for 'chain 'AK' and resid 74 through 81' Processing helix chain 'Ct' and resid 5 through 13 removed outlier: 3.845A pdb=" N ILECt 12 " --> pdb=" O GLNCt 8 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N METCt 13 " --> pdb=" O ILECt 9 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 31 through 44 removed outlier: 4.767A pdb=" N LEUCt 35 " --> pdb=" O GLYCt 31 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.790A 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 Processing helix chain 'Ct' and resid 170 through 191 Processing helix chain 'Ct' and resid 224 through 235 removed outlier: 4.267A pdb=" N PHECt 228 " --> pdb=" O THRCt 224 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N METCt 231 " --> pdb=" O GLNCt 227 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALACt 234 " --> pdb=" O GLUCt 230 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 245 through 263 removed outlier: 4.210A pdb=" N LYSCt 251 " --> pdb=" O ALACt 247 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TRPCt 261 " --> pdb=" O METCt 257 " (cutoff:3.500A) removed outlier: 5.432A 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: 4.397A pdb=" N GLNCt 291 " --> pdb=" O ARGCt 287 " (cutoff:3.500A) removed outlier: 6.099A 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: 4.417A pdb=" N GLUCt 317 " --> pdb=" O ALACt 313 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYSCt 318 " --> pdb=" O LYSCt 314 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 325 through 330 removed outlier: 4.617A pdb=" N ASPCt 329 " --> pdb=" O SERCt 325 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 333 through 344 removed outlier: 5.654A pdb=" N LYSCt 337 " --> pdb=" O LYSCt 333 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEUCt 344 " --> pdb=" O METCt 340 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 345 through 358 removed outlier: 4.270A pdb=" N ALACt 349 " --> pdb=" O PROCt 345 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEUCt 350 " --> pdb=" O ALACt 346 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N HISCt 357 " --> pdb=" O METCt 353 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEUCt 358 " --> pdb=" O ILECt 354 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 360 through 373 removed outlier: 5.751A pdb=" N GLUCt 370 " --> pdb=" O LYSCt 366 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEUCt 371 " --> pdb=" O TYRCt 367 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 379 through 388 removed outlier: 6.540A pdb=" N METCt 383 " --> pdb=" O ASPCt 379 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLYCt 384 " --> pdb=" O GLUCt 380 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 474 through 479 removed outlier: 4.652A pdb=" N PHECt 478 " --> pdb=" O GLYCt 474 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 513 through 532 removed outlier: 4.797A pdb=" N LEUCt 517 " --> pdb=" O ASNCt 513 " (cutoff:3.500A) Proline residue: Ct 518 - end of helix Proline residue: Ct 532 - end of helix Processing helix chain 'Ct' and resid 550 through 564 removed outlier: 4.722A pdb=" N ASPCt 564 " --> pdb=" O ASPCt 560 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 612 through 620 removed outlier: 3.904A pdb=" N ASPCt 618 " --> pdb=" O ALACt 614 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 627 through 638 removed outlier: 3.934A pdb=" N TYRCt 634 " --> pdb=" O GLNCt 630 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEUCt 635 " --> pdb=" O ARGCt 631 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 642 through 649 Processing helix chain 'Ct' and resid 673 through 690 removed outlier: 4.940A pdb=" N ASPCt 677 " --> pdb=" O ASNCt 673 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SERCt 678 " --> pdb=" O GLUCt 674 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLYCt 690 " --> pdb=" O ALACt 686 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 717 through 737 removed outlier: 5.701A pdb=" N ILECt 721 " --> pdb=" O GLYCt 717 " (cutoff:3.500A) Proline residue: Ct 723 - end of helix removed outlier: 4.010A pdb=" N ALACt 736 " --> pdb=" O SERCt 732 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLNCt 737 " --> pdb=" O VALCt 733 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 753 through 767 removed outlier: 4.482A pdb=" N GLYCt 757 " --> pdb=" O GLUCt 753 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLYCt 758 " --> pdb=" O GLNCt 754 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLYCt 761 " --> pdb=" O GLYCt 757 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VALCt 762 " --> pdb=" O GLYCt 758 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEUCt 763 " --> pdb=" O ILECt 759 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASNCt 764 " --> pdb=" O TYRCt 760 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 789 through 794 removed outlier: 4.202A 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: 4.361A pdb=" N ARGCt 841 " --> pdb=" O GLUCt 837 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYSCt 842 " --> pdb=" O THRCt 838 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 849 through 854 removed outlier: 4.865A pdb=" N PHECt 853 " --> pdb=" O ALACt 849 " (cutoff:3.500A) removed outlier: 4.144A 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 'AA' and resid 47 through 50 removed outlier: 3.834A pdb=" N ASPAA 47 " --> pdb=" O LYSAA 60 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYSAA 60 " --> pdb=" O LYSAA 46 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'AA' and resid 110 through 114 removed outlier: 3.916A pdb=" N THRAA 111 " --> pdb=" O VALAA 136 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SERAA 154 " --> pdb=" O LEUAA 150 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'AA' and resid 58 through 65 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'BA' and resid 24 through 28 removed outlier: 5.513A pdb=" N HISBA 24 " --> pdb=" O ILEBA 49 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYRBA 47 " --> pdb=" O GLYBA 26 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THRBA 28 " --> pdb=" O GLYBA 45 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLYBA 45 " --> pdb=" O THRBA 28 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'BA' and resid 121 through 125 Processing sheet with id= 6, first strand: chain 'AB' and resid 53 through 59 removed outlier: 6.815A pdb=" N ILEAB 78 " --> pdb=" O ALAAB 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEUAB 347 " --> pdb=" O PHEAB 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYSAB 50 " --> pdb=" O ARGAB 343 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARGAB 343 " --> pdb=" O LYSAB 50 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VALAB 344 " --> pdb=" O VALAB 222 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VALAB 222 " --> pdb=" O VALAB 344 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N HISAB 275 " --> pdb=" O THRAB 223 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'AB' and resid 98 through 102 removed outlier: 7.073A pdb=" N GLYAB 91 " --> pdb=" O PHEAB 102 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VALAB 87 " --> pdb=" O ALAAB 107 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'AB' and resid 180 through 184 Processing sheet with id= 9, first strand: chain 'AB' and resid 286 through 290 removed outlier: 3.974A pdb=" N LYSAB 286 " --> pdb=" O METAB 332 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLYAB 288 " --> pdb=" O PHEAB 330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHEAB 330 " --> pdb=" O GLYAB 288 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLYAB 290 " --> pdb=" O ASNAB 328 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASNAB 328 " --> pdb=" O GLYAB 290 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'AB' and resid 76 through 80 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'AB' and resid 84 through 88 removed outlier: 6.275A pdb=" N ILEAB 163 " --> pdb=" O VALAB 87 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'AB' and resid 84 through 87 removed outlier: 4.124A pdb=" N GLNAB 203 " --> pdb=" O VALAB 86 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'AB' and resid 215 through 218 removed outlier: 4.160A pdb=" N GLUAB 215 " --> pdb=" O ILEAB 284 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYSAB 282 " --> pdb=" O ILEAB 217 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'BB' and resid 45 through 48 removed outlier: 4.284A pdb=" N GLYBB 45 " --> pdb=" O VALBB 33 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'BB' and resid 66 through 70 removed outlier: 8.005A pdb=" N HISBB 101 " --> pdb=" O METBB 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEUBB 105 " --> pdb=" O ARGBB 213 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ARGBB 213 " --> pdb=" O LEUBB 105 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYSBB 214 " --> pdb=" O PHEBB 138 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THRBB 143 " --> pdb=" O THRBB 119 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THRBB 119 " --> pdb=" O THRBB 143 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'AC' and resid 6 through 10 No H-bonds generated for sheet with id= 16 Processing sheet with id= 17, first strand: chain 'AC' and resid 207 through 210 