Starting phenix.real_space_refine (version: dev) on Wed May 18 06:26:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/05_2022/6hd7_0202_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/05_2022/6hd7_0202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/05_2022/6hd7_0202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/05_2022/6hd7_0202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/05_2022/6hd7_0202_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/05_2022/6hd7_0202_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 18": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 326": "NH1" <-> "NH2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H ARG 140": "NH1" <-> "NH2" Residue "J ARG 30": "NH1" <-> "NH2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "L ARG 23": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 56": "NH1" <-> "NH2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R ARG 128": "NH1" <-> "NH2" Residue "R ARG 175": "NH1" <-> "NH2" Residue "R ARG 181": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 176": "NH1" <-> "NH2" Residue "S ARG 178": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "T ARG 163": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 117": "NH1" <-> "NH2" Residue "U ARG 155": "NH1" <-> "NH2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V ARG 108": "NH1" <-> "NH2" Residue "V ARG 139": "NH1" <-> "NH2" Residue "V PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 32": "NH1" <-> "NH2" Residue "Z ARG 125": "NH1" <-> "NH2" Residue "Z ARG 138": "NH1" <-> "NH2" Residue "a ARG 121": "NH1" <-> "NH2" Residue "b ARG 84": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "f ARG 70": "NH1" <-> "NH2" Residue "h TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 105": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 23": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "s ARG 109": "NH1" <-> "NH2" Residue "s ARG 152": "NH1" <-> "NH2" Residue "s ARG 153": "NH1" <-> "NH2" Residue "s ARG 177": "NH1" <-> "NH2" Residue "t PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 141153 Number of models: 1 Model: "" Number of chains: 52 Chain: "1" Number of atoms: 71309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3335, 71309 Classifications: {'RNA': 3335} Modifications used: {'rna3p_pyr': 1407, 'rna2p_pur': 135, 'rna3p_pur': 1696, 'rna2p_pyr': 97} Link IDs: {'rna3p': 3102, 'rna2p': 232} Chain breaks: 6 Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna3p_pyr': 57, 'rna2p_pur': 3, 'rna3p_pur': 60, 'rna2p_pyr': 1} Link IDs: {'rna3p': 116, 'rna2p': 4} Chain: "4" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna3p_pyr': 76, 'rna2p_pur': 7, 'rna3p_pur': 71, 'rna2p_pyr': 4} Link IDs: {'rna3p': 146, 'rna2p': 11} Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1611 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 35, 'rna2p_pyr': 1, 'rna3p_pyr': 38} Link IDs: {'rna3p': 72, 'rna2p': 3} Chain: "B" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 38, 'p5*END': 1, 'rna3p_pur': 35, 'rna2p_pur': 3} Link IDs: {'rna3p': 72, 'rna2p': 4} Chain: "C" 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: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "E" 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: {'PTRANS': 10, 'TRANS': 240, 'PCIS': 1} 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: "F" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 371, 'PCIS': 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 343, 'PCIS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" 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: "I" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 147, 'PCIS': 1} Chain breaks: 1 Chain: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain: "U" 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: "V" 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: "W" 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: "X" 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: "Y" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 699 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "Z" 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: "a" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "g" 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: "h" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 101, 'PCIS': 1} Chain: "i" 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: "j" 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: "k" 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: "l" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 84, 'PCIS': 1} Chain: "m" 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: "n" 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: "o" 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: "p" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "r" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "s" 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: "t" Number of atoms: 6650 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 838, 6650 Classifications: {'peptide': 838} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 27, 'TRANS': 810} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "u" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1798 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 227} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "v" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1259 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "z" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'3HE': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PHE v 36 " occ=0.79 ... (9 atoms not shown) pdb=" CZ PHE v 36 " occ=0.79 Time building chain proxies: 59.34, per 1000 atoms: 0.42 Number of scatterers: 141153 At special positions: 0 Unit cell: (251.488, 289.428, 261.244, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 134 16.00 P 3766 15.00 O 37044 8.00 N 25871 7.00 C 74338 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 Atom "ATOM 5705 O4' G 1 269 .