Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 21:22:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs5_14926/04_2023/7zs5_14926.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs5_14926/04_2023/7zs5_14926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs5_14926/04_2023/7zs5_14926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs5_14926/04_2023/7zs5_14926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs5_14926/04_2023/7zs5_14926.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs5_14926/04_2023/7zs5_14926.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3603 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 66547 2.51 5 N 23532 2.21 5 O 34064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ASP 33": "OD1" <-> "OD2" Residue "BC TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ASP 161": "OD1" <-> "OD2" Residue "BC ASP 176": "OD1" <-> "OD2" Residue "BD ASP 289": "OD1" <-> "OD2" Residue "BD ASP 299": "OD1" <-> "OD2" Residue "BD PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE GLU 211": "OE1" <-> "OE2" Residue "BE PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ASP 259": "OD1" <-> "OD2" Residue "BF PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF GLU 188": "OE1" <-> "OE2" Residue "BG TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI GLU 144": "OE1" <-> "OE2" Residue "BI PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ ASP 171": "OD1" <-> "OD2" Residue "BJ TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL GLU 77": "OE1" <-> "OE2" Residue "BL GLU 81": "OE1" <-> "OE2" Residue "BL TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BO GLU 103": "OE1" <-> "OE2" Residue "BO TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP GLU 40": "OE1" <-> "OE2" Residue "BP PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BS ASP 25": "OD1" <-> "OD2" Residue "BS GLU 31": "OE1" <-> "OE2" Residue "BS GLU 86": "OE1" <-> "OE2" Residue "BS ASP 116": "OD1" <-> "OD2" Residue "BT PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW ASP 89": "OD1" <-> "OD2" Residue "BW PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW ASP 124": "OD1" <-> "OD2" Residue "BY GLU 70": "OE1" <-> "OE2" Residue "Ba TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba GLU 119": "OE1" <-> "OE2" Residue "Bb TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb GLU 97": "OE1" <-> "OE2" Residue "Bd TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bd PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Be PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bf GLU 30": "OE1" <-> "OE2" Residue "Bg TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bg TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi GLU 15": "OE1" <-> "OE2" Residue "Bi PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bj GLU 66": "OE1" <-> "OE2" Residue "Bn ASP 92": "OD1" <-> "OD2" Residue "BK TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 127849 Number of models: 1 Model: "" Number of chains: 50 Chain: "1" Number of atoms: 69452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3248, 69452 Classifications: {'RNA': 3248} Modifications used: {'rna2p_pur': 160, 'rna2p_pyr': 103, 'rna3p_pur': 1630, 'rna3p_pyr': 1355} Link IDs: {'rna2p': 263, 'rna3p': 2984} Chain breaks: 4 Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 59, 'rna3p_pyr': 57} Link IDs: {'rna2p': 5, 'rna3p': 115} Chain: "4" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 70, 'rna3p_pyr': 75} Link IDs: {'rna2p': 13, 'rna3p': 144} Chain: "A" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1633 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "2" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 13, 'rna3p': 62} Chain: "BA" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 847 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "BB" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "BC" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1914 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "BD" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "BE" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "BF" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2375 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "BG" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "BH" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "BI" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "BJ" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "BL" 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: "BM" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "BN" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "BO" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "BP" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "BQ" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1420 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "BR" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "BS" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1286 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain: "BT" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1445 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "BU" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "BV" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "BW" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "BX" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 553 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "BY" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "BZ" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Chain: "Ba" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "Bb" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "Bc" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "Bd" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "Be" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Bf" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "Bg" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "Bh" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Bi" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "Bj" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "Bk" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Chain: "Bl" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Bm" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Bn" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "BK" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 209} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "1" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "BQ" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "Bm" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'UNK:plan-1': 3} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 46.54, per 1000 atoms: 0.36 Number of scatterers: 127849 At special positions: 0 Unit cell: (226.765, 224.675, 261.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 3603 15.00 Mg 1 11.99 O 34064 8.00 N 23532 7.00 C 66547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 51.60 Conformation dependent library (CDL) restraints added in 5.9 seconds 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11990 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 66 sheets defined 35.2% alpha, 12.9% beta 1143 base pairs and 1784 stacking pairs defined. Time for finding SS restraints: 37.03 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.554A pdb=" N PHE A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 12 through 16' Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.689A pdb=" N ALA A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 38 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.522A pdb=" N GLY A 55 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.602A pdb=" N GLY A 144 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 removed outlier: 3.577A pdb=" N LEU A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.889A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'BA' and resid 37 through 48 Processing helix chain 'BB' and resid 8 through 15 Processing helix chain 'BB' and resid 20 through 34 removed outlier: 3.685A pdb=" N LEUBB 29 " --> pdb=" O GLNBB 25 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLNBB 32 " --> pdb=" O LYSBB 28 " (cutoff:3.500A) Processing helix chain 'BB' and resid 73 through 92 removed outlier: 4.552A pdb=" N THRBB 78 " --> pdb=" O ALABB 74 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VALBB 79 " --> pdb=" O ALABB 75 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARGBB 80 " --> pdb=" O ALABB 76 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SERBB 81 " --> pdb=" O ALABB 77 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLUBB 88 " --> pdb=" O ARGBB 84 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N METBB 89 " --> pdb=" O ARGBB 85 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VALBB 90 " --> pdb=" O LEUBB 86 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLUBB 91 " --> pdb=" O ARGBB 87 " (cutoff:3.500A) Processing helix chain 'BC' and resid 33 through 38 Processing helix chain 'BC' and resid 105 through 107 No H-bonds generated for 'chain 'BC' and resid 105 through 107' Processing helix chain 'BC' and resid 173 through 177 removed outlier: 3.641A pdb=" N ASPBC 176 " --> pdb=" O GLYBC 173 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYSBC 177 " --> pdb=" O ARGBC 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 173 through 177' Processing helix chain 'BC' and resid 181 through 190 removed outlier: 3.577A pdb=" N ALABC 185 " --> pdb=" O LYSBC 181 " (cutoff:3.500A) Processing helix chain 'BD' and resid 111 through 118 removed outlier: 3.801A pdb=" N PHEBD 118 " --> pdb=" O VALBD 114 " (cutoff:3.500A) Processing helix chain 'BD' and resid 133 through 139 removed outlier: 3.672A pdb=" N TYRBD 137 " --> pdb=" O SERBD 134 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLNBD 139 " --> pdb=" O LYSBD 136 " (cutoff:3.500A) Processing helix chain 'BD' and resid 141 through 154 removed outlier: 4.346A pdb=" N GLUBD 147 " --> pdb=" O GLYBD 143 " (cutoff:3.500A) Processing helix chain 'BD' and resid 187 through 197 removed outlier: 3.958A pdb=" N GLUBD 197 " --> pdb=" O ASPBD 193 " (cutoff:3.500A) Processing helix chain 'BD' and resid 229 through 234 removed outlier: 3.671A pdb=" N TRPBD 233 " --> pdb=" O VALBD 229 " (cutoff:3.500A) Processing helix chain 'BD' and resid 372 through 381 Processing helix chain 'BE' and resid 31 through 43 removed outlier: 3.832A pdb=" N SERBE 41 " --> pdb=" O THRBE 37 " (cutoff:3.500A) Processing helix chain 'BE' and resid 44 through 47 Processing helix chain 'BE' and resid 114 through 130 removed outlier: 3.957A pdb=" N ALABE 130 " --> pdb=" O ILEBE 126 " (cutoff:3.500A) Processing helix chain 'BE' and resid 131 through 137 removed outlier: 3.595A pdb=" N VALBE 135 " --> pdb=" O VALBE 131 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALABE 137 " --> pdb=" O SERBE 133 " (cutoff:3.500A) Processing helix