Processing sheet with id= 18, first strand: chain 'BC' and resid 103 through 107 removed outlier: 4.292A pdb=" N LYSBC 103 " --> pdb=" O GLYBC 131 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHEBC 127 " --> pdb=" O LEUBC 107 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'BC' and resid 183 through 187 removed outlier: 4.226A pdb=" N ALABC 198 " --> pdb=" O ASPBC 221 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASPBC 221 " --> pdb=" O ALABC 198 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALBC 205 " --> pdb=" O CYSBC 222 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THRBC 224 " --> pdb=" O VALBC 205 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'BC' and resid 124 through 132 Processing sheet with id= 21, first strand: chain 'BD' and resid 34 through 42 removed outlier: 7.331A pdb=" N TYRBD 34 " --> pdb=" O THRBD 53 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THRBD 53 " --> pdb=" O TYRBD 34 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLUBD 47 " --> pdb=" O ARGBD 40 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THRBD 42 " --> pdb=" O ARGBD 45 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARGBD 45 " --> pdb=" O THRBD 42 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'BD' and resid 148 through 155 removed outlier: 3.725A pdb=" N GLYBD 140 " --> pdb=" O LYSBD 148 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLYBD 133 " --> pdb=" O METBD 189 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'BF' and resid 123 through 127 Processing sheet with id= 24, first strand: chain 'BK' and resid 20 through 24 removed outlier: 3.769A pdb=" N METBK 21 " --> pdb=" O TRPBK 69 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'BM' and resid 74 through 80 removed outlier: 4.100A pdb=" N ASNBM 75 " --> pdb=" O HISBM 48 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SERBM 107 " --> pdb=" O ALABM 53 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'BP' and resid 75 through 78 removed outlier: 4.154A pdb=" N SERBP 92 " --> pdb=" O ILEBP 107 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BQ' and resid 9 through 15 removed outlier: 5.653A pdb=" N ALABQ 21 " --> pdb=" O GLYBQ 14 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THRBQ 20 " --> pdb=" O LYSBQ 73 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BT' and resid 81 through 86 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'BT' and resid 113 through 117 removed outlier: 6.435A pdb=" N GLUBT 114 " --> pdb=" O ARGBT 121 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARGBT 121 " --> pdb=" O GLUBT 114 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASPBT 116 " --> pdb=" O GLYBT 119 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BU' and resid 56 through 66 removed outlier: 5.569A pdb=" N LYSBU 86 " --> pdb=" O PROBU 57 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEUBU 61 " --> pdb=" O METBU 82 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N METBU 82 " --> pdb=" O LEUBU 61 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILEBU 20 " --> pdb=" O LEUBU 91 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLYBU 109 " --> pdb=" O ARGBU 27 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BZ' and resid 97 through 100 removed outlier: 7.467A pdb=" N ILEBZ 108 " --> pdb=" O VALBZ 100 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Bc' and resid 9 through 13 Processing sheet with id= 33, first strand: chain 'Bc' and resid 18 through 22 removed outlier: 3.738A pdb=" N GLYBc 19 " --> pdb=" O GLNBc 29 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Bf' and resid 138 through 141 No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'Bg' and resid 3 through 8 removed outlier: 6.927A pdb=" N VALBg 309 " --> pdb=" O ARGBg 8 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLYBg 9 " --> pdb=" O VALBg 309 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Bg' and resid 19 through 23 removed outlier: 4.784A pdb=" N GLNBg 20 " --> pdb=" O ALABg 34 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASPBg 29 " --> pdb=" O LEUBg 45 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N METBg 42 " --> pdb=" O GLNBg 56 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYRBg 52 " --> pdb=" O THRBg 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Bg' and resid 67 through 72 removed outlier: 5.661A pdb=" N PHEBg 77 " --> pdb=" O SERBg 72 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THRBg 86 " --> pdb=" O SERBg 82 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARGBg 99 " --> pdb=" O LEUBg 89 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Bg' and resid 109 through 114 removed outlier: 5.520A pdb=" N GLNBg 119 " --> pdb=" O SERBg 114 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THRBg 128 " --> pdb=" O SERBg 124 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Bg' and resid 153 through 158 removed outlier: 5.655A pdb=" N CYSBg 153 " --> pdb=" O CYSBg 168 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILEBg 164 " --> pdb=" O SERBg 157 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VALBg 176 " --> pdb=" O LYSBg 185 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Bg' and resid 197 through 201 removed outlier: 5.676A pdb=" N LEUBg 206 " --> pdb=" O SERBg 201 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SERBg 205 " --> pdb=" O LEUBg 221 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLYBg 214 " --> pdb=" O GLYBg 232 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYRBg 228 " --> pdb=" O LEUBg 218 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Bg' and resid 238 through 242 removed outlier: 3.798A pdb=" N ALABg 238 " --> pdb=" O ALABg 251 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TRPBg 247 " --> pdb=" O SERBg 242 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N TYRBg 246 " --> pdb=" O LEUBg 261 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SERBg 255 " --> pdb=" O THRBg 252 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILEBg 258 " --> pdb=" O VALBg 267 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILEBg 265 " --> pdb=" O ASPBg 260 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Bg' and resid 288 through 292 removed outlier: 3.541A pdb=" N SERBg 288 " --> pdb=" O GLYBg 301 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THRBg 297 " --> pdb=" O SERBg 292 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Bg' and resid 39 through 42 removed outlier: 3.853A pdb=" N ARGBg 57 " --> pdb=" O METBg 42 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Bg' and resid 173 through 176 removed outlier: 3.650A pdb=" N THRBg 186 " --> pdb=" O VALBg 176 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Bg' and resid 255 through 258 removed outlier: 3.867A pdb=" N ASPBg 268 " --> pdb=" O ILEBg 258 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Bg' and resid 296 through 301 removed outlier: 7.133A pdb=" N GLNBg 296 " --> pdb=" O VALBg 312 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BE' and resid 87 through 91 removed outlier: 4.281A pdb=" N ASPBE 88 " --> pdb=" O LEUBE 101 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BE' and resid 123 through 126 removed outlier: 4.515A pdb=" N ASPBE 158 " --> pdb=" O VALBE 126 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYSBE 168 " --> pdb=" O ASPBE 163 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BE' and resid 129 through 133 removed outlier: 6.859A pdb=" N THRBE 130 " --> pdb=" O PROBE 137 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLYBE 132 " --> pdb=" O GLYBE 135 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARGBE 145 " --> pdb=" O THRBE 141 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BE' and resid 180 through 184 removed outlier: 3.640A pdb=" N ARGBE 191 " --> pdb=" O VALBE 183 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BE' and resid 196 through 200 Processing sheet with id= 52, first strand: chain 'BE' and resid 158 through 161 removed outlier: 3.678A pdb=" N GLNBE 161 " --> pdb=" O ASNBE 171 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASNBE 171 " --> pdb=" O GLNBE 161 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'BG' and resid 11 through 18 removed outlier: 6.187A pdb=" N ASNBG 110 " --> pdb=" O SERBG 53 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VALBG 49 " --> pdb=" O VALBG 114 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYRBG 48 " --> pdb=" O ALABG 38 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEBG 52 " --> pdb=" O THRBG 34 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THRBG 34 " --> pdb=" O ILEBG 52 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BG' and resid 159 through 164 removed outlier: 6.913A pdb=" N LYSBG 168 " --> pdb=" O LYSBG 164 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BG' and resid 54 through 57 removed outlier: 3.853A pdb=" N GLYBG 54 " --> pdb=" O ASNBG 110 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BH' and resid 47 through 53 removed outlier: 4.643A pdb=" N ALABH 47 " --> pdb=" O PHEBH 63 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARGBH 57 " --> pdb=" O VALBH 53 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N HISBH 91 " --> pdb=" O LYSBH 58 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'BH' and