*. O " rejected from bonding due to valence issues. Atom "ATOM 67387 O5' A 13213 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59402 O5' A 12837 .*. O " rejected from bonding due to valence issues. Atom "ATOM 34002 O4' A 11589 .*. O " rejected from bonding due to valence issues. Atom "ATOM 34090 O5' A 11593 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59402 O5' A 12837 .*. O " rejected from bonding due to valence issues. Atom "ATOM 67409 O5' U 13214 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59402 O5' A 12837 .*. O " rejected from bonding due to valence issues. Atom "ATOM 9609 O5' G 1 450 .*. O " rejected from bonding due to valence issues. Atom "ATOM 1485 O5' C 1 72 .*. O " rejected from bonding due to valence issues. Atom "ATOM 1999 O5' G 1 96 .*. O " rejected from bonding due to valence issues. Atom "ATOM 9612 O4' G 1 450 .*. O " rejected from bonding due to valence issues. Atom "ATOM 74585 O5' U 4 34 .*. O " rejected from bonding due to valence issues. Atom "ATOM 25470 O4' U 11191 .*. O " rejected from bonding due to valence issues. Atom "ATOM 41698 O5' G 11949 .*. O " rejected from bonding due to valence issues. Atom "ATOM 43083 O4' C 12013 .*. O " rejected from bonding due to valence issues. Atom "ATOM 25937 O5' G 11213 .*. O " rejected from bonding due to valence issues. Atom "ATOM 44346 O5' A 12093 .*. O " rejected from bonding due to valence issues. Atom "ATOM 25937 O5' G 11213 .*. O " rejected from bonding due to valence issues. Atom "ATOM 43103 O4' U 12014 .*. O " rejected from bonding due to valence issues. Atom "ATOM 28256 O4' G 11321 .*. O " rejected from bonding due to valence issues. Atom "ATOM 44495 O5' A 12100 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 53.26 Conformation dependent library (CDL) restraints added in 7.1 seconds 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14538 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 260 helices and 50 sheets defined 44.9% alpha, 9.6% beta 1118 base pairs and 1738 stacking pairs defined. Time for finding SS restraints: 60.06 Creating SS restraints... Processing helix chain 'C' and resid 37 through 49 removed outlier: 5.755A pdb=" N GLY C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 34 removed outlier: 5.027A pdb=" N ARG D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 29 " --> pdb=" O GLN D 25 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 92 removed outlier: 4.438A pdb=" N THR D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ARG D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N MET D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.812A pdb=" N GLY E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA E 12 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 39 removed outlier: 3.734A pdb=" N ARG E 37 " --> pdb=" O ASP E 33 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 39' Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.009A pdb=" N VAL E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Proline residue: E 108 - end of helix No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.791A pdb=" N ALA E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU E 191 " --> pdb=" O HIS E 187 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG E 193 " --> pdb=" O TYR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 205 removed outlier: 4.211A pdb=" N MET E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASN E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 205' Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.744A pdb=" N LYS F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 removed outlier: 5.644A pdb=" N LYS F 126 " --> pdb=" O TRP F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 138 removed outlier: 4.601A pdb=" N TYR F 137 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 Processing helix chain 'F' and resid 165 through 170 removed outlier: 4.022A pdb=" N THR F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Proline residue: F 170 - end of helix No H-bonds generated for 'chain 'F' and resid 165 through 170' Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 204 through 209 removed outlier: 4.308A pdb=" N VAL F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 4.463A pdb=" N ARG F 232 " --> pdb=" O GLY F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 removed outlier: 7.343A pdb=" N LEU F 351 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU F 352 " --> pdb=" O ARG F 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 347 through 352' Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'G' and resid 31 through 47 removed outlier: 4.248A pdb=" N LYS G 44 " --> pdb=" O THR G 40 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 130 removed outlier: 4.396A pdb=" N ALA G 130 " --> pdb=" O ILE G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 139 removed outlier: 3.999A pdb=" N ARG G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY G 139 " --> pdb=" O VAL G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 removed outlier: 4.406A pdb=" N SER G 158 " --> pdb=" O THR G 154 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 159' Processing helix chain 'G' and resid 161 through 173 removed outlier: 3.524A pdb=" N ALA G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 185 removed outlier: 3.691A pdb=" N VAL G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU G 182 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER G 184 " --> pdb=" O LYS G 180 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS G 185 " --> pdb=" O VAL G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 removed outlier: 4.006A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASN G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 Proline residue: G 240 - end of helix Processing helix chain 'G' and resid 251 through 262 removed outlier: 4.010A pdb=" N ASP G 259 " --> pdb=" O PHE G 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 292 removed outlier: 4.497A pdb=" N ILE G 289 " --> pdb=" O ASP G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 300 removed outlier: 4.364A pdb=" N SER G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA G 298 " --> pdb=" O GLU G 294 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG G 300 " --> pdb=" O GLN G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 329 removed outlier: 4.148A pdb=" N LEU G 327 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN G 328 " --> pdb=" O LEU G 324 " (cutoff:3.500A) Proline residue: G 329 - end of helix Processing helix chain 'G' and resid 330 through 338 Processing helix chain 'G' and resid 352 through 361 Processing helix chain 'G' and resid 56 through 61 removed outlier: 5.440A pdb=" N GLN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR G 60 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER G 61 " --> pdb=" O HIS G 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 61' Processing helix chain 'H' and resid 9 through 16 removed outlier: 4.240A pdb=" N ARG H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE H 16 " --> pdb=" O TYR H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 26 removed outlier: 3.909A pdb=" N GLU H 25 " --> pdb=" O ARG H 21 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 4.383A pdb=" N ARG H 35 " --> pdb=" O TYR H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 4.833A pdb=" N LEU H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Proline residue: H 84 - end of helix removed outlier: 3.577A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 79 through 87' Processing helix chain 'H' and resid 94 through 114 removed outlier: 3.561A pdb=" N LEU H 113 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 120 removed outlier: 4.926A pdb=" N TYR H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 115 through 120' Processing helix chain 'H' and resid 157 through 170 removed outlier: 3.578A pdb=" N GLY H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY H 170 " --> pdb=" O ALA H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 201 removed outlier: 3.866A pdb=" N LEU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 214 removed outlier: 3.560A pdb=" N ASP H 214 " --> pdb=" O GLU H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 223 removed outlier: 4.024A pdb=" N PHE H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE H 223 " --> pdb=" O PHE H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 230 Processing helix chain 'H' and resid 232 through 251 removed outlier: 3.960A pdb=" N LEU H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP H 238 " --> pdb=" O ASP H 234 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER H 242 " --> pdb=" O ASP H 238 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA H 243 " --> pdb=" O ILE H 239 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Proline residue: H 251 - end of helix Processing helix chain 'H' and resid 261 through 274 removed outlier: 3.749A pdb=" N TYR H 265 " --> pdb=" O THR H 261 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR H 272 " --> pdb=" O GLU H 268 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG H 273 " --> pdb=" O SER H 269 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN H 274 " --> pdb=" O LYS H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 294 removed outlier: 3.596A pdb=" N ARG H 282 " --> pdb=" O SER H 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 107 removed outlier: 4.180A pdb=" N PHE I 106 " --> pdb=" O ASN I 102 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA I 107 " --> pdb=" O VAL I 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 102 through 107' Processing helix chain 'I' and resid 131 through 150 removed outlier: 3.877A pdb=" N VAL I 135 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 162 removed outlier: 4.286A pdb=" N TYR I 158 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER I 160 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA I 161 " --> pdb=" O GLN I 157 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N SER I 162 " --> pdb=" O TYR I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 73 removed outlier: 3.825A pdb=" N GLY J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 120 through 131 removed outlier: 4.201A pdb=" N LEU J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 151 removed outlier: 5.497A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 removed outlier: 4.185A pdb=" N ILE J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.571A pdb=" N LEU J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 203 removed outlier: 4.131A pdb=" N ALA J 198 " --> pdb=" O HIS J 194 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TRP J 203 " --> pdb=" O ASN J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 244 removed outlier: 4.919A pdb=" N ASN J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS J 238 " --> pdb=" O GLU J 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 69 Processing helix chain 'K' and resid 72 through 77 removed outlier: 4.942A pdb=" N ALA K 76 " --> pdb=" O PRO K 72 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLN K 77 " --> pdb=" O PRO K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 77' Processing helix chain 'K' and resid 83 through 98 removed outlier: 4.001A pdb=" N LYS K 96 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR K 97 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG K 98 " --> pdb=" O PHE K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 119 Processing helix chain 'K' and resid 135 