chain 'BE' and resid 153 through 159 Processing helix chain 'BE' and resid 161 through 173 Processing helix chain 'BE' and resid 174 through 181 Processing helix chain 'BE' and resid 190 through 195 Processing helix chain 'BE' and resid 214 through 220 Processing helix chain 'BE' and resid 234 through 239 Processing helix chain 'BE' and resid 240 through 243 Processing helix chain 'BE' and resid 252 through 262 removed outlier: 4.610A pdb=" N ASPBE 259 " --> pdb=" O PHEBE 255 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLNBE 260 " --> pdb=" O THRBE 256 " (cutoff:3.500A) Processing helix chain 'BE' and resid 286 through 292 Processing helix chain 'BE' and resid 295 through 299 Processing helix chain 'BE' and resid 320 through 327 removed outlier: 3.683A pdb=" N LEUBE 324 " --> pdb=" O ASNBE 320 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEUBE 327 " --> pdb=" O VALBE 323 " (cutoff:3.500A) Processing helix chain 'BE' and resid 329 through 337 removed outlier: 4.456A pdb=" N VALBE 333 " --> pdb=" O PROBE 329 " (cutoff:3.500A) Processing helix chain 'BE' and resid 352 through 361 removed outlier: 3.771A pdb=" N THRBE 356 " --> pdb=" O ALABE 352 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLUBE 357 " --> pdb=" O ALABE 353 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THRBE 358 " --> pdb=" O VALBE 354 " (cutoff:3.500A) Processing helix chain 'BF' and resid 9 through 15 Processing helix chain 'BF' and resid 20 through 25 removed outlier: 3.563A pdb=" N GLUBF 25 " --> pdb=" O ARGBF 21 " (cutoff:3.500A) Processing helix chain 'BF' and resid 29 through 38 removed outlier: 4.315A pdb=" N ARGBF 35 " --> pdb=" O TYRBF 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEUBF 36 " --> pdb=" O GLNBF 32 " (cutoff:3.500A) Processing helix chain 'BF' and resid 40 through 44 Processing helix chain 'BF' and resid 82 through 87 removed outlier: 3.604A pdb=" N TYRBF 86 " --> pdb=" O GLUBF 82 " (cutoff:3.500A) Processing helix chain 'BF' and resid 94 through 114 removed outlier: 3.582A pdb=" N ALABF 98 " --> pdb=" O ASNBF 94 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYRBF 99 " --> pdb=" O TRPBF 95 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEUBF 110 " --> pdb=" O ALABF 106 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLNBF 111 " --> pdb=" O ARGBF 107 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYSBF 112 " --> pdb=" O ARGBF 108 " (cutoff:3.500A) Processing helix chain 'BF' and resid 158 through 169 removed outlier: 3.964A pdb=" N ALABF 162 " --> pdb=" O ARGBF 158 " (cutoff:3.500A) Processing helix chain 'BF' and resid 191 through 200 Processing helix chain 'BF' and resid 201 through 214 removed outlier: 3.721A pdb=" N GLUBF 209 " --> pdb=" O SERBF 205 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASPBF 214 " --> pdb=" O GLUBF 210 " (cutoff:3.500A) Processing helix chain 'BF' and resid 215 through 222 removed outlier: 3.686A pdb=" N PHEBF 219 " --> pdb=" O ASPBF 215 " (cutoff:3.500A) Processing helix chain 'BF' and resid 223 through 230 removed outlier: 3.504A pdb=" N LEUBF 227 " --> pdb=" O PHEBF 223 " (cutoff:3.500A) Processing helix chain 'BF' and resid 232 through 250 removed outlier: 3.886A pdb=" N GLUBF 237 " --> pdb=" O ALABF 233 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASPBF 238 " --> pdb=" O ASPBF 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYRBF 240 " --> pdb=" O LEUBF 236 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLUBF 245 " --> pdb=" O THRBF 241 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALABF 246 " --> pdb=" O SERBF 242 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARGBF 248 " --> pdb=" O HISBF 244 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASPBF 250 " --> pdb=" O ALABF 246 " (cutoff:3.500A) Processing helix chain 'BF' and resid 261 through 271 removed outlier: 3.576A pdb=" N TYRBF 265 " --> pdb=" O THRBF 261 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SERBF 269 " --> pdb=" O TYRBF 265 " (cutoff:3.500A) Processing helix chain 'BF' and resid 278 through 293 Processing helix chain 'BG' and resid 80 through 82 No H-bonds generated for 'chain 'BG' and resid 80 through 82' Processing helix chain 'BG' and resid 102 through 106 Processing helix chain 'BG' and resid 131 through 150 removed outlier: 3.772A pdb=" N VALBG 135 " --> pdb=" O LYSBG 131 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASPBG 137 " --> pdb=" O GLUBG 133 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYSBG 143 " --> pdb=" O LYSBG 139 " (cutoff:3.500A) Processing helix chain 'BH' and resid 28 through 72 removed outlier: 3.522A pdb=" N GLUBH 56 " --> pdb=" O GLNBH 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLNBH 64 " --> pdb=" O ARGBH 60 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSBH 70 " --> pdb=" O LYSBH 66 " (cutoff:3.500A) Processing helix chain 'BH' and resid 96 through 106 Processing helix chain 'BH' and resid 120 through 131 removed outlier: 4.310A pdb=" N LEUBH 126 " --> pdb=" O ALABH 122 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEUBH 127 " --> pdb=" O THRBH 123 " (cutoff:3.500A) Processing helix chain 'BH' and resid 140 through 151 Processing helix chain 'BH' and resid 167 through 174 Processing helix chain 'BH' and resid 175 through 177 No H-bonds generated for 'chain 'BH' and resid 175 through 177' Processing helix chain 'BH' and resid 180 through 191 removed outlier: 3.658A pdb=" N ILEBH 189 " --> pdb=" O ILEBH 185 " (cutoff:3.500A) Processing helix chain 'BH' and resid 195 through 202 removed outlier: 3.877A pdb=" N LEUBH 202 " --> pdb=" O ALABH 198 " (cutoff:3.500A) Processing helix chain 'BH' and resid 232 through 234 No H-bonds generated for 'chain 'BH' and resid 232 through 234' Processing helix chain 'BH' and resid 235 through 244 removed outlier: 3.705A pdb=" N LEUBH 239 " --> pdb=" O PHEBH 235 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SERBH 242 " --> pdb=" O LYSBH 238 " (cutoff:3.500A) Processing helix chain 'BI' and resid 53 through 69 removed outlier: 3.582A pdb=" N GLNBI 61 " --> pdb=" O ARGBI 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYSBI 63 " --> pdb=" O GLNBI 59 " (cutoff:3.500A) Processing helix chain 'BI' and resid 83 through 96 removed outlier: 3.533A pdb=" N LYSBI 96 " --> pdb=" O LYSBI 92 " (cutoff:3.500A) Processing helix chain 'BI' and resid 101 through 119 removed outlier: 4.007A pdb=" N LEUBI 109 " --> pdb=" O LYSBI 105 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THRBI 110 " --> pdb=" O LYSBI 106 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYSBI 111 " --> pdb=" O GLUBI 107 " (cutoff:3.500A) Processing helix chain 'BI' and resid 135 through 145 removed outlier: 4.018A pdb=" N ALABI 141 " --> pdb=" O ASNBI 137 " (cutoff:3.500A) Processing helix chain 'BI' and resid 165 through 174 Processing helix chain 'BI' and resid 183 through 189 removed outlier: 3.683A pdb=" N LEUBI 189 " --> pdb=" O ARGBI 185 " (cutoff:3.500A) Processing helix chain 'BI' and resid 208 through 223 removed outlier: 3.727A pdb=" N ASNBI 221 " --> pdb=" O THRBI 217 " (cutoff:3.500A) Processing helix chain 'BI' and resid 225 through 232 removed outlier: 3.772A pdb=" N VALBI 229 " --> pdb=" O LYSBI 225 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYSBI 231 " --> pdb=" O ASPBI 227 " (cutoff:3.500A) Processing helix chain 'BI' and resid 239 through 254 Processing helix chain 'BJ' and resid 61 through 84 removed outlier: 3.617A pdb=" N ARGBJ 69 " --> pdb=" O VALBJ 65 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THRBJ 70 " --> pdb=" O ALABJ 66 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 151 through 165 removed outlier: 3.825A pdb=" N CYSBJ 165 " --> pdb=" O LEUBJ 161 " (cutoff:3.500A) Processing helix chain 'BL' and resid 27 through 42 removed outlier: 4.155A pdb=" N THRBL 31 " --> pdb=" O GLYBL 27 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VALBL 36 " --> pdb=" O ARGBL 32 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEUBL 37 " --> pdb=" O ALABL 33 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLUBL 38 " --> pdb=" O SERBL 34 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLNBL 39 " --> pdb=" O LYSBL 35 " (cutoff:3.500A) Processing helix chain 'BL' and resid 76 through 85 removed outlier: 4.070A pdb=" N LEUBL 80 " --> pdb=" O ALABL 76 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLUBL 81 " --> pdb=" O GLUBL 77 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARGBL 82 " --> pdb=" O GLUBL 78 " (cutoff:3.500A) Processing helix chain 'BL' and resid 108 through 113 Processing helix chain 'BL' and resid 135 through 141 removed outlier: 3.603A pdb=" N VALBL 138 " --> pdb=" O GLYBL 135 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THRBL 139 " --> pdb=" O ALABL 136 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARGBL 141 " --> pdb=" O VALBL 138 " (cutoff:3.500A) Processing helix chain 'BL' and resid 149 through 153 Processing helix chain 'BL' and resid 155 through 165 removed outlier: 3.671A pdb=" N GLNBL 165 " --> pdb=" O SERBL 161 " (cutoff:3.500A) Processing helix chain 'BM' and resid 17 through 20 removed outlier: 3.567A pdb=" N GLUBM 20 " --> pdb=" O HISBM 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'BM' and resid 17 through 20' Processing helix chain 'BM' and resid 28 through 46 removed outlier: 3.509A pdb=" N ALABM 38 " --> pdb=" O SERBM 34 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALABM 44 " --> pdb=" O ALABM 40 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYSBM 45 " --> pdb=" O THRBM 41 " (cutoff:3.500A) Processing helix chain 'BM' and resid 77 through 84 Processing helix chain 'BM' and resid 86 through 94 removed outlier: 3.786A pdb=" N ALABM 90 " --> pdb=" O THRBM 86 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARGBM 91 " --> pdb=" O ALABM 87 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THRBM 92 " --> pdb=" O ALABM 88 " (cutoff:3.500A) Processing helix chain 'BM' and resid 105 through 121 removed outlier: 3.614A pdb=" N TYRBM 119 " --> pdb=" O ARGBM 115 " (cutoff:3.500A) Processing helix chain 'BM' and resid 166 through 187 removed outlier: 3.884A pdb=" N LYSBM 178 " --> pdb=" O ARGBM 174 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLYBM 181 " --> pdb=" O LYSBM 177 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILEBM 182 " --> pdb=" O LYSBM 178 " (cutoff:3.500A) Processing helix chain 'BM' and resid 188 through 193 removed outlier: 3.781A pdb=" N GLUBM 192 " --> pdb=" O ARGBM 188 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALABM 193 " --> pdb=" O GLUBM 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'BM' and resid 188 through 193' Processing helix chain 'BN' and resid 77 through 88 removed outlier: 3.565A pdb=" N ALABN 86 " --> pdb=" O SERBN 82 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALABN 87 " --> pdb=" O LYSBN 83 " (cutoff:3.500A) Processing helix chain 'BN' and resid 89 through 97 Processing helix chain 