resid 141 through 146 removed outlier: 3.699A pdb=" N GLYBH 141 " --> pdb=" O HISBH 157 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BI' and resid 42 through 48 removed outlier: 6.940A pdb=" N ARGBI 42 " --> pdb=" O LEUBI 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASNBI 52 " --> pdb=" O VALBI 48 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'BI' and resid 71 through 76 removed outlier: 3.964A pdb=" N CYSBI 72 " --> pdb=" O TRPBI 67 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLYBI 68 " --> pdb=" O VALBI 189 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYSBI 100 " --> pdb=" O ILEBI 175 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'BL' and resid 71 through 76 removed outlier: 5.366A pdb=" N ARGBL 71 " --> pdb=" O GLUBL 130 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THRBL 127 " --> pdb=" O LEUBL 143 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'BL' and resid 85 through 95 No H-bonds generated for sheet with id= 61 Processing sheet with id= 62, first strand: chain 'BO' and resid 40 through 46 removed outlier: 3.540A pdb=" N LYSBO 125 " --> pdb=" O THRBO 91 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILEBO 95 " --> pdb=" O GLYBO 127 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'BV' and resid 15 through 18 removed outlier: 4.521A pdb=" N ARGBV 15 " --> pdb=" O ILEBV 24 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARGBV 22 " --> pdb=" O CYSBV 17 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'BV' and resid 32 through 38 removed outlier: 5.965A pdb=" N GLNBV 49 " --> pdb=" O GLUBV 38 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'BW' and resid 23 through 28 removed outlier: 6.698A pdb=" N ARGBW 23 " --> pdb=" O LEUBW 65 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VALBW 25 " --> pdb=" O VALBW 63 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VALBW 63 " --> pdb=" O VALBW 25 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALABW 58 " --> pdb=" O ASPBW 55 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASPBW 55 " --> pdb=" O ALABW 58 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLUBW 49 " --> pdb=" O ASNBW 64 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THRBW 66 " --> pdb=" O ILEBW 47 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILEBW 47 " --> pdb=" O THRBW 66 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'BW' and resid 71 through 74 removed outlier: 3.938A pdb=" N GLYBW 127 " --> pdb=" O VALBW 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VALBW 103 " --> pdb=" O GLYBW 127 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'BX' and resid 46 through 51 removed outlier: 4.864A pdb=" N ASPBX 98 " --> pdb=" O VALBX 51 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEUBX 101 " --> pdb=" O VALBX 123 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'BX' and resid 52 through 59 removed outlier: 3.515A pdb=" N GLUBX 53 " --> pdb=" O ARGBX 71 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALABX 65 " --> pdb=" O ALABX 59 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VALBX 70 " --> pdb=" O ALABX 83 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LYSBX 79 " --> pdb=" O LEUBX 74 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'BY' and resid 5 through 10 removed outlier: 3.657A pdb=" N THRBY 6 " --> pdb=" O LEUBY 28 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VALBY 24 " --> pdb=" O ARGBY 10 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYSBY 11 " --> pdb=" O VALBY 24 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'BY' and resid 54 through 61 removed outlier: 6.590A pdb=" N VALBY 54 " --> pdb=" O TYRBY 76 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHEBY 60 " --> pdb=" O THRBY 70 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THRBY 70 " --> pdb=" O PHEBY 60 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'BY' and resid 20 through 30 Processing sheet with id= 72, first strand: chain 'Ba' and resid 36 through 43 Processing sheet with id= 73, first strand: chain 'Bb' and resid 43 through 47 Processing sheet with id= 74, first strand: chain 'Bb' and resid 54 through 57 removed outlier: 6.769A pdb=" N VALBb 54 " --> pdb=" O LEUBb 63 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THRBb 61 " --> pdb=" O CYSBb 56 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Bb' and resid 64 through 67 removed outlier: 3.654A pdb=" N ARGBb 72 " --> pdb=" O GLNBb 65 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THRBb 67 " --> pdb=" O LYSBb 70 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYSBb 70 " --> pdb=" O THRBb 67 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'AD' and resid 60 through 66 removed outlier: 3.910A pdb=" N VALAD 53 " --> pdb=" O ASPAD 147 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'AE' and resid 186 through 190 removed outlier: 4.782A pdb=" N ARGAE 187 " --> pdb=" O VALAE 175 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VALAE 175 " --> pdb=" O ARGAE 187 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEUAE 174 " --> pdb=" O LEUAE 165 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYSAE 160 " --> pdb=" O ILEAE 152 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THRAE 148 " --> pdb=" O PHEAE 164 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LYSAE 166 " --> pdb=" O PROAE 146 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILEAE 149 " --> pdb=" O THRAE 197 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'AF' and resid 139 through 144 removed outlier: 7.926A pdb=" N TYRAF 139 " --> pdb=" O ILEAF 95 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASNAF 119 " --> pdb=" O ARGAF 94 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHEAF 118 " --> pdb=" O LEUAF 213 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'AF' and resid 158 through 161 removed outlier: 8.883A pdb=" N GLYAF 158 " --> pdb=" O LEUAF 169 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'AG' and resid 180 through 185 Processing sheet with id= 81, first strand: chain 'AH' and resid 5 through 12 removed outlier: 5.123A pdb=" N LYSAH 53 " --> pdb=" O ILEAH 12 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'AH' and resid 17 through 20 Processing sheet with id= 83, first strand: chain 'AH' and resid 102 through 106 removed outlier: 6.417A pdb=" N LEUAH 111 " --> pdb=" O GLNAH 106 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SERAH 110 " --> pdb=" O METAH 128 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'AH' and resid 132 through 137 removed outlier: 5.480A pdb=" N GLUAH 143 " --> pdb=" O SERAH 137 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASPAH 142 " --> pdb=" O SERAH 94 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'AI' and resid 85 through 90 removed outlier: 7.070A pdb=" N ILEAI 135 " --> pdb=" O ARGAI 90 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N METAI 136 " --> pdb=" O METAI 52 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'AI' and resid 189 through 192 removed outlier: 6.362A pdb=" N ARGAI 189 " --> pdb=" O ILEAI 200 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILEAI 200 " --> pdb=" O ARGAI 189 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'AJ' and resid 19 through 26 removed outlier: 5.328A pdb=" N ILEAJ 68 " --> pdb=" O VALAJ 26 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALAAJ 69 " --> pdb=" O SERAJ 51 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'AJ' and resid 104 through 110 removed outlier: 5.791A pdb=" N PHEAJ 130 " --> pdb=" O PHEAJ 107 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'AL' and resid 57 through 60 Processing sheet with id= 90, first strand: chain 'AM' and resid 10 through 16 removed outlier: 3.905A pdb=" N ARGAM 11 " --> pdb=" O ILEAM 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYSAM 23 " --> pdb=" O VALAM 15 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEUAM 37 " --> pdb=" O VALAM 28 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'AN' and resid 35 through 39 removed outlier: 6.239A pdb=" N ALAAN 35 " --> pdb=" O ARGAN 65 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILEAN 61 " --> pdb=" O ALAAN 39 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLYAN 58 " --> pdb=" O ASPAN 136 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILEAN 133 " --> pdb=" O LEUAN 116 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'AN' and resid 117 through 121 removed outlier: 3.818A pdb=" N ASNAN 117 " --> pdb=" O ILEAN 133 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHEAN 129 " --> pdb=" O VALAN 121 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'AO' and resid 5 through 10 Processing sheet with id= 94, first strand: chain 'AP' and resid 16 through 20 removed outlier: 6.713A pdb=" N ILEAP 149 " --> pdb=" O GLUAP 115 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'AP' and resid 116 through 122 Processing sheet with id= 96, first strand: chain 'AP' and resid 124 through 131 No H-bonds generated for sheet with id= 96 Processing sheet with id= 97, first strand: chain 'AQ' and resid 118 through 121 removed outlier: 3.586A pdb=" N LYSAQ 119 " --> pdb=" O LEUAQ 98 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALAAQ 102 " --> pdb=" O LEUAQ 121 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYSAQ 99 " --> pdb=" O LYSAQ 78 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'AS' and resid 27 through 34 removed outlier: 3.662A pdb=" N VALAS 12 " --> pdb=" O METAS 30 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VALAS 13 " --> pdb=" O VALAS 62 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'AS' and resid 91 through 99 removed outlier: 4.109A pdb=" N ASNAS 77 " --> pdb=" O ILEAS 132 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYSAS 128 " --> pdb=" O TRPAS 81 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'AS' and resid 9 through 13 removed outlier: 4.809A pdb=" N GLUAS 9 " --> pdb=" O VALAS 67 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'AT' and resid 39 through 43 removed outlier: 4.028A pdb=" N LYSAT 60 " --> pdb=" O ILEAT 42 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VALAT 80 " --> pdb=" O LYSAT 83 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYSAT 83 " --> pdb=" O VALAT 80 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'AU' and resid 69 through 74 removed outlier: 6.283A pdb=" N GLUAU 108 " --> pdb=" O LYSAU 20 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEUAU 112 " --> pdb=" O ASPAU 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARGAU 113 " --> pdb=" O ARGAU 101 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARGAU 101 " --> pdb=" O ARGAU 113 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'AV' and resid 82 through 85 removed outlier: 4.639A pdb=" N ARGAV 85 " --> pdb=" O ASPAV 100 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASPAV 100 " --> pdb=" O ARGAV 85 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASNAV 101 " --> pdb=" O VALAV 25 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALAAV 24 " --> pdb=" O ILEAV 39 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYSAV 35 " --> pdb=" O CYSAV 28 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N METAV 62 " --> pdb=" O ILEAV 40 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'AV' and resid 78 through 81 Processing sheet with id=105, first strand: chain 'AW' and resid 18 through 22 Processing sheet with id=106, first strand: chain 'AX' and resid 95 through 100 removed outlier: 3.747A pdb=" N GLUAX 133 " --> pdb=" O ARGAX 129 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'AY' and resid 72 through 75 removed outlier: 3.629A pdb=" N GLNAY 72 " --> pdb=" O TYRAY 81 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'AY' and resid 86 through 89 removed outlier: 5.025A pdb=" N THRAY 93 " --> pdb=" O LYSAY 89 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'AZ' and resid 9 through 14 removed outlier: 4.525A pdb=" N LYSAZ 9 " --> pdb=" O ILEAZ 25 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VALAZ 13 " --> pdb=" O ARGAZ 21 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARGAZ 21 " --> pdb=" O VALAZ 13 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEUAZ 42 " --> pdb=" O VALAZ 26 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'Ac' and resid 69 through 75 removed outlier: 3.963A pdb=" N LEUAc 45 " --> pdb=" O ILEAc 96 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'Ad' and resid 61 through 64 removed outlier: 4.723A pdb=" N ASPAd 61 " --> pdb=" O LEUAd 102 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VALAd 21 " --> pdb=" O ARGAd 90 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THRAd 22 " --> pdb=" O VALAd 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VALAd 120 " --> pdb=" O GLUAd 24 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'Ae' and resid 74 through 80 Processing sheet with id=113, first strand: chain 'Af' and resid 67 through 74 removed outlier: 5.031A pdb=" N LYSAf 45 " --> pdb=" O VALAf 74 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARGAf 46 " --> pdb=" O METAf 104 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VALAf 50 " --> pdb=" O ARGAf 100 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARGAf 100 " --> pdb=" O VALAf 50 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEUAf 27 " --> pdb=" O ALAAf 12 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'Ag' and resid 20 through 24 Processing sheet with id=115, first strand: chain 'Ak' and resid 2 through 5 removed outlier: 4.610A pdb=" N VALAk 46 " --> pdb=" O ILEAk 5 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SERAk 22 " --> pdb=" O ARGAk 37 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYSAk 27 " --> pdb=" O LEUAk 69 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'Ao' and resid 20 through 25 removed outlier: 4.273A pdb=" N ILEAo 66 " --> pdb=" O ILEAo 85 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SERAo 79 " --> pdb=" O CYSAo 72 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'Ap' and resid 47 through 50 removed outlier: 5.482A pdb=" N ILEAp 54 " --> pdb=" O ARGAp 50 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLYAp 53 " --> pdb=" O GLYAp 66 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'At' and resid 46 through 53 removed outlier: 8.468A pdb=" N ARGAt 46 " --> pdb=" O ARGAt 67 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARGAt 67 " --> pdb=" O ARGAt 46 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THRAt 48 " --> pdb=" O LYSAt 65 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N SERAt 76 " --> pdb=" O ARGAt 66 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'Au' and resid 50 through 53 Processing sheet with id=120, first strand: chain 'Au' and resid 110 through 113 Processing sheet with id=121, first strand: chain 'Au' and resid 163 through 168 removed outlier: 6.090A pdb=" N LEUAu 163 " --> pdb=" O LEUAu 38 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEUAu 204 " --> pdb=" O LEUAu 216 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'Aq' and resid 13 through 18 removed outlier: 3.819A pdb=" N THRAq 59 " --> pdb=" O THRAq 18 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VALAq 60 " --> pdb=" O PROAq 75 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'AK' and resid 51 through 55 removed outlier: 3.854A pdb=" N LYSAK 26 " --> pdb=" O THRAK 91 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILEAK 29 " --> pdb=" O GLNAK 190 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'AK' and resid 125 through 129 removed outlier: 4.535A pdb=" N GLNAK 126 " --> pdb=" O ILEAK 154 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILEAK 154 " --> pdb=" O GLNAK 126 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILEAK 152 " --> pdb=" O THRAK 128 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THRAK 144 " --> pdb=" O LEUAK 155 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'AK' and resid 26 through 29 removed outlier: 3.594A pdb=" N GLNAK 191 " --> pdb=" O ILEAK 29 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'Ct' and resid 72 through 80 removed outlier: 3.759A pdb=" N SERCt 105 " --> pdb=" O VALCt 24 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALACt 26 " --> pdb=" O SERCt 105 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYSCt 152 " --> pdb=" O ASPCt 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALACt 125 " --> pdb=" O LYSCt 152 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THRCt 211 " --> pdb=" O PROCt 153 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'Ct' and resid 395 through 399 Processing sheet with id=128, first strand: chain 'Ct' and resid 400 through 403 removed outlier: 4.123A pdb=" N LYSCt 400 " --> pdb=" O PHECt 413 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'Ct' and resid 504 through 509 removed outlier: 4.721A pdb=" N HISCt 544 " --> pdb=" O VALCt 509 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'Ct' and resid 579 through 583 removed outlier: 6.624A pdb=" N LYSCt 785 " --> pdb=" O PHECt 771 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain 'Ct' and resid 590 through 595 removed outlier: 5.678A pdb=" N ASNCt 600 " --> pdb=" O SERCt 595 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYRCt 603 " --> pdb=" O HISCt 705 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VALCt 704 " --> pdb=" O THRCt 663 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 'Ct' and resid 599 through 603 removed outlier: 9.231A pdb=" N HISCt 599 " --> pdb=" O HISCt 710 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HISCt 710 " --> pdb=" O HISCt 599 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASPCt 706 " --> pdb=" O TYRCt 603 " (cutoff:3.500A) Processing sheet with id=133, first strand: chain 'Ct' and resid 745 through 751 removed outlier: 6.351A pdb=" N GLUCt 748 " --> pdb=" O GLNCt 811 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHECt 809 " --> pdb=" O GLNCt 750 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'Ct' and resid 740 through 745 No H-bonds generated for sheet with id=134 Processing sheet with id=135, first strand: chain 'Ct' and resid 772 through 775 removed outlier: 3.665A pdb=" N GLUCt 772 " --> pdb=" O LYSCt 785 " (cutoff:3.500A) 3847 hydrogen bonds defined for protein. 