'BN' and resid 97 through 111 removed outlier: 3.868A pdb=" N LYSBN 101 " --> pdb=" O SERBN 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYSBN 102 " --> pdb=" O SERBN 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILEBN 103 " --> pdb=" O TRPBN 99 " (cutoff:3.500A) Processing helix chain 'BN' and resid 113 through 135 removed outlier: 3.708A pdb=" N GLNBN 119 " --> pdb=" O PHEBN 115 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N METBN 121 " --> pdb=" O ARGBN 117 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VALBN 122 " --> pdb=" O PHEBN 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYSBN 133 " --> pdb=" O TYRBN 129 " (cutoff:3.500A) Processing helix chain 'BO' and resid 3 through 13 removed outlier: 4.322A pdb=" N LEUBO 7 " --> pdb=" O ALABO 3 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLUBO 8 " --> pdb=" O TYRBO 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYSBO 13 " --> pdb=" O GLUBO 9 " (cutoff:3.500A) Processing helix chain 'BO' and resid 16 through 32 removed outlier: 3.687A pdb=" N LEUBO 22 " --> pdb=" O VALBO 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARGBO 24 " --> pdb=" O ARGBO 20 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRPBO 28 " --> pdb=" O ARGBO 24 " (cutoff:3.500A) Processing helix chain 'BO' and resid 44 through 51 Processing helix chain 'BO' and resid 75 through 79 removed outlier: 3.912A pdb=" N GLYBO 78 " --> pdb=" O VALBO 75 " (cutoff:3.500A) Processing helix chain 'BO' and resid 97 through 110 removed outlier: 3.765A pdb=" N ARGBO 109 " --> pdb=" O ARGBO 105 " (cutoff:3.500A) Processing helix chain 'BO' and resid 139 through 144 Processing helix chain 'BO' and resid 145 through 157 removed outlier: 5.195A pdb=" N TRPBO 150 " --> pdb=" O ARGBO 147 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILEBO 151 " --> pdb=" O TYRBO 148 " (cutoff:3.500A) Proline residue: BO 154 - end of helix Processing helix chain 'BO' and resid 159 through 163 Processing helix chain 'BO' and resid 165 through 172 Processing helix chain 'BO' and resid 186 through 195 Processing helix chain 'BP' and resid 15 through 29 removed outlier: 3.579A pdb=" N LYSBP 25 " --> pdb=" O SERBP 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLNBP 26 " --> pdb=" O VALBP 22 " (cutoff:3.500A) Processing helix chain 'BP' and resid 37 through 40 removed outlier: 3.943A pdb=" N GLUBP 40 " --> pdb=" O ARGBP 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 37 through 40' Processing helix chain 'BP' and resid 46 through 59 Processing helix chain 'BP' and resid 65 through 69 removed outlier: 3.531A pdb=" N ARGBP 68 " --> pdb=" O ASNBP 65 " (cutoff:3.500A) Processing helix chain 'BP' and resid 75 through 86 removed outlier: 3.739A pdb=" N GLYBP 86 " --> pdb=" O LYSBP 82 " (cutoff:3.500A) Processing helix chain 'BP' and resid 92 through 100 removed outlier: 3.518A pdb=" N GLUBP 100 " --> pdb=" O LYSBP 96 " (cutoff:3.500A) Processing helix chain 'BP' and resid 110 through 114 removed outlier: 4.458A pdb=" N LYSBP 114 " --> pdb=" O PROBP 111 " (cutoff:3.500A) Processing helix chain 'BP' and resid 120 through 123 Processing helix chain 'BP' and resid 124 through 129 removed outlier: 3.708A pdb=" N ARGBP 128 " --> pdb=" O LEUBP 124 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEUBP 129 " --> pdb=" O ARGBP 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 124 through 129' Processing helix chain 'BP' and resid 138 through 144 Processing helix chain 'BP' and resid 149 through 186 removed outlier: 3.541A pdb=" N LEUBP 156 " --> pdb=" O VALBP 152 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VALBP 162 " --> pdb=" O ALABP 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SERBP 163 " --> pdb=" O LYSBP 159 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYRBP 167 " --> pdb=" O SERBP 163 " (cutoff:3.500A) Processing helix chain 'BP' and resid 188 through 197 removed outlier: 3.604A pdb=" N LYSBP 192 " --> pdb=" O SERBP 188 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLNBP 193 " --> pdb=" O ASPBP 189 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 29 through 35 Processing helix chain 'BQ' and resid 40 through 53 removed outlier: 4.171A pdb=" N LYSBQ 46 " --> pdb=" O THRBQ 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASPBQ 53 " --> pdb=" O GLUBQ 49 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 70 through 77 removed outlier: 4.007A pdb=" N GLYBQ 73 " --> pdb=" O THRBQ 70 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYSBQ 74 " --> pdb=" O ALABQ 71 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLUBQ 75 " --> pdb=" O GLNBQ 72 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 85 through 105 removed outlier: 3.992A pdb=" N LYSBQ 89 " --> pdb=" O ALABQ 85 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHEBQ 90 " --> pdb=" O LYSBQ 86 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEUBQ 94 " --> pdb=" O PHEBQ 90 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASNBQ 97 " --> pdb=" O GLYBQ 93 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALABQ 98 " --> pdb=" O LEUBQ 94 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLUBQ 103 " --> pdb=" O ALABQ 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALABQ 104 " --> pdb=" O ALABQ 100 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 169 through 183 removed outlier: 3.716A pdb=" N ARGBQ 175 " --> pdb=" O ARGBQ 171 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILEBQ 176 " --> pdb=" O GLNBQ 172 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLNBQ 179 " --> pdb=" O ARGBQ 175 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYSBQ 180 " --> pdb=" O ILEBQ 176 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARGBQ 181 " --> pdb=" O ALABQ 177 " (cutoff:3.500A) Processing helix chain 'BR' and resid 23 through 40 removed outlier: 3.514A pdb=" N LEUBR 28 " --> pdb=" O VALBR 24 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHEBR 35 " --> pdb=" O LYSBR 31 " (cutoff:3.500A) Processing helix chain 'BR' and resid 42 through 53 removed outlier: 4.081A pdb=" N LYSBR 46 " --> pdb=" O ALABR 42 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHEBR 53 " --> pdb=" O LEUBR 49 " (cutoff:3.500A) Processing helix chain 'BR' and resid 63 through 73 removed outlier: 3.734A pdb=" N ILEBR 67 " --> pdb=" O SERBR 63 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALABR 68 " --> pdb=" O VALBR 64 " (cutoff:3.500A) Processing helix chain 'BR' and resid 107 through 117 removed outlier: 4.142A pdb=" N VALBR 115 " --> pdb=" O ARGBR 111 " (cutoff:3.500A) Processing helix chain 'BR' and resid 123 through 131 removed outlier: 3.519A pdb=" N LEUBR 127 " --> pdb=" O THRBR 123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALABR 128 " --> pdb=" O LEUBR 124 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VALBR 129 " --> pdb=" O ASPBR 125 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARGBR 130 " --> pdb=" O GLNBR 126 " (cutoff:3.500A) Processing helix chain 'BR' and resid 148 through 153 removed outlier: 3.552A pdb=" N ARGBR 151 " --> pdb=" O GLUBR 148 " (cutoff:3.500A) Processing helix chain 'BS' and resid 4 through 16 Processing helix chain 'BS' and resid 18 through 22 removed outlier: 3.944A pdb=" N VALBS 22 " --> pdb=" O LYSBS 19 " (cutoff:3.500A) Processing helix chain 'BS' and resid 28 through 33 removed outlier: 4.087A pdb=" N ILEBS 32 " --> pdb=" O GLUBS 28 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALABS 33 " --> pdb=" O THRBS 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'BS' and resid 28 through 33' Processing helix chain 'BS' and resid 37 through 47 removed outlier: 3.734A pdb=" N LYSBS 46 " --> pdb=" O ARGBS 42 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASNBS 47 " --> pdb=" O LYSBS 43 " (cutoff:3.500A) Processing helix chain 'BS' and resid 60 through 73 removed outlier: 3.516A pdb=" N ARGBS 64 " --> pdb=" O LYSBS 60 " (cutoff:3.500A) Processing helix chain 'BS' and resid 77 through 81 removed outlier: 3.600A pdb=" N ARGBS 81 " --> pdb=" O TYRBS 78 " (cutoff:3.500A) Processing helix chain 'BS' and resid 84 through 89 Processing helix chain 'BS' and resid 90 through 111 removed outlier: 3.823A pdb=" N VALBS 101 " --> pdb=" O ARGBS 97 " (cutoff:3.500A) Processing helix chain 'BS' and resid 116 through 129 removed outlier: 3.666A pdb=" N TYRBS 120 " --> pdb=" O ASPBS 116 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HISBS 121 " --> pdb=" O LYSBS 117 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VALBS 122 " --> pdb=" O HISBS 118 " (cutoff:3.500A) Processing helix chain 'BS' and resid 134 through 161 removed outlier: 3.799A pdb=" N GLUBS 140 " --> pdb=" O ARGBS 136 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HISBS 141 " --> pdb=" O ALABS 137 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALABS 161 " --> pdb=" O GLUBS 157 " (cutoff:3.500A) Processing helix chain 'BT' and resid 33 through 46 removed outlier: 3.680A pdb=" N SERBT 39 " --> pdb=" O VALBT 35 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRPBT 42 " --> pdb=" O LYSBT 38 " (cutoff:3.500A) Processing helix chain 'BT' and resid 98 through 115 removed outlier: 3.724A pdb=" N GLNBT 108 " --> pdb=" O GLUBT 104 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARGBT 113 " --> pdb=" O ASPBT 109 " (cutoff:3.500A) Processing helix chain 'BT' and resid 117 through 119 No H-bonds generated for 'chain 'BT' and resid 117 through 119' Processing helix chain 'BT' and resid 137 through 142 removed outlier: 3.748A pdb=" N LYSBT 141 " --> pdb=" O ARGBT 137 " (cutoff:3.500A) Processing helix chain 'BU' and resid 99 through 123 removed outlier: 3.929A pdb=" N GLNBU 103 " --> pdb=" O SERBU 99 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLUBU 104 " --> pdb=" O LYSBU 100 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHEBU 105 " --> pdb=" O CYSBU 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEUBU 106 " --> pdb=" O ARGBU 102 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLUBU 107 " --> pdb=" O GLNBU 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALABU 117 " --> pdb=" O ALABU 113 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLUBU 118 " --> pdb=" O ALABU 114 " (cutoff:3.500A) Processing helix chain 'BV' and resid 19 through 24 Processing helix chain 'BV' and resid 29 through 38 removed outlier: 3.593A pdb=" N TYRBV 33 " --> pdb=" O ASPBV 29 " (cutoff:3.500A) Processing helix chain 'BV' and resid 72 through 87 removed outlier: 3.612A pdb=" N LEUBV 76 " --> pdb=" O SERBV 72 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYSBV 77 " --> pdb=" O GLYBV 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASNBV 87 " --> pdb=" O TYRBV 83 " (cutoff:3.500A) Processing helix chain 'BW' and resid 67 through 70 Processing helix chain 'BW' and resid 119 through 126 removed outlier: 3.738A pdb=" N LEUBW 125 " --> pdb=" O GLUBW 121 " (cutoff:3.500A) Processing helix chain 'BW' and resid 126 through 132 Processing helix chain 