11436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4300 hydrogen bonds 7196 hydrogen bond angles 0 basepair planarities 1672 basepair parallelities 3035 stacking parallelities Total time for adding SS restraints: 440.30 Time building geometry restraints manager: 78.13 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: 38253 1.33 - 1.45: 91855 1.45 - 1.58: 99322 1.58 - 1.70: 11496 1.70 - 1.82: 747 Bond restraints: 241673 Sorted by residual: bond pdb=" N3B GNPCt 901 " pdb=" PG GNPCt 901 " ideal model delta sigma weight residual 1.801 1.704 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" O5' GNPCt 901 " pdb=" PA GNPCt 901 " ideal model delta sigma weight residual 1.660 1.572 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C ARGAu 60 " pdb=" N PROAu 61 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.47e+01 bond pdb=" C LEUAG 170 " pdb=" N PROAG 171 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.07e+01 bond pdb=" C ASPBD 162 " pdb=" N PROBD 163 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.90e+00 ... (remaining 241668 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.87: 27054 104.87 - 112.86: 140019 112.86 - 120.86: 116624 120.86 - 128.85: 65131 128.85 - 136.85: 5245 Bond angle restraints: 354073 Sorted by residual: angle pdb=" C ALAAJ 53 " pdb=" N ARGAJ 54 " pdb=" CA ARGAJ 54 " ideal model delta sigma weight residual 121.54 134.87 -13.33 1.91e+00 2.74e-01 4.87e+01 angle pdb=" C GLUBI 132 " pdb=" N GLUBI 133 " pdb=" CA GLUBI 133 " ideal model delta sigma weight residual 122.36 131.81 -9.45 1.47e+00 4.63e-01 4.13e+01 angle pdb=" C ASPCt 463 " pdb=" N VALCt 464 " pdb=" CA VALCt 464 " ideal model delta sigma weight residual 122.13 133.16 -11.03 1.85e+00 2.92e-01 3.55e+01 angle pdb=" N ILECt 12 " pdb=" CA ILECt 12 " pdb=" C ILECt 12 " ideal model delta sigma weight residual 111.77 105.68 6.09 1.04e+00 9.25e-01 3.43e+01 angle pdb=" C VALBc 32 " pdb=" N GLUBc 33 " pdb=" CA GLUBc 33 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 ... (remaining 354068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 129371 35.97 - 71.95: 3880 71.95 - 107.92: 297 107.92 - 143.89: 19 143.89 - 179.86: 50 Dihedral angle restraints: 133617 sinusoidal: 96978 harmonic: 36639 Sorted by residual: 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 -110.88 -69.12 0 5.00e+00 4.00e-02 1.91e+02 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 -111.22 -68.78 0 5.00e+00 4.00e-02 1.89e+02 dihedral pdb=" CA ALAAq 29 " pdb=" C ALAAq 29 " pdb=" N PROAq 30 " pdb=" CA PROAq 30 " ideal model delta harmonic sigma weight residual -180.00 -127.66 -52.34 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 133614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 41267 0.083 - 0.165: 2528 0.165 - 0.248: 149 0.248 - 0.330: 20 0.330 - 0.413: 3 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 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB THRAL 63 " pdb=" CA THRAL 63 " pdb=" OG1 THRAL 63 " pdb=" CG2 THRAL 63 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.76e+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 3.10e+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 4.32e-02 1.87e+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 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CA22298 " 0.054 2.00e-02 2.50e+03 2.74e-02 1.69e+01 pdb=" N1 CA22298 " -0.058 2.00e-02 2.50e+03 pdb=" C2 CA22298 " -0.007 2.00e-02 2.50e+03 pdb=" O2 CA22298 " -0.005 2.00e-02 2.50e+03 pdb=" N3 CA22298 " 0.002 2.00e-02 2.50e+03 pdb=" C4 CA22298 " 0.010 2.00e-02 2.50e+03 pdb=" N4 CA22298 " 0.013 2.00e-02 2.50e+03 pdb=" C5 CA22298 " 0.004 2.00e-02 2.50e+03 pdb=" C6 CA22298 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYRAf 106 " -0.066 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PROAf 107 " 0.172 5.00e-02 4.00e+02 pdb=" CA PROAf 107 " -0.054 5.00e-02 4.00e+02 pdb=" CD PROAf 107 " -0.052 5.00e-02 4.00e+02 ... (remaining 23437 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.76: 36782 2.76 - 3.47: 289255 3.47 - 4.19: 669063 4.19 - 4.90: 948995 Nonbonded interactions: 1944097 Sorted by model distance: nonbonded pdb="MG MGB11914 " pdb="MG MGB11960 " model vdw 1.337 1.300 nonbonded pdb="MG MGA25133 " pdb="MG MGA25152 " model vdw 1.356 1.300 nonbonded pdb=" OP1 UA21618 " pdb="MG MGA25197 " model vdw 2.082 2.170 nonbonded pdb=" O3' AA24515 " pdb="MG MGA25189 " model vdw 2.086 2.170 nonbonded pdb=" OP1 GA24482 " pdb="MG MGA25295 " model vdw 2.090 2.170 ... (remaining 1944092 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: 0.150 Extract box with map and model: 26.540 Check model and map are aligned: 2.170 Convert atoms to be neutral: 1.230 Process input model: 854.960 Find NCS groups from input model: 5.710 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 897.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 241673 Z= 0.231 Angle : 0.812 15.145 354073 Z= 0.409 Chirality : 0.041 0.413 43967 Planarity : 0.006 0.099 23440 Dihedral : 14.041 179.864 109979 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.89 % Favored : 90.89 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.04 % Twisted Proline : 0.75 % Twisted General : 0.23 % 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: -3.81 (0.06), residues: 12536 helix: -2.39 (0.06), residues: 4198 sheet: -1.50 (0.11), residues: 1805 loop : -2.98 (0.06), residues: 6533 *********************** 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 5202 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 5178 time to evaluate : 10.337 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: 24 outliers final: 9 residues processed: 5193 average time/residue: 2.1292 time to fit residues: 18268.3481 Evaluate side-chains 3224 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 3215 time to evaluate : 10.321 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 1.7125 time to fit residues: 40.4965 ------------------------------------------------------------------------------- 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: 9.9990 chunk 759 optimal weight: 40.0000 chunk 467 optimal weight: 10.0000 chunk 923 optimal weight: 9.9990 chunk 731 optimal weight: 50.0000 chunk 1415 optimal weight: 0.9990 chunk 547 optimal weight: 20.0000 chunk 860 optimal weight: 9.9990 chunk 1053 optimal weight: 20.0000 chunk 1640 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 8 GLN AA 50 HIS AA 83 HIS ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 140 ASN ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 209 HIS AA 218 HIS BA 29 ASN BA 169 HIS AB 179 HIS AB 203 GLN AB 213 GLN AB 245 HIS AB 301 ASN AB 302 ASN AB 322 HIS AB 380 GLN BB 76 ASN BB 124 HIS BB 149 GLN BB 158 HIS AC 38 ASN ** AC 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 85 HIS AC 112 HIS AC 187 GLN AC 215 ASN BC 134 ASN BC 235 ASN BC 272 HIS BD 74 GLN ** BD 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 159 HIS BF 74 ASN BF 95 HIS BF 179 ASN BF 186 ASN ** BF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 42 ASN BK 61 GLN BM 55 ASN BM 72 HIS ** BP 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 114 HIS BQ 8 GLN ** BQ 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 17 ASN BS 19 ASN BS 120 HIS BS 125 HIS ** BT 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 137 GLN BZ 106 GLN BZ 112 ASN Bc 24 GLN Bc 26 GLN Bd 26 ASN Bf 91 ASN ** Bg 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 143 GLN Bg 187 ASN Bg 226 HIS Bg 311 GLN BE 161 GLN BE 171 ASN ** BE 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 230 ASN BE 232 ASN BG 4 ASN BG 56 ASN BG 70 HIS BG 202 ASN ** BG 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 157 HIS BI 181 GLN BJ 75 ASN BJ 124 HIS BJ 125 HIS ** BJ 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 140 GLN BJ 143 ASN BJ 156 HIS BL 11 GLN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BO 43 HIS BV 29 HIS ** BV 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 5 ASN BW 44 HIS BW 56 HIS BW 70 ASN BW 98 GLN BW 113 HIS BX 20 GLN ** BX 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 61 GLN ** BX 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 110 HIS BX 127 ASN BY 29 HIS Ba 25 ASN ** Bb 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AE 279 ASN AF 126 ASN AF 163 ASN AF 206 ASN ** AG 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 64 GLN AG 100 HIS AG 227 ASN ** AH 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 130 HIS AI 147 HIS ** AJ 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 115 GLN AL 175 ASN AL 188 ASN ** AM 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 86 HIS ** AN 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 109 HIS AN 182 HIS ** AN 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 199 GLN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 14 HIS AO 65 ASN AP 40 HIS ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 44 ASN AQ 57 ASN AR 58 HIS AR 141 HIS AR 178 GLN AS 92 ASN AS 125 GLN AT 90 ASN AU 38 ASN AV 101 ASN AW 45 ASN AW 50 ASN AY 56 GLN AY 61 HIS ** AZ 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 17 HIS Aa 60 HIS Aa 74 ASN Ab 12 GLN ** Ab 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Ac 19 GLN Ac 40 GLN Ad 34 HIS Ad 79 ASN Ae 107 ASN Af 24 HIS Af 99 HIS Ag 28 ASN Ag 73 HIS ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 12 ASN Aj 57 ASN Al 20 ASN Al 43 HIS Am 120 ASN Ao 3 ASN Ao 18 HIS Ao 25 GLN Ao 45 GLN Ap 56 HIS At 6 GLN ** At 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 70 GLN Au 21 ASN Au 143 ASN ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 188 ASN Au 197 ASN Au 199 GLN AK 34 ASN ** AK 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 179 ASN AK 195 ASN Ct 91 GLN Ct 145 GLN ** Ct 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 306 ASN Ct 492 HIS Ct 588 ASN Ct 626 GLN Ct 696 ASN Ct 705 HIS Ct 710 HIS ** Ct 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 769 HIS Total number of N/Q/H flips: 164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.127 241673 Z= 0.443 Angle : 0.771 17.280 354073 Z= 0.392 Chirality : 0.042 0.314 43967 Planarity : 0.007 0.127 23440 Dihedral : 15.042 179.754 83290 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.37 % Favored : 90.43 % Rotamer Outliers : 4.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.16 % 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: -2.44 (0.07), residues: 12536 helix: -0.46 (0.07), residues: 4235 sheet: -1.30 (0.12), residues: 1877 loop : -2.60 (0.07), residues: 6424 *********************** 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 3981 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 545 poor density : 3436 time to evaluate : 10.738 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 outliers start: 545 outliers final: 317 residues processed: 3695 average time/residue: 1.7734 time to fit residues: 11317.0813 Evaluate side-chains 3310 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 2993 time to evaluate : 10.693 Switching outliers to nearest non-outliers outliers start: 317 outliers final: 0 residues processed: 317 average time/residue: 1.4082 time to fit residues: 856.2207 ------------------------------------------------------------------------------- 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: 6.9990 chunk 508 optimal weight: 30.0000 chunk 1364 optimal weight: 3.9990 chunk 1116 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 1643 optimal weight: 6.9990 chunk 1774 optimal weight: 8.9990 chunk 1463 optimal weight: 6.9990 chunk 1629 optimal weight: 2.9990 chunk 560 optimal weight: 10.0000 chunk 1318 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 95 ASN BB 124 HIS ** BB 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 208 HIS ** AC 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 198 ASN BC 172 ASN ** BD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 ASN ** BF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BP 103 ASN BQ 80 GLN BZ 103 HIS Bd 26 ASN Bf 135 HIS ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 311 GLN BE 17 HIS BE 161 GLN ** BE 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 227 GLN BI 7 ASN BI 116 HIS ** BI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 168 GLN BJ 75 ASN BJ 113 GLN ** BJ 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 143 ASN BJ 177 ASN BL 19 ASN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BO 79 GLN BV 29 HIS BW 16 ASN ** BW 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BW 98 GLN ** BX 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 72 HIS AD 122 GLN AD 198 HIS ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AF 206 ASN ** AG 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 100 HIS AG 149 ASN ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 8 GLN AH 42 ASN AH 102 ASN AJ 10 ASN AJ 98 ASN AJ 104 ASN ** AJ 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 188 ASN ** AM 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 78 GLN AN 87 HIS AN 158 HIS ** AN 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AS 77 ASN AS 92 ASN AS 122 HIS AT 90 ASN AU 38 ASN AV 31 ASN AV 77 HIS AV 135 ASN AX 107 HIS AY 56 GLN Aa 25 HIS ** Aa 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 49 HIS ** Ab 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Ac 40 GLN Af 24 HIS ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 48 ASN ** Al 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 90 ASN Ao 18 HIS Ao 25 GLN At 4 HIS At 6 GLN ** At 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 95 HIS At 100 ASN ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 179 ASN Ct 145 GLN ** Ct 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 179 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 241673 Z= 0.308 Angle : 0.664 13.077 354073 Z= 0.339 Chirality : 0.038 0.304 43967 Planarity : 0.006 0.101 23440 Dihedral : 14.990 179.793 83290 Min Nonbonded Distance : 1.123 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.77 % Favored : 91.04 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.16 % 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: -2.00 (0.07), residues: 12536 helix: 0.11 (0.08), residues: 4233 sheet: -1.18 (0.12), residues: 1885 loop : -2.45 (0.07), residues: 6418 *********************** 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 3519 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 3172 time to evaluate : 10.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 347 outliers final: 167 residues processed: 3349 average time/residue: 1.8148 time to fit residues: 10558.2334 Evaluate side-chains 3094 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 2927 time to evaluate : 10.498 Switching outliers to nearest non-outliers outliers start: 167 outliers final: 0 residues processed: 167 average time/residue: 1.4504 time to fit residues: 472.3169 ------------------------------------------------------------------------------- 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: 10.0000 chunk 852 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 784 optimal weight: 30.0000 chunk 1103 optimal weight: 8.9990 chunk 1648 optimal weight: 9.9990 chunk 1745 optimal weight: 10.0000 chunk 861 optimal weight: 10.0000 chunk 1562 optimal weight: 4.9990 chunk 470 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 9 GLN BA 29 ASN AB 109 HIS AB 302 ASN AB 315 ASN BB 157 GLN ** AC 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 ASN ** BF 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 44 HIS ** BK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 53 GLN ** BR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 37 ASN Bf 135 HIS ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 187 ASN BE 8 HIS BE 17 HIS ** BE 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 216 ASN BE 224 ASN ** BG 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 91 HIS BH 193 GLN BI 7 ASN BI 165 GLN BJ 75 ASN ** BJ 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BL 39 ASN BN 13 GLN BO 79 GLN BV 35 ASN ** BW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 98 GLN ** BX 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 122 GLN AD 198 HIS ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AG 66 GLN AG 100 HIS ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 8 GLN ** AJ 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 113 ASN AM 56 GLN ** AN 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AR 178 GLN AS 144 GLN AU 38 ASN AU 41 GLN AV 31 ASN AW 96 GLN AX 125 ASN Aa 44 ASN Aa 67 GLN ** Ab 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Af 24 HIS ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 117 HIS At 6 GLN ** At 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ct 138 GLN Ct 158 ASN Ct 352 GLN ** Ct 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.111 241673 Z= 0.383 Angle : 0.716 17.594 354073 Z= 0.366 Chirality : 0.040 0.360 43967 Planarity : 0.006 0.123 23440 Dihedral : 15.146 179.826 83290 Min Nonbonded Distance : 1.061 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.17 % Favored : 89.65 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.94 % 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: -1.84 (0.07), residues: 12536 helix: 0.28 (0.08), residues: 4237 sheet: -1.17 (0.12), residues: 1932 loop : -2.37 (0.07), residues: 6367 *********************** 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 3558 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 423 poor density : 3135 time to evaluate : 10.597 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 outliers start: 423 outliers final: 241 residues processed: 3336 average time/residue: 1.8234 time to fit residues: 10582.3227 Evaluate side-chains 3166 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 2925 time to evaluate : 10.615 Switching outliers to nearest non-outliers outliers start: 241 outliers final: 0 residues processed: 241 average time/residue: 1.5346 time to fit residues: 716.1912 ------------------------------------------------------------------------------- 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: 8.9990 chunk 990 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 1299 optimal weight: 6.9990 chunk 720 optimal weight: 9.9990 chunk 1489 optimal weight: 2.9990 chunk 1206 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 891 optimal weight: 0.6980 chunk 1566 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 162 ASN BA 113 GLN BB 124 HIS BB 208 HIS AC 38 ASN ** BD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 28 HIS ** BK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 53 GLN ** BQ 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 26 ASN Bf 135 HIS ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 17 HIS BE 161 