'BX' and resid 33 through 42 Processing helix chain 'BX' and resid 45 through 49 removed outlier: 3.758A pdb=" N ILEBX 49 " --> pdb=" O PROBX 46 " (cutoff:3.500A) Processing helix chain 'BX' and resid 52 through 59 removed outlier: 3.857A pdb=" N ARGBX 56 " --> pdb=" O THRBX 52 " (cutoff:3.500A) Processing helix chain 'BX' and resid 63 through 68 removed outlier: 3.888A pdb=" N VALBX 67 " --> pdb=" O THRBX 64 " (cutoff:3.500A) Processing helix chain 'BY' and resid 69 through 80 removed outlier: 3.603A pdb=" N LYSBY 74 " --> pdb=" O GLUBY 70 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYSBY 75 " --> pdb=" O THRBY 71 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VALBY 76 " --> pdb=" O ALABY 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLUBY 77 " --> pdb=" O METBY 73 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASPBY 78 " --> pdb=" O LYSBY 74 " (cutoff:3.500A) Processing helix chain 'BY' and resid 91 through 103 removed outlier: 3.822A pdb=" N LYSBY 97 " --> pdb=" O TYRBY 93 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALABY 98 " --> pdb=" O GLNBY 94 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYSBY 100 " --> pdb=" O LYSBY 96 " (cutoff:3.500A) Processing helix chain 'BY' and resid 132 through 139 removed outlier: 3.575A pdb=" N ARGBY 138 " --> pdb=" O ASPBY 134 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILEBY 139 " --> pdb=" O ILEBY 135 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 11 through 21 Processing helix chain 'BZ' and resid 36 through 43 Processing helix chain 'BZ' and resid 100 through 102 No H-bonds generated for 'chain 'BZ' and resid 100 through 102' Processing helix chain 'BZ' and resid 114 through 122 removed outlier: 3.671A pdb=" N ILEBZ 119 " --> pdb=" O ARGBZ 115 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLNBZ 120 " --> pdb=" O LYSBZ 116 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 59 through 64 Processing helix chain 'Ba' and resid 78 through 80 No H-bonds generated for 'chain 'Ba' and resid 78 through 80' Processing helix chain 'Ba' and resid 106 through 123 removed outlier: 4.257A pdb=" N ALABa 110 " --> pdb=" O GLNBa 106 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYSBa 115 " --> pdb=" O LYSBa 111 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 6 through 11 Processing helix chain 'Bb' and resid 41 through 46 Processing helix chain 'Bb' and resid 83 through 92 removed outlier: 3.710A pdb=" N ASPBb 88 " --> pdb=" O GLUBb 84 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLNBb 89 " --> pdb=" O ASPBb 85 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYRBb 90 " --> pdb=" O LYSBb 86 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEUBb 91 " --> pdb=" O ARGBb 87 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYSBb 92 " --> pdb=" O ASPBb 88 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 105 through 108 Processing helix chain 'Bb' and resid 131 through 141 removed outlier: 3.590A pdb=" N GLUBb 135 " --> pdb=" O SERBb 131 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLUBb 136 " --> pdb=" O LYSBb 132 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYSBb 137 " --> pdb=" O LEUBb 133 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILEBb 138 " --> pdb=" O ALABb 134 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 11 through 17 Processing helix chain 'Bc' and resid 18 through 20 No H-bonds generated for 'chain 'Bc' and resid 18 through 20' Processing helix chain 'Bc' and resid 36 through 58 removed outlier: 3.702A pdb=" N LYSBc 52 " --> pdb=" O HISBc 48 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYSBc 58 " --> pdb=" O LEUBc 54 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 10 through 21 removed outlier: 5.299A pdb=" N LYSBd 19 " --> pdb=" O ALABd 15 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 27 through 36 removed outlier: 3.737A pdb=" N ARGBd 35 " --> pdb=" O VALBd 31 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLNBd 36 " --> pdb=" O LYSBd 32 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 49 through 63 removed outlier: 3.585A pdb=" N GLUBd 55 " --> pdb=" O LEUBd 51 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEUBd 56 " --> pdb=" O ARGBd 52 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLUBd 57 " --> pdb=" O LYSBd 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYRBd 58 " --> pdb=" O SERBd 54 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 73 through 82 removed outlier: 3.773A pdb=" N THRBd 79 " --> pdb=" O ASNBd 75 " (cutoff:3.500A) Processing helix chain 'Be' and resid 27 through 45 removed outlier: 3.617A pdb=" N LYSBe 37 " --> pdb=" O VALBe 33 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYSBe 38 " --> pdb=" O LYSBe 34 " (cutoff:3.500A) Processing helix chain 'Be' and resid 52 through 60 removed outlier: 3.513A pdb=" N TRPBe 60 " --> pdb=" O ASNBe 56 " (cutoff:3.500A) Processing helix chain 'Be' and resid 61 through 63 No H-bonds generated for 'chain 'Be' and resid 61 through 63' Processing helix chain 'Bf' and resid 54 through 58 Processing helix chain 'Bf' and resid 60 through 64 removed outlier: 3.589A pdb=" N LYSBf 64 " --> pdb=" O LYSBf 61 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 78 through 84 removed outlier: 3.519A pdb=" N LEUBf 82 " --> pdb=" O ASNBf 78 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRBf 84 " --> pdb=" O LYSBf 80 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 101 through 116 removed outlier: 3.501A pdb=" N ARGBf 105 " --> pdb=" O SERBf 101 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VALBf 106 " --> pdb=" O ALABf 102 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VALBf 107 " --> pdb=" O LYSBf 103 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 37 through 44 removed outlier: 3.823A pdb=" N PHEBg 43 " --> pdb=" O GLNBg 39 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYRBg 44 " --> pdb=" O ASPBg 40 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 15 through 18 Processing helix chain 'Bh' and resid 59 through 64 Processing helix chain 'Bh' and resid 66 through 70 Processing helix chain 'Bh' and resid 82 through 112 removed outlier: 3.550A pdb=" N VALBh 101 " --> pdb=" O GLUBh 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALABh 111 " --> pdb=" O GLUBh 107 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 13 through 36 removed outlier: 4.063A pdb=" N VALBi 22 " --> pdb=" O ALABi 18 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLUBi 27 " --> pdb=" O ASPBi 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VALBi 33 " --> pdb=" O ALABi 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEUBi 36 " --> pdb=" O LYSBi 32 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 42 through 70 removed outlier: 4.189A pdb=" N THRBi 46 " --> pdb=" O PROBi 42 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VALBi 47 " --> pdb=" O LYSBi 43 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SERBi 50 " --> pdb=" O THRBi 46 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALABi 52 " --> pdb=" O ARGBi 48 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYRBi 70 " --> pdb=" O VALBi 66 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 85 through 90 Processing helix chain 'Bi' and resid 93 through 99 Processing helix chain 'Bi' and resid 101 through 111 Processing helix chain 'Bj' and resid 35 through 49 removed outlier: 3.533A pdb=" N PHEBj 39 " --> pdb=" O ASNBj 35 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLUBj 46 " --> pdb=" O SERBj 42 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 51 through 64 Processing helix chain 'Bj' and resid 65 through 77 removed outlier: 3.569A pdb=" N LYSBj 71 " --> pdb=" O LYSBj 67 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 79 through 99 removed outlier: 3.792A pdb=" N ALABj 85 " --> pdb=" O THRBj 81 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASNBj 92 " --> pdb=" O GLUBj 88 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 4 through 8 Processing helix chain 'Bk' and resid 51 through 56 Processing helix chain 'Bk' and resid 66 through 77 removed outlier: 3.543A pdb=" N VALBk 70 " --> pdb=" O TYRBk 66 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SERBk 71 " --> pdb=" O LEUBk 67 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARGBk 72 " --> pdb=" O LYSBk 68 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASNBk 76 " --> pdb=" O ARGBk 72 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 7 through 16 removed outlier: 3.712A pdb=" N GLUBl 13 " --> pdb=" O LYSBl 9 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARGBl 16 " --> pdb=" O LEUBl 12 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 61 through 67 removed outlier: 3.579A pdb=" N LEUBl 65 " --> pdb=" O LYSBl 61 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 6 through 20 Processing helix chain 'Bm' and resid 24 through 30 Processing helix chain 'Bn' and resid 79 through 91 removed outlier: 3.886A pdb=" N LYSBn 83 " --> pdb=" O GLUBn 79 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALABn 84 " --> pdb=" O PROBn 80 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEUBn 85 " --> pdb=" O SERBn 81 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYRBn 89 " --> pdb=" O LEUBn 85 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASNBn 90 " --> pdb=" O ALABn 86 " (cutoff:3.500A) Processing helix chain 'BK' and resid 60 through 79 removed outlier: 3.512A pdb=" N TYRBK 74 " --> pdb=" O CYSBK 70 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THRBK 77 " --> pdb=" O LYSBK 73 " (cutoff:3.500A) Processing helix chain 'BK' and resid 80 through 83 Processing helix chain 'BK' and resid 140 through 142 No H-bonds generated for 'chain 'BK' and resid 140 through 142' Processing helix chain 'BK' and resid 143 through 156 removed outlier: 3.530A pdb=" N GLUBK 149 " --> pdb=" O ASPBK 145 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYRBK 156 " --> pdb=" O ARGBK 152 " (cutoff:3.500A) Processing helix chain 'BK' and resid 176 through 187 removed outlier: 4.077A pdb=" N GLUBK 185 " --> pdb=" O LEUBK 181 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALABK 186 " --> pdb=" O LYSBK 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLYBK 187 " --> pdb=" O LYSBK 183 " (cutoff:3.500A) Processing helix chain 'BK' and resid 204 through 212 removed outlier: 3.899A pdb=" N ASNBK 208 " --> pdb=" O SERBK 204 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARGBK 210 " --> pdb=" O GLUBK 206 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLUBK 211 " --> pdb=" O ASNBK 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.064A pdb=" N THR A 3 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 203 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 198 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.243A pdb=" N ALA A 115 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.778A pdb=" N SER A 155 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY A 159 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BA' and resid 7 through 11 removed outlier: 3.585A pdb=" N THRBA 10 " --> pdb=" O THRBA 21 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALABA 81 " --> pdb=" O LEUBA 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'BB' and resid 47 through 49 Processing sheet with id=AA8, first strand: chain 'BC' and resid 40 through 41 removed outlier: 3.530A pdb=" N ALABC 90 " --> pdb=" O ILEBC 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'BC' and resid 44 through 47 removed outlier: 7.000A pdb=" N LYSBC 60 " --> pdb=" O LYSBC 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'BC' and resid 101 through 103 removed outlier: 6.245A pdb=" N ILEBC 136 " --> pdb=" O ARGBC 149 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARGBC 149 " --> pdb=" O ILEBC 136 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLYBC 138 " --> pdb=" O ARGBC 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'BC' and resid 224 through 225 Processing sheet with id=AB3, first strand: chain 'BD' and resid 356 through 359 removed outlier: 6.451A pdb=" N VALBD 57 " --> pdb=" O LYSBD 357 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILEBD 359 " --> pdb=" O THRBD 55 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THRBD 55 " --> pdb=" O ILEBD 359 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILEBD 335 " --> pdb=" O VALBD 220 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VALBD 220 " --> pdb=" O ILEBD 335 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALABD 217 " --> pdb=" O ILEBD 278 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILEBD 278 " --> pdb=" O ALABD 217 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALABD 219 " --> pdb=" O THRBD 276 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THRBD 276 " --> pdb=" O ALABD 219 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYSBD 281 " --> pdb=" O LYSBD 325 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N METBD 323 " --> pdb=" O TYRBD 283 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VALBD 285 " --> pdb=" O PHEBD 321 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHEBD 321 " --> pdb=" O VALBD 285 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VALBD 324 " --> pdb=" O THRBD 77 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARGBD 70 " --> pdb=" O ASPBD 59 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASPBD 59 " --> pdb=" O ARGBD 70 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VALBD 72 " --> pdb=" O VALBD 57 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VALBD 57 " --> pdb=" O VALBD 72 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLUBD 74 " --> pdb=" O THRBD 55 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THRBD 55 " --> pdb=" O GLUBD 74 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VALBD 76 " --> pdb=" O METBD 53 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N METBD 53 " --> pdb=" O VALBD 76 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VALBD 78 " --> pdb=" O ALABD 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'BD' and resid 100 through 106 removed outlier: 3.567A pdb=" N LEUBD 102 " --> pdb=" O GLYBD 91 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLYBD 91 " --> pdb=" O LEUBD 102 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THRBD 104 " --> pdb=" O VALBD 89 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VALBD 89 " --> pdb=" O THRBD 104 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TRPBD 106 " --> pdb=" O VALBD 87 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VALBD 87 " --> pdb=" O TRPBD 106 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VALBD 86 " --> pdb=" O HISBD 163 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HISBD 163 " --> pdb=" O VALBD 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'BD' and resid 225 through 227 Processing sheet with id=AB6, first strand: chain 'BE' and resid 6 through 10 removed outlier: 5.718A pdb=" N ASNBE 18 " --> pdb=" O VALBE 8 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SERBE 10 " --> pdb=" O THRBE 16 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THRBE 16 " --> pdb=" O SERBE 10 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'BE' and resid 62 through 64 Processing sheet with id=AB8, first strand: chain 'BE' and resid 150 through 152 removed outlier: 6.551A pdb=" N LEUBE 150 " --> pdb=" O TRPBE 250 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEUBE 206 " --> pdb=" O ILEBE 249 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THRBE 251 " --> pdb=" O LEUBE 206 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VALBE 208 " --> pdb=" O THRBE 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYRBE 209 " --> pdb=" O ALABE 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'BF' and resid 73 through 79 removed outlier: 6.535A pdb=" N ILEBF 64 " --> pdb=" O LEUBF 75 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALABF 77 " --> pdb=" O CYSBF 62 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N CYSBF 62 " --> pdb=" O ALABF 77 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYRBF 79 " --> pdb=" O ILEBF 60 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILEBF 60 " --> pdb=" O TYRBF 79 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASPBF 59 " --> pdb=" O THRBF 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLNBF 63 " --> pdb=" O VALBF 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'BG' and resid 77 through 79 removed outlier: 3.713A pdb=" N ARGBG 77 " --> pdb=" O ILEBG 65 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEUBG 64 " --> pdb=" O LEUBG 55 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THRBG 38 " --> pdb=" O TYRBG 54 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THRBG 89 " --> pdb=" O VALBG 39 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILEBG 41 " --> pdb=" O THRBG 87 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THRBG 87 " --> pdb=" O ILEBG 41 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'BH' and resid 75 through 77 removed outlier: 3.942A pdb=" N TYRBH 75 " --> pdb=" O VALBU 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'BH' and resid 134 through 137 removed outlier: 3.785A pdb=" N VALBH 87 " --> pdb=" O ALABH 135 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SERBH 113 " --> pdb=" O ARGBH 88 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'BI' and resid 70 through 71 removed outlier: 3.725A pdb=" N GLYBI 234 " --> pdb=" O VALBI 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'BI' and resid 133 through 134 removed outlier: 3.890A pdb=" N ALABI 199 " --> pdb=" O LYSBI 133 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEUBI 150 " --> pdb=" O LEUBI 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VALBI 151 " --> pdb=" O ALABI 178 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VALBI 180 " --> pdb=" O VALBI 151 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILEBI 153 " --> pdb=" O VALBI 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'BJ' and resid 3 through 11 removed outlier: 6.751A pdb=" N ILEBJ 4 " --> pdb=" O ASNBJ 59 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'BJ' and resid 17 through 21 Processing sheet with id=AC8, first strand: chain 'BJ' and resid 132 through 136 removed outlier: 6.208A pdb=" N ARGBJ 91 " --> pdb=" O VALBJ 181 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VALBJ 181 " --> pdb=" O ARGBJ 91 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VALBJ 93 " --> pdb=" O ILEBJ 179 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILEBJ 179 " --> pdb=" O VALBJ 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'BJ' and resid 100 through 104 Processing sheet with id=AD1, first strand: chain 'BL' and resid 46 through 48 removed outlier: 3.648A pdb=" N ALABL 66 " --> pdb=" O SERBL 48 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VALBL 67 " --> pdb=" O ILEBL 21 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILEBL 21 " --> pdb=" O VALBL 67 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VALBL 130 " --> pdb=" O GLUBL 15 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEUBL 17 " --> pdb=" O TYRBL 128 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYRBL 128 " --> pdb=" O LEUBL 17 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEUBL 19 " --> pdb=" O ASPBL 126 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASPBL 126 " --> pdb=" O LEUBL 19 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHEBL 102 " --> pdb=" O VALBL 129 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'BM' and resid 22 through 24 Processing sheet with id=AD3, first strand: chain 'BM' and resid 57 through 59 Processing sheet with id=AD4, first strand: chain 'BM' and resid 123 through 125 removed outlier: 3.583A pdb=" N ALABi 117 " --> pdb=" O ILEBM 124 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'BM' and resid 156 through 157 removed outlier: 3.620A pdb=" N ARGBM 157 " --> pdb=" O ALABb 99 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYSBb 126 " --> pdb=" O PROBb 100 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILEBb 102 " --> pdb=" O LYSBb 126 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VALBb 125 " --> pdb=" O GLUBb 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'BN' and resid 56 through 59 removed outlier: 8.127A pdb=" N LYSBN 43 " --> pdb=" O ILEBN 38 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILEBN 38 " --> pdb=" O LYSBN 43 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEUBN 45 " --> pdb=" O VALBN 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALABN 33 " --> pdb=" O VALBN 21 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'BO' and resid 36 through 39 removed outlier: 3.925A pdb=" N ILEBO 61 " --> pdb=" O ALABO 39 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TYRBO 127 " --> pdb=" O ASNBO 122 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASNBO 122 " --> pdb=" O TYRBO 127 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYRBO 129 " --> pdb=" O TRPBO 120 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TRPBO 120 " --> pdb=" O TYRBO 129 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLUBO 131 " --> pdb=" O SERBO 118 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SERBO 118 " --> pdb=" O GLUBO 131 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILEBO 133 " --> pdb=" O LEUBO 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'BP' and resid 6 through 10 removed outlier: 5.878A pdb=" N VALBP 7 " --> pdb=" O VALBP 34 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VALBP 36 " --> pdb=" O VALBP 7 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILEBP 9 " --> pdb=" O VALBP 36 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYSBP 103 " --> pdb=" O ILEBP 33 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'BP' and resid 42 through 44 Processing sheet with id=AE1, first strand: chain 'BQ' and resid 14 through 17 