GLN BG 65 GLN ** BG 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 7 ASN BJ 75 ASN ** BJ 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 140 GLN ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BN 13 GLN BO 26 ASN BO 79 GLN BW 98 GLN ** BX 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 110 HIS Bb 51 GLN AD 39 GLN AD 45 ASN ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AE 250 GLN AG 100 HIS ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 167 GLN AL 188 ASN AN 57 GLN AN 196 ASN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AS 92 ASN AS 144 GLN AU 38 ASN ** Ab 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 28 ASN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 25 GLN At 6 GLN ** At 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 95 HIS ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 139 GLN Ct 158 ASN Ct 565 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.130 241673 Z= 0.180 Angle : 0.611 14.732 354073 Z= 0.311 Chirality : 0.035 0.314 43967 Planarity : 0.005 0.137 23440 Dihedral : 14.998 179.897 83290 Min Nonbonded Distance : 1.168 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.23 % Favored : 91.64 % Rotamer Outliers : 2.60 % 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: -1.56 (0.07), residues: 12536 helix: 0.62 (0.08), residues: 4219 sheet: -1.06 (0.12), residues: 1957 loop : -2.25 (0.07), residues: 6360 *********************** 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 3348 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 3064 time to evaluate : 10.519 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 outliers start: 284 outliers final: 135 residues processed: 3203 average time/residue: 1.7535 time to fit residues: 9806.4425 Evaluate side-chains 2994 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 2859 time to evaluate : 10.443 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 135 outliers final: 1 residues processed: 135 average time/residue: 1.3836 time to fit residues: 369.0137 ------------------------------------------------------------------------------- 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: 20.0000 chunk 1572 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 chunk 1024 optimal weight: 5.9990 chunk 430 optimal weight: 40.0000 chunk 1747 optimal weight: 10.0000 chunk 1450 optimal weight: 20.0000 chunk 809 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 578 optimal weight: 10.0000 chunk 917 optimal weight: 0.0070 overall best weight: 6.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 29 ASN BA 113 GLN AB 138 GLN AB 315 ASN AC 38 ASN ** AC 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 82 ASN ** BF 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 26 ASN Bf 135 HIS ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 17 HIS ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 146 ASN ** BH 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 76 GLN BJ 75 ASN ** BJ 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 62 GLN BO 26 ASN BV 47 ASN ** BW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 20 GLN ** BX 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 51 GLN AD 45 ASN AD 198 HIS ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AF 39 GLN AG 100 HIS ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 167 GLN AM 125 ASN AN 57 GLN AN 149 GLN AN 199 GLN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 28 ASN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AR 118 HIS AS 125 GLN AU 38 ASN AV 135 ASN AY 20 ASN Aa 67 GLN ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 28 ASN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 36 HIS Ao 45 GLN At 41 ASN ** At 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 171 HIS ** 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 179 ASN Ct 588 ASN ** Ct 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.196 241673 Z= 0.333 Angle : 0.668 15.190 354073 Z= 0.340 Chirality : 0.039 0.359 43967 Planarity : 0.006 0.117 23440 Dihedral : 15.030 179.537 83290 Min Nonbonded Distance : 1.084 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.75 % Favored : 90.12 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.16 % 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: -1.56 (0.07), residues: 12536 helix: 0.62 (0.08), residues: 4252 sheet: -1.07 (0.12), residues: 1952 loop : -2.26 (0.07), residues: 6332 *********************** 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 3246 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 2953 time to evaluate : 10.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 293 outliers final: 177 residues processed: 3064 average time/residue: 1.8875 time to fit residues: 10144.2114 Evaluate side-chains 3037 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 2860 time to evaluate : 11.681 Switching outliers to nearest non-outliers outliers start: 177 outliers final: 0 residues processed: 177 average time/residue: 1.5765 time to fit residues: 543.8184 ------------------------------------------------------------------------------- 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: 6.9990 chunk 196 optimal weight: 10.0000 chunk 995 optimal weight: 20.0000 chunk 1276 optimal weight: 5.9990 chunk 988 optimal weight: 8.9990 chunk 1470 optimal weight: 0.9990 chunk 975 optimal weight: 0.9990 chunk 1740 optimal weight: 5.9990 chunk 1089 optimal weight: 4.9990 chunk 1061 optimal weight: 0.6980 chunk 803 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 162 ASN BA 29 ASN BB 186 ASN BB 208 HIS AC 38 ASN AC 187 GLN ** BF 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 7 ASN BK 42 ASN ** BK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 74 GLN BU 81 GLN Bf 135 HIS ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 17 HIS ** BH 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 76 GLN ** BI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 75 ASN ** BJ 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 62 GLN BV 47 ASN Ba 7 ASN Bb 51 GLN ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AF 39 GLN AG 100 HIS ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 8 GLN AJ 46 GLN AJ 167 GLN AL 188 ASN AN 149 GLN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 34 GLN ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 137 ASN ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AS 125 GLN AS 144 GLN AU 38 ASN AU 41 GLN AV 135 ASN AY 20 ASN ** Ab 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Ag 28 ASN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 179 ASN ** Ct 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.224 241673 Z= 0.168 Angle : 0.606 14.649 354073 Z= 0.308 Chirality : 0.035 0.309 43967 Planarity : 0.005 0.115 23440 Dihedral : 14.948 179.746 83290 Min Nonbonded Distance : 1.181 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.41 % Favored : 91.50 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.14 % 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: -1.39 (0.07), residues: 12536 helix: 0.78 (0.08), residues: 4231 sheet: -0.97 (0.12), residues: 1951 loop : -2.17 (0.07), residues: 6354 *********************** 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 3149 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 2949 time to evaluate : 10.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 200 outliers final: 92 residues processed: 3035 average time/residue: 1.8065 time to fit residues: 9563.2707 Evaluate side-chains 2896 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 2804 time to evaluate : 10.475 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 1.5111 time to fit residues: 271.7266 ------------------------------------------------------------------------------- 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: 7.9990 chunk 695 optimal weight: 10.0000 chunk 1039 optimal weight: 4.9990 chunk 524 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 1106 optimal weight: 20.0000 chunk 1185 optimal weight: 9.9990 chunk 860 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 1368 optimal weight: 0.0770 overall best weight: 6.