Processing sheet with id=AE2, first strand: chain 'BQ' and resid 14 through 17 removed outlier: 3.640A pdb=" N ASNBQ 120 " --> pdb=" O HISBQ 145 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLUBQ 147 " --> pdb=" O GLNBQ 118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'BQ' and resid 58 through 59 removed outlier: 3.522A pdb=" N ARGBQ 82 " --> pdb=" O ILEBQ 58 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'BQ' and resid 128 through 131 removed outlier: 3.681A pdb=" N ARGBQ 135 " --> pdb=" O ARGBQ 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'BR' and resid 121 through 122 removed outlier: 6.733A pdb=" N VALBR 101 " --> pdb=" O ILEBR 122 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VALBR 81 " --> pdb=" O ALABR 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'BR' and resid 86 through 87 Processing sheet with id=AE7, first strand: chain 'BT' and resid 58 through 62 removed outlier: 6.560A pdb=" N ILEBT 10 " --> pdb=" O VALBT 59 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILEBT 61 " --> pdb=" O GLNBT 8 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLNBT 8 " --> pdb=" O ILEBT 61 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARGBT 28 " --> pdb=" O LEUBU 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'BT' and resid 86 through 94 removed outlier: 3.651A pdb=" N GLYBT 86 " --> pdb=" O SERBT 83 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALBT 79 " --> pdb=" O METBT 90 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLYBT 76 " --> pdb=" O VALBT 126 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VALBT 126 " --> pdb=" O GLYBT 76 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRPBT 78 " --> pdb=" O LEUBT 124 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'BU' and resid 83 through 92 removed outlier: 3.672A pdb=" N ASNBU 66 " --> pdb=" O GLYBU 73 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILEBU 75 " --> pdb=" O VALBU 64 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VALBU 64 " --> pdb=" O ILEBU 75 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASNBU 77 " --> pdb=" O GLYBU 62 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N GLYBU 62 " --> pdb=" O ASNBU 77 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLYBU 62 " --> pdb=" O VALBU 40 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'BV' and resid 57 through 58 removed outlier: 7.559A pdb=" N GLUBV 102 " --> pdb=" O THRBV 98 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THRBV 98 " --> pdb=" O GLUBV 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'BW' and resid 22 through 25 removed outlier: 6.330A pdb=" N ARGBW 32 " --> pdb=" O CYSBW 25 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALABW 31 " --> pdb=" O GLYBW 65 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLYBW 65 " --> pdb=" O ALABW 31 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASNBW 33 " --> pdb=" O LYSBW 63 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYSBW 63 " --> pdb=" O ASNBW 33 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N METBW 59 " --> pdb=" O ILEBW 37 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VALBW 39 " --> pdb=" O METBW 57 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N METBW 57 " --> pdb=" O VALBW 39 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALABW 99 " --> pdb=" O VALBW 79 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLYBW 100 " --> pdb=" O ILEBW 22 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASNBW 24 " --> pdb=" O GLYBW 100 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILEBW 102 " --> pdb=" O ASNBW 24 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'BW' and resid 85 through 86 removed outlier: 6.425A pdb=" N PHEBW 92 " --> pdb=" O LEUBX 20 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N VALBX 22 " --> pdb=" O PHEBW 92 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYRBW 94 " --> pdb=" O VALBX 22 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'BX' and resid 4 through 5 removed outlier: 4.657A pdb=" N GLUBX 4 " --> pdb=" O ILEBX 13 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'BY' and resid 63 through 66 removed outlier: 3.942A pdb=" N GLNBY 65 " --> pdb=" O GLNBY 85 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYSBY 120 " --> pdb=" O VALBY 86 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYSBY 109 " --> pdb=" O ARGBY 125 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'BZ' and resid 79 through 82 removed outlier: 7.354A pdb=" N ALABZ 79 " --> pdb=" O VALBZ 73 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VALBZ 73 " --> pdb=" O ALABZ 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLNBZ 81 " --> pdb=" O SERBZ 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLUBZ 55 " --> pdb=" O THRBZ 107 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'BZ' and resid 86 through 88 Processing sheet with id=AF8, first strand: chain 'Ba' and resid 10 through 12 removed outlier: 6.865A pdb=" N LEUBa 42 " --> pdb=" O VALBa 26 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N HISBa 40 " --> pdb=" O PROBa 28 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Ba' and resid 46 through 48 removed outlier: 6.547A pdb=" N LYSBa 69 " --> pdb=" O GLUBa 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Bb' and resid 72 through 74 removed outlier: 3.522A pdb=" N LEUBb 113 " --> pdb=" O LEUBb 73 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Bd' and resid 23 through 24 removed outlier: 3.503A pdb=" N SERBd 91 " --> pdb=" O THRBd 24 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEUBd 41 " --> pdb=" O ILEBd 92 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILEBd 42 " --> pdb=" O TYRBd 68 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHEBd 70 " --> pdb=" O ILEBd 42 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILEBd 44 " --> pdb=" O PHEBd 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Be' and resid 49 through 50 removed outlier: 4.440A pdb=" N THRBe 9 " --> pdb=" O VALBe 109 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Bf' and resid 72 through 76 removed outlier: 6.320A pdb=" N LYSBf 72 " --> pdb=" O ALABf 93 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLUBf 95 " --> pdb=" O LYSBf 72 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHEBf 74 " --> pdb=" O GLUBf 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'Bg' and resid 9 through 16 removed outlier: 4.333A pdb=" N LEUBg 29 " --> pdb=" O LEUBg 14 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARGBg 73 " --> pdb=" O ARGBg 82 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THRBg 84 " --> pdb=" O VALBg 71 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VALBg 71 " --> pdb=" O THRBg 84 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYSBg 63 " --> pdb=" O ALABg 55 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALABg 55 " --> pdb=" O LYSBg 63 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VALBg 52 " --> pdb=" O SERBg 97 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SERBg 97 " --> pdb=" O VALBg 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Bh' and resid 20 through 24 Processing sheet with id=AG7, first strand: chain 'Bk' and resid 16 through 17 Processing sheet with id=AG8, first strand: chain 'Bl' and resid 51 through 56 removed outlier: 4.626A pdb=" N THRBl 22 " --> pdb=" O ARGBl 46 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALABl 23 " --> pdb=" O ASNBl 76 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Bn' and resid 102 through 103 Processing sheet with id=AH1, first strand: chain 'BK' and resid 35 through 36 Processing sheet with id=AH2, first strand: chain 'BK' and resid 133 through 136 removed outlier: 3.670A pdb=" N HISBK 50 " --> pdb=" O ILEBK 165 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILEBK 165 " --> pdb=" O HISBK 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'BK' and resid 94 through 98 removed outlier: 6.485A pdb=" N HISBK 94 " --> pdb=" O LEUBK 124 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEUBK 124 " --> pdb=" O HISBK 94 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEUBK 96 " --> pdb=" O HISBK 122 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2810 hydrogen bonds 4500 hydrogen bond angles 0 basepair planarities 1143 basepair parallelities 1784 stacking parallelities Total time for adding SS restraints: 199.36 Time building geometry restraints manager: 55.87 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: 21839 1.33 - 1.45: 53685 1.45 - 1.57: 55029 1.57 - 1.69: 7199 1.69 - 1.81: 159 Bond restraints: 137911 Sorted by residual: bond pdb=" CB PRO A 213 " pdb=" CG PRO A 213 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.73e+00 bond pdb=" O3' G 1 616 " pdb=" P G 1 617 " ideal model delta sigma weight residual 1.607 1.571 0.036 1.50e-02 4.44e+03 5.71e+00 bond pdb=" CB LYSBW 66 " pdb=" CG LYSBW 66 " ideal model delta sigma weight residual 1.520 1.588 -0.068 3.00e-02 1.11e+03 5.08e+00 bond pdb=" N7 G 4 75 " pdb=" C5 G 4 75 " ideal model delta sigma weight residual 1.388 1.348 0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" O5' G 12249 " pdb=" C5' G 12249 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.71e+00 ... (remaining 137906 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.57: 16327 104.57 - 112.45: 78509 112.45 - 120.32: 57707 120.32 - 128.20: 45615 128.20 - 136.08: 5645 Bond angle restraints: 203803 Sorted by residual: angle pdb=" CA PRO A 213 " pdb=" N PRO A 213 " pdb=" CD PRO A 213 " ideal model delta sigma weight residual 112.00 100.49 11.51 1.40e+00 5.10e-01 6.76e+01 angle pdb=" C ASPBL 173 " pdb=" CA ASPBL 173 " pdb=" CB ASPBL 173 " ideal model delta sigma weight residual 116.54 110.11 6.43 1.15e+00 7.56e-01 3.13e+01 angle pdb=" O4' U 12269 " pdb=" C1' U 12269 " pdb=" C2' U 12269 " ideal model delta sigma weight residual 107.60 102.06 5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" C PHEBF 260 " pdb=" CA PHEBF 260 " pdb=" CB PHEBF 260 " ideal model delta sigma weight residual 115.79 109.69 6.10 1.19e+00 7.06e-01 2.63e+01 angle pdb=" C LYSBM 131 " pdb=" CA LYSBM 131 " pdb=" CB LYSBM 131 " ideal model delta sigma weight residual 117.23 110.68 6.55 1.36e+00 5.41e-01 2.32e+01 ... (remaining 203798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 72116 35.99 - 71.98: 2609 71.98 - 107.98: 260 107.98 - 143.97: 36 143.97 - 179.96: 60 Dihedral angle restraints: 75081 sinusoidal: 56488 harmonic: 18593 Sorted by residual: dihedral pdb=" C4' C 11793 " pdb=" C3' C 11793 " pdb=" C2' C 11793 " pdb=" C1' C 11793 " ideal model delta sinusoidal sigma weight residual -35.00 34.52 -69.52 1 8.00e+00 1.56e-02 9.75e+01 dihedral pdb=" C4' A 11557 " pdb=" C3' A 11557 " pdb=" C2' A 11557 " pdb=" C1' A 11557 " ideal model delta sinusoidal sigma weight residual -35.00 34.42 -69.42 1 8.00e+00 1.56e-02 9.73e+01 dihedral pdb=" C5' C 11793 " pdb=" C4' C 11793 " pdb=" C3' C 11793 " pdb=" O3' C 11793 " ideal model delta sinusoidal sigma weight residual 147.00 79.21 67.79 1 8.00e+00 1.56e-02 9.33e+01 ... (remaining 75078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 24278 0.071 - 0.142: 1320 0.142 - 0.213: 79 0.213 - 0.284: 14 0.284 - 0.355: 5 Chirality restraints: 25696 Sorted by residual: chirality pdb=" C3' U 12269 " pdb=" C4' U 12269 " pdb=" O3' U 12269 " pdb=" C2' U 12269 " both_signs ideal model delta sigma weight residual False -2.48 -2.12 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB ILEBM 9 " pdb=" CA ILEBM 9 " pdb=" CG1 ILEBM 9 " pdb=" CG2 ILEBM 9 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' A 11557 " pdb=" C4' A 11557 " pdb=" O3' A 11557 " pdb=" C2' A 11557 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 25693 not shown) Planarity restraints: 12438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 12269 " 0.053 2.00e-02 2.50e+03 2.72e-02 1.67e+01 pdb=" N1 U 12269 " -0.054 2.00e-02 2.50e+03 pdb=" C2 U 12269 " -0.006 2.00e-02 2.50e+03 pdb=" O2 U 12269 " -0.009 2.00e-02 2.50e+03 pdb=" N3 U 12269 " 0.011 2.00e-02 2.50e+03 pdb=" C4 U 12269 " 0.011 2.00e-02 2.50e+03 pdb=" O4 U 12269 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U 12269 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U 12269 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 12708 " -0.013 2.00e-02 2.50e+03 2.42e-02 1.32e+01 pdb=" N1 C 12708 " 0.010 2.00e-02 2.50e+03 pdb=" C2 C 12708 " 0.059 2.00e-02 2.50e+03 pdb=" O2 C 12708 " -0.034 2.00e-02 2.50e+03 pdb=" N3 C 12708 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C 12708 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C 12708 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C 12708 " -0.010 2.00e-02 2.50e+03 pdb=" C6 C 12708 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASNBX 45 " 0.059 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PROBX 46 " -0.150 5.00e-02 4.00e+02 pdb=" CA PROBX 46 " 0.044 5.00e-02 4.00e+02 pdb=" CD PROBX 46 " 0.048 5.00e-02 4.00e+02 ... (remaining 12435 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 9 2.04 - 2.76: 19981 2.76 - 3.47: 175322 3.47 - 4.19: 393916 4.19 - 4.90: 549309 Nonbonded interactions: 1138537 Sorted by model distance: nonbonded pdb=" C UNK 13405 " pdb=" N UNKBQ 204 " model vdw 1.329 3.350 nonbonded pdb=" C UNK 13403 " pdb=" N UNKBE 401 " model vdw 1.329 3.350 nonbonded pdb=" N UNK 13402 " pdb=" C UNKBQ 203 " model vdw 1.329 3.350 nonbonded pdb=" N UNKBQ 201 " pdb=" C UNKBm 103 " model vdw 1.329 3.350 nonbonded pdb=" N UNK 13406 " pdb=" C UNKBQ 204 " model vdw 1.330 3.350 ... (remaining 1138532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.300 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: 0.090 Extract box with map and model: 39.950 Check model and map are aligned: 1.370 Set scattering table: 0.830 Process input model: 421.660 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 480.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.148 137911 Z= 0.132 Angle : 0.551 11.507 203803 Z= 0.292 Chirality : 0.034 0.355 25696 Planarity : 0.004 0.087 12438 Dihedral : 16.111 179.961 63091 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.50 % Favored : 97.12 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.10), residues: 6330 helix: -0.76 (0.12), residues: 1783 sheet: -0.90 (0.18), residues: 804 loop : -1.25 (0.10), residues: 3743 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1192 time to evaluate : 6.151 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 outliers start: 1 outliers final: 0 residues processed: 1192 average time/residue: 1.1176 time to fit residues: 2298.0757 Evaluate side-chains 988 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 988 time to evaluate : 6.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 829 optimal weight: 6.9990 chunk 744 optimal weight: 6.9990 chunk 413 optimal weight: 0.0030 chunk 254 optimal weight: 7.9990 chunk 502 optimal weight: 5.9990 chunk 397 optimal weight: 0.7980 chunk 769 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 468 optimal weight: 8.9990 chunk 572 optimal weight: 2.9990 chunk 891 optimal weight: 0.9980 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 38 GLN ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 144 ASN BD 279 ASN BE 9 HIS BE 221 ASN BG 57 HIS BH 48 ASN BH 146 GLN BH 157 ASN BI 38 GLN BI 95 ASN ** BJ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 9 GLN ** BJ 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 156 GLN BL 152 HIS BM 66 ASN ** BN 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 55 HIS BP 65 ASN BR 45 ASN BR 58 ASN BS 130 ASN BT 46 GLN BT 65 ASN BT 142 GLN ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 66 GLN BZ 100 HIS ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 44 ASN Bd 47 ASN Bd 75 ASN Be 43 HIS Bf 52 GLN Bg 26 ASN Bg 77 ASN Bg 88 ASN Bh 69 HIS ** Bj 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bl 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 11 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 137911 Z= 0.256 Angle : 0.622 11.940 203803 Z= 0.321 Chirality : 0.038 0.326 25696 Planarity : 0.005 0.066 12438 Dihedral : 15.999 179.742 50375 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.69 % Favored : 93.92 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 6330 helix: -0.40 (0.12), residues: 1892 sheet: -0.91 (0.18), residues: 827 loop : -1.40 (0.10), residues: 3611 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1089 time to evaluate : 6.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 73 residues processed: 1123 average time/residue: 1.1508 time to fit residues: 2238.9099 Evaluate side-chains 1053 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 980 time to evaluate : 6.143 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.9307 time to fit residues: 135.6471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 495 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 742 optimal weight: 0.4980 chunk 607 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 893 optimal weight: 6.9990 chunk 965 optimal weight: 2.9990 chunk 795 optimal weight: 4.9990 chunk 885 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 716 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 3 ASN BA 38 GLN BC 38 HIS ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 9 HIS ** BE 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 90 HIS BH 80 GLN BH 146 GLN ** BI 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 156 GLN BN 126 GLN BP 55 HIS BR 58 ASN ** BT 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 120 ASN Bg 77 ASN Bh 69 HIS Bi 108 GLN ** Bj 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bl 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 32 ASN Bm 11 GLN ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 137911 Z= 0.261 Angle : 0.620 9.609 203803 Z= 0.322 Chirality : 0.038 0.325 25696 Planarity : 0.005 0.066 12438 Dihedral : 16.079 179.938 50375 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.86 % Favored : 92.75 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.52 (0.10), residues: 6330 helix: -0.24 (0.12), residues: 1900 sheet: -1.06 (0.18), residues: 821 loop : -1.43 (0.10), residues: 3609 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1046 time to evaluate : 6.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 58 residues processed: 1103 average time/residue: 1.2595 time to fit residues: 2414.3377 Evaluate side-chains 1022 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 964 time to evaluate : 6.171 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.9544 time to fit residues: 111.8230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 882 optimal weight: 0.1980 chunk 671 optimal weight: 5.9990 chunk 463 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 426 optimal weight: 2.9990 chunk 599 optimal weight: 0.0020 chunk 896 optimal weight: 0.0670 chunk 949 optimal weight: 1.9990 chunk 468 optimal weight: 10.0000 chunk 849 optimal weight: 0.7980 chunk 255 optimal weight: 6.9990 overall best weight: 0.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN BA 3 ASN BA 38 GLN ** BC 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 217 GLN BD 273 HIS BE 9 HIS BE 304 GLN ** BG 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 80 GLN BH 146 GLN BH 157 ASN BI 38 GLN BI 41 GLN ** BI 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 9 GLN BJ 156 GLN ** BJ 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 55 HIS BR 58 ASN ** BT 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 11 HIS Bb 49 HIS Bb 120 ASN Bd 75 ASN Be 43 HIS Bg 77 ASN Bh 69 HIS ** Bj 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 32 ASN ** Bm 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.073 137911 Z= 0.139 Angle : 0.552 11.427 203803 Z= 0.286 Chirality : 0.034 0.279 25696 Planarity : 0.004 0.066 12438 Dihedral : 15.900 179.480 50375 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.72 % Favored : 93.89 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.31 (0.10), residues: 6330 helix: -0.03 (0.12), residues: 1923 sheet: -0.99 (0.18), residues: 829 loop : -1.32 (0.10), residues: 3578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1085 time to evaluate : 6.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 32 residues processed: 1120 average time/residue: 1.2067 time to fit residues: 2333.4664 Evaluate side-chains 1015 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 983 time to evaluate : 6.169 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.9590 time to fit residues: 65.3460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 790 optimal weight: 1.9990 chunk 538 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 706 optimal weight: 7.9990 chunk 391 optimal weight: 0.6980 chunk 809 optimal weight: 3.9990 chunk 656 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 484 optimal weight: 0.9990 chunk 851 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 3 ASN ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 111 GLN BG 28 GLN BG 57 HIS BH 80 GLN BH 146 GLN BI 41 GLN ** BI 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 252 ASN BJ 156 GLN ** BJ 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 126 GLN BP 50 ASN BP 55 HIS ** BQ 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 58 ASN BT 65 ASN BT 142 GLN BU 66 ASN ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 44 ASN Bh 69 HIS Bj 12 ASN ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 137911 Z= 0.167 Angle : 0.560 13.309 203803 Z= 0.289 Chirality : 0.035 0.292 25696 Planarity : 0.004 0.065 12438 Dihedral : 15.881 179.911 50375 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.32 % Favored : 93.29 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.24 (0.10), residues: 6330 helix: 0.11 (0.12), residues: 1895 sheet: -0.93 (0.18), residues: 830 loop : -1.32 (0.10), residues: 3605 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1034 time to evaluate : 6.