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 8 GLN ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 138 GLN AB 315 ASN BB 186 ASN AC 38 ASN ** AC 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 172 ASN ** BD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 65 GLN ** BF 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 81 GLN Bd 10 HIS Bd 26 ASN Bf 135 HIS ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 187 ASN ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 146 ASN BG 227 GLN ** BH 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 76 GLN BH 157 HIS BJ 125 HIS ** BJ 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BN 62 GLN BO 26 ASN BO 79 GLN ** BV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 47 ASN ** BX 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 198 HIS ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN ** AF 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 100 HIS ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 8 GLN AJ 98 ASN AJ 112 HIS AJ 167 GLN AM 125 ASN AN 57 GLN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 50 ASN AO 72 HIS ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AS 92 ASN AT 69 GLN AX 73 HIS AY 20 ASN ** AZ 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Ac 19 GLN Ag 28 ASN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 12 ASN ** At 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 179 ASN ** Ct 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.531 241673 Z= 0.351 Angle : 0.680 22.261 354073 Z= 0.347 Chirality : 0.039 0.319 43967 Planarity : 0.006 0.122 23440 Dihedral : 15.021 179.542 83290 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.00 % Favored : 89.86 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.14 % 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: 0.71 (0.08), residues: 4255 sheet: -1.02 (0.12), residues: 1962 loop : -2.21 (0.07), residues: 6319 *********************** 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 3146 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 2929 time to evaluate : 11.626 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 outliers start: 217 outliers final: 149 residues processed: 3007 average time/residue: 1.8439 time to fit residues: 9732.6341 Evaluate side-chains 2979 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 2830 time to evaluate : 10.446 Switching outliers to nearest non-outliers outliers start: 149 outliers final: 0 residues processed: 149 average time/residue: 1.5222 time to fit residues: 439.4944 ------------------------------------------------------------------------------- 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: 0.2980 chunk 1521 optimal weight: 9.9990 chunk 1622 optimal weight: 9.9990 chunk 976 optimal weight: 9.9990 chunk 706 optimal weight: 10.0000 chunk 1273 optimal weight: 2.9990 chunk 497 optimal weight: 10.0000 chunk 1465 optimal weight: 7.9990 chunk 1534 optimal weight: 5.9990 chunk 1616 optimal weight: 5.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 169 HIS AB 315 ASN BB 186 ASN BB 208 HIS ** AC 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 7 ASN BK 28 HIS BR 29 HIS BU 81 GLN Bd 10 HIS Bd 26 ASN Bf 135 HIS ** Bg 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 146 ASN BH 76 GLN BH 157 HIS ** BJ 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BO 79 GLN ** BV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 47 ASN ** BX 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 51 GLN ** Be 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN AF 126 ASN ** AG 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 100 HIS ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 8 GLN AH 156 ASN AH 162 GLN AL 188 ASN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AQ 160 HIS AS 92 ASN AT 69 GLN ** AU 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 20 ASN AZ 28 ASN Aa 89 ASN ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Ac 19 GLN Ag 28 ASN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 87 GLN At 70 GLN ** At 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 72 ASN AK 179 ASN ** Ct 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.229 241673 Z= 0.277 Angle : 0.659 18.020 354073 Z= 0.337 Chirality : 0.037 0.470 43967 Planarity : 0.006 0.131 23440 Dihedral : 15.030 179.212 83290 Min Nonbonded Distance : 1.121 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.36 % Favored : 90.52 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.07), residues: 12536 helix: 0.72 (0.08), residues: 4247 sheet: -0.99 (0.12), residues: 1948 loop : -2.21 (0.07), residues: 6341 *********************** 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 2992 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 2881 time to evaluate : 10.520 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 outliers start: 111 outliers final: 60 residues processed: 2919 average time/residue: 1.7268 time to fit residues: 9004.2085 Evaluate side-chains 2869 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 2809 time to evaluate : 10.583 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 1.4712 time to fit residues: 184.3690 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1715 optimal weight: 20.0000 chunk 1046 optimal weight: 8.9990 chunk 813 optimal weight: 5.9990 chunk 1192 optimal weight: 4.9990 chunk 1799 optimal weight: 0.9980 chunk 1655 optimal weight: 4.9990 chunk 1432 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 1106 optimal weight: 2.9990 chunk 878 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 138 GLN ** AC 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 28 HIS BT 12 GLN BU 81 GLN Bd 10 HIS Bd 26 ASN Bf 135 HIS ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 161 GLN ** BG 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 146 ASN BH 76 GLN BH 157 HIS BN 62 GLN BO 26 ASN BV 47 ASN BW 70 ASN ** BX 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 45 ASN ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN ** AE 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 126 ASN ** AG 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 100 HIS ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 106 GLN AH 108 ASN AH 162 GLN AJ 98 ASN AL 188 ASN AM 125 ASN ** AN 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AS 92 ASN AS 144 GLN AT 69 GLN AW 48 GLN AY 20 ASN Aa 25 HIS Ab 61 ASN Ac 19 GLN Ag 28 ASN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 87 GLN At 70 GLN ** At 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 179 ASN ** Ct 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.426 241673 Z= 0.216 Angle : 0.633 25.818 354073 Z= 0.323 Chirality : 0.035 0.335 43967 Planarity : 0.005 0.131 23440 Dihedral : 14.947 179.845 83290 Min Nonbonded Distance : 1.151 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.33 % Favored : 90.57 % Rotamer Outliers : 0.67 % 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: -1.33 (0.07), residues: 12536 helix: 0.83 (0.08), residues: 4234 sheet: -0.94 (0.12), residues: 1923 loop : -2.13 (0.07), residues: 6379 ********************** 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 2976 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 2903 time to evaluate : 10.601 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 outliers start: 73 outliers final: 41 residues processed: 2931 average time/residue: 1.7858 time to fit residues: 9142.5042 Evaluate side-chains 2843 residues out of total 10924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 2802 time to evaluate : 11.618 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 1.6431 time to fit residues: 139.9196 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1526 optimal weight: 6.9990 chunk 438 optimal weight: 40.0000 chunk 1321 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 1435 optimal weight: 7.9990 chunk 600 optimal weight: 10.0000 chunk 1473 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 157 GLN ** AC 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 119 GLN ** BC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 65 GLN ** BF 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 186 ASN BK 28 HIS Bc 26 GLN Bd 10 HIS Bd 26 ASN Bf 135 HIS ** Bg 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 76 GLN BH 157 HIS ** BI 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 125 HIS BN 62 GLN ** BO 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 47 ASN ** BX 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 45 ASN AD 175 HIS AD 198 HIS ** AD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 191 GLN ** AE 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 126 ASN ** AG 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 100 HIS ** AG 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 162 GLN AL 188 ASN ** AM 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 57 ASN AS 92 ASN AS 156 HIS AY 20 ASN ** AZ 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 61 ASN Ac 19 GLN Ad 100 ASN Ag 28 ASN ** Ah 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 51 GLN ** At 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 179 ASN ** Ct 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 833 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 = 0.3455 r_free = 0.3455 target = 0.100712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.073792 restraints weight = 503813.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076105 restraints weight = 173984.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.077465 restraints weight = 95317.618| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.179 241673 Z= 0.452 Angle : 0.766 17.559 354073 Z= 0.390 Chirality : 0.043 0.384 43967 Planarity : 0.006 0.132 23440 Dihedral : 15.218 179.809 83290 Min Nonbonded Distance : 1.069 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.74 % Favored : 89.09 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.05 % Twisted Proline : 0.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.07), residues: 12536 helix: 0.62 (0.08), residues: 4247 sheet: -1.09 (0.11), residues: 1982 loop : -2.24 (0.07), residues: 6307 =============================================================================== Job complete usr+sys time: 124651.73 seconds wall clock time: 2133 minutes 49.00 seconds (128029.00 seconds total)