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 46 residues processed: 1080 average time/residue: 1.1455 time to fit residues: 2142.4311 Evaluate side-chains 1021 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 975 time to evaluate : 6.075 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.9193 time to fit residues: 87.2903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 319 optimal weight: 8.9990 chunk 854 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 557 optimal weight: 1.9990 chunk 234 optimal weight: 30.0000 chunk 950 optimal weight: 0.0050 chunk 788 optimal weight: 0.4980 chunk 439 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 498 optimal weight: 9.9990 overall best weight: 3.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 3 ASN BA 38 GLN ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 217 GLN BD 139 GLN BE 9 HIS BH 146 GLN BH 157 ASN BI 38 GLN BI 41 GLN ** BI 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 221 ASN BJ 9 GLN BJ 156 GLN ** BL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 126 GLN BP 55 HIS BQ 72 GLN BR 58 ASN BT 63 GLN ** BT 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 142 GLN ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 120 ASN Bg 77 ASN Bh 69 HIS Bi 34 GLN ** Bi 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bl 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 137911 Z= 0.340 Angle : 0.685 12.442 203803 Z= 0.353 Chirality : 0.041 0.343 25696 Planarity : 0.005 0.063 12438 Dihedral : 16.236 179.840 50375 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.90 % Favored : 91.71 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.47 (0.10), residues: 6330 helix: -0.08 (0.12), residues: 1902 sheet: -1.11 (0.18), residues: 799 loop : -1.45 (0.10), residues: 3629 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1003 time to evaluate : 5.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 89 residues processed: 1069 average time/residue: 1.2316 time to fit residues: 2285.9612 Evaluate side-chains 1032 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 943 time to evaluate : 6.156 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 1.0235 time to fit residues: 180.6536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 916 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 541 optimal weight: 0.0270 chunk 693 optimal weight: 2.9990 chunk 537 optimal weight: 0.8980 chunk 799 optimal weight: 1.9990 chunk 530 optimal weight: 0.9980 chunk 946 optimal weight: 0.9990 chunk 592 optimal weight: 0.9980 chunk 577 optimal weight: 1.9990 chunk 436 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 3 ASN BA 38 GLN ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 217 GLN BD 139 GLN ** BG 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 80 GLN BH 146 GLN BI 41 GLN BJ 156 GLN BL 20 ASN ** BM 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 55 HIS BQ 72 GLN BQ 96 GLN BR 58 ASN BT 142 GLN ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 120 ASN Bg 88 ASN Bh 69 HIS ** Bl 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.069 137911 Z= 0.154 Angle : 0.578 15.923 203803 Z= 0.299 Chirality : 0.035 0.295 25696 Planarity : 0.004 0.061 12438 Dihedral : 15.972 179.661 50375 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.37 % Favored : 93.24 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.27 (0.10), residues: 6330 helix: 0.07 (0.12), residues: 1917 sheet: -0.91 (0.18), residues: 793 loop : -1.35 (0.10), residues: 3620 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1025 time to evaluate : 6.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 28 residues processed: 1056 average time/residue: 1.1406 time to fit residues: 2079.6936 Evaluate side-chains 1005 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 977 time to evaluate : 6.141 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.9508 time to fit residues: 56.5731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 585 optimal weight: 7.9990 chunk 377 optimal weight: 50.0000 chunk 565 optimal weight: 2.9990 chunk 285 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 601 optimal weight: 6.9990 chunk 644 optimal weight: 4.9990 chunk 467 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 743 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 3 ASN BA 38 GLN BC 97 ASN ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 217 GLN BD 139 GLN BG 28 GLN BH 80 GLN BH 146 GLN BH 157 ASN BI 41 GLN BJ 156 GLN ** BL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 55 HIS BQ 72 GLN BR 45 ASN BR 58 ASN BT 89 ASN BT 142 GLN BT 157 GLN ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 44 ASN Bc 43 HIS Bd 47 ASN Bg 77 ASN Bh 69 HIS ** Bl 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.121 137911 Z= 0.443 Angle : 0.785 14.921 203803 Z= 0.401 Chirality : 0.046 0.357 25696 Planarity : 0.006 0.082 12438 Dihedral : 16.512 179.754 50375 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.88 % Favored : 90.74 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.71 (0.10), residues: 6330 helix: -0.26 (0.12), residues: 1906 sheet: -1.29 (0.18), residues: 808 loop : -1.61 (0.10), residues: 3616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 984 time to evaluate : 6.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 80 residues processed: 1028 average time/residue: 1.2348 time to fit residues: 2203.8981 Evaluate side-chains 1017 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 937 time to evaluate : 6.192 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 1.0047 time to fit residues: 159.3338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 860 optimal weight: 1.9990 chunk 906 optimal weight: 1.9990 chunk 827 optimal weight: 3.9990 chunk 882 optimal weight: 3.9990 chunk 530 optimal weight: 0.9980 chunk 384 optimal weight: 3.9990 chunk 692 optimal weight: 10.0000 chunk 270 optimal weight: 5.9990 chunk 797 optimal weight: 0.9980 chunk 834 optimal weight: 0.3980 chunk 878 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 3 ASN BC 97 ASN ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 217 GLN BG 57 HIS ** BH 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 146 GLN BI 41 GLN BJ 156 GLN ** BL 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 105 ASN BO 117 ASN BR 45 ASN BR 58 ASN BT 142 GLN ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 44 ASN Bc 43 HIS Bd 47 ASN Be 43 HIS Be 56 ASN Bg 88 ASN Bh 69 HIS ** Bl 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 137911 Z= 0.171 Angle : 0.611 15.549 203803 Z= 0.316 Chirality : 0.036 0.335 25696 Planarity : 0.004 0.067 12438 Dihedral : 16.093 179.488 50375 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.57 % Favored : 93.02 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.44 (0.10), residues: 6330 helix: -0.03 (0.12), residues: 1911 sheet: -1.06 (0.18), residues: 828 loop : -1.46 (0.10), residues: 3591 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1013 time to evaluate : 6.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 1035 average time/residue: 1.1962 time to fit residues: 2103.2866 Evaluate side-chains 997 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 979 time to evaluate : 6.234 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 1.0411 time to fit residues: 40.5280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 579 optimal weight: 2.9990 chunk 932 optimal weight: 7.9990 chunk 569 optimal weight: 2.9990 chunk 442 optimal weight: 2.9990 chunk 648 optimal weight: 2.9990 chunk 978 optimal weight: 0.5980 chunk 900 optimal weight: 1.9990 chunk 779 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 601 optimal weight: 5.9990 chunk 477 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 3 ASN BA 38 GLN ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 146 GLN BH 157 ASN BI 41 GLN BJ 156 GLN BP 55 HIS BR 45 ASN BR 58 ASN BT 142 GLN BT 157 GLN ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 5 HIS Bg 77 ASN Bg 88 ASN Bh 52 GLN Bh 69 HIS ** Bl 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 137911 Z= 0.271 Angle : 0.654 15.117 203803 Z= 0.337 Chirality : 0.039 0.328 25696 Planarity : 0.005 0.065 12438 Dihedral : 16.181 179.846 50375 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.10 % Favored : 91.48 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.10), residues: 6330 helix: -0.02 (0.12), residues: 1895 sheet: -0.98 (0.18), residues: 811 loop : -1.50 (0.10), residues: 3624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12660 Ramachandran restraints generated. 6330 Oldfield, 0 Emsley, 6330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 998 time to evaluate : 6.294 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 outliers start: 26 outliers final: 20 residues processed: 1005 average time/residue: 1.1509 time to fit residues: 1996.9782 Evaluate side-chains 988 residues out of total 5354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 968 time to evaluate : 6.142 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.8857 time to fit residues: 41.0731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 618 optimal weight: 6.9990 chunk 829 optimal weight: 0.2980 chunk 238 optimal weight: 10.0000 chunk 718 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 780 optimal weight: 0.0570 chunk 326 optimal weight: 9.9990 chunk 801 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 overall best weight: 4.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 3 ASN BA 38 GLN BC 97 ASN ** BC 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 217 GLN ** BH 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 80 GLN BH 146 GLN ** BI 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 252 ASN BJ 64 HIS BJ 156 GLN ** BL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 55 HIS BR 45 ASN BR 58 ASN BS 118 HIS BT 142 GLN ** BW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 59 HIS ** Ba 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 43 HIS Bg 88 ASN Bh 69 HIS Bi 108 GLN ** Bl 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.104245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.080290 restraints weight = 357832.908| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.92 r_work: 0.3193 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.119 137911 Z= 0.471 Angle : 0.824 13.855 203803 Z= 0.420 Chirality : 0.048 0.384 25696 Planarity : 0.006 0.070 12438 Dihedral : 16.763 179.872 50375 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.61 % Favored : 89.97 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.91 (0.10), residues: 6330 helix: -0.43 (0.12), residues: 1912 sheet: -1.32 (0.18), residues: 823 loop : -1.75 (0.10), residues: 3595 =============================================================================== Job complete usr+sys time: 33520.27 seconds wall clock time: 587 minutes 31.77 seconds (35251.77 seconds total)