through 146 Processing helix chain 'K' and resid 159 through 174 removed outlier: 4.670A pdb=" N VAL K 163 " --> pdb=" O PRO K 159 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL K 164 " --> pdb=" O ILE K 160 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE K 165 " --> pdb=" O GLU K 161 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) Proline residue: K 167 - end of helix Processing helix chain 'K' and resid 182 through 191 removed outlier: 5.505A pdb=" N LEU K 186 " --> pdb=" O GLY K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 233 removed outlier: 3.568A pdb=" N LEU K 211 " --> pdb=" O ASP K 207 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA K 212 " --> pdb=" O GLU K 208 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP K 224 " --> pdb=" O ALA K 220 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS K 225 " --> pdb=" O ASN K 221 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR K 226 " --> pdb=" O PHE K 222 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASP K 227 " --> pdb=" O ALA K 223 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLU K 228 " --> pdb=" O ASP K 224 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL K 229 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TRP K 233 " --> pdb=" O VAL K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 254 Processing helix chain 'L' and resid 61 through 84 Processing helix chain 'L' and resid 150 through 166 removed outlier: 4.813A pdb=" N VAL L 154 " --> pdb=" O SER L 150 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS L 165 " --> pdb=" O LEU L 161 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG L 166 " --> pdb=" O GLN L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 176 removed outlier: 3.707A pdb=" N PHE L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU L 176 " --> pdb=" O ILE L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 171 through 176' Processing helix chain 'M' and resid 27 through 41 removed outlier: 3.846A pdb=" N THR M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 88 removed outlier: 4.649A pdb=" N GLU M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU M 88 " --> pdb=" O LEU M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 141 removed outlier: 3.579A pdb=" N ARG M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 167 removed outlier: 3.710A pdb=" N THR M 159 " --> pdb=" O THR M 155 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN M 165 " --> pdb=" O SER M 161 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS M 166 " --> pdb=" O TRP M 162 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR M 167 " --> pdb=" O PHE M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 22 removed outlier: 4.513A pdb=" N ARG N 21 " --> pdb=" O HIS N 17 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL N 22 " --> pdb=" O TRP N 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 17 through 22' Processing helix chain 'N' and resid 27 through 47 removed outlier: 5.219A pdb=" N LYS N 31 " --> pdb=" O ASP N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 4.645A pdb=" N VAL N 80 " --> pdb=" O THR N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 94 Processing helix chain 'N' and resid 105 through 124 removed outlier: 3.803A pdb=" N PHE N 109 " --> pdb=" O ASN N 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS N 122 " --> pdb=" O GLU N 118 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE N 123 " --> pdb=" O TYR N 119 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE N 124 " --> pdb=" O GLN N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 146 removed outlier: 5.841A pdb=" N THR N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Proline residue: N 146 - end of helix No H-bonds generated for 'chain 'N' and resid 140 through 146' Processing helix chain 'N' and resid 165 through 193 removed outlier: 5.102A pdb=" N THR N 169 " --> pdb=" O SER N 165 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLY N 181 " --> pdb=" O LYS N 177 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE N 182 " --> pdb=" O LYS N 178 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS N 190 " --> pdb=" O ARG N 186 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA N 191 " --> pdb=" O ALA N 187 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU N 192 " --> pdb=" O ARG N 188 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA N 193 " --> pdb=" O GLU N 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 64 removed outlier: 3.749A pdb=" N VAL O 63 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 59 through 64' Processing helix chain 'O' and resid 77 through 89 removed outlier: 3.577A pdb=" N ALA O 88 " --> pdb=" O LYS O 84 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA O 89 " --> pdb=" O TRP O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 98 removed outlier: 5.736A pdb=" N SER O 98 " --> pdb=" O TRP O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 112 removed outlier: 3.743A pdb=" N ALA O 111 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU O 112 " --> pdb=" O ARG O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 136 removed outlier: 4.827A pdb=" N ALA O 136 " --> pdb=" O LYS O 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 removed outlier: 4.112A pdb=" N LEU P 7 " --> pdb=" O ALA P 3 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG P 12 " --> pdb=" O GLU P 8 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 34 removed outlier: 3.817A pdb=" N LEU P 22 " --> pdb=" O VAL P 18 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG P 31 " --> pdb=" O VAL P 27 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN P 32 " --> pdb=" O TRP P 28 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 52 removed outlier: 3.662A pdb=" N ARG P 50 " --> pdb=" O ASP P 46 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU P 51 " --> pdb=" O LYS P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 88 removed outlier: 4.870A pdb=" N GLN P 87 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLY P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 83 through 88' Processing helix chain 'P' and resid 97 through 111 Processing helix chain 'P' and resid 139 through 145 removed outlier: 5.304A pdb=" N ASP P 145 " --> pdb=" O ALA P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 153 removed outlier: 5.537A pdb=" N TRP P 150 " --> pdb=" O ALA P 146 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE P 151 " --> pdb=" O ARG P 147 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N CYS P 152 " --> pdb=" O TYR P 148 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP P 153 " --> pdb=" O ASN P 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 146 through 153' Processing helix chain 'P' and resid 158 through 163 removed outlier: 4.058A pdb=" N ARG P 162 " --> pdb=" O HIS P 158 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY P 163 " --> pdb=" O ARG P 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 158 through 163' Processing helix chain 'P' and resid 165 through 173 removed outlier: 3.912A pdb=" N LYS P 169 " --> pdb=" O THR P 165 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS P 170 " --> pdb=" O ALA P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 196 removed outlier: 3.575A pdb=" N GLN P 194 " --> pdb=" O THR P 190 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR P 196 " --> pdb=" O LYS P 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.713A pdb=" N VAL Q 22 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS Q 25 " --> pdb=" O SER Q 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN Q 29 " --> pdb=" O LYS Q 25 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY Q 30 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 61 removed outlier: 3.613A pdb=" N ARG Q 59 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS Q 60 " --> pdb=" O ASP Q 56 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA Q 61 " --> pdb=" O PHE Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 89 removed outlier: 3.518A pdb=" N PHE Q 80 " --> pdb=" O PRO Q 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY Q 86 " --> pdb=" O LYS Q 82 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N MET Q 87 " --> pdb=" O ALA Q 83 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER Q 89 " --> pdb=" O ARG Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 103 removed outlier: 3.649A pdb=" N LEU Q 99 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU Q 100 " --> pdb=" O LYS Q 96 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG Q 101 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU Q 102 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS Q 103 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 129 removed outlier: 3.541A pdb=" N ARG Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 146 removed outlier: 3.698A pdb=" N SER Q 144 " --> pdb=" O LYS Q 140 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL Q 145 " --> pdb=" O LEU Q 141 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY Q 146 " --> pdb=" O SER Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 186 removed outlier: 3.715A pdb=" N VAL Q 162 " --> pdb=" O ALA Q 158 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS Q 177 " --> pdb=" O ALA Q 173 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER Q 180 " --> pdb=" O LYS Q 176 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA Q 185 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA Q 186 " --> pdb=" O ASN Q 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 198 removed outlier: 3.847A pdb=" N LYS Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 15 removed outlier: 3.910A pdb=" N SER R 14 " --> pdb=" O ASN R 10 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA R 15 " --> pdb=" O PRO R 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 10 through 15' Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.528A pdb=" N GLU R 31 " --> pdb=" O LYS R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 54 removed outlier: 3.814A pdb=" N LYS R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 106 removed outlier: 5.071A pdb=" N VAL R 88 " --> pdb=" O PRO R 84 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE R 90 " --> pdb=" O LYS R 86 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU R 94 " --> pdb=" O PHE R 90 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN R 97 " --> pdb=" O GLY R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 183 removed outlier: 3.584A pdb=" N ARG R 173 " --> pdb=" O THR R 169 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG R 175 " --> pdb=" O ARG R 171 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE R 176 " --> pdb=" O GLN R 172 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN R 179 " --> pdb=" O ARG R 175 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS R 180 " --> pdb=" O ILE R 176 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE R 182 " --> pdb=" O ALA R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 76 removed outlier: 4.253A pdb=" N GLY R 73 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS R 74 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU R 75 " --> pdb=" O GLN R 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE R 76 " --> pdb=" O GLY R 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 70 through 76' Processing helix chain 'S' and resid 23 through 40 removed outlier: 3.800A pdb=" N LEU S 29 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG S 39 " --> pdb=" O PHE S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 54 removed outlier: 3.623A pdb=" N LYS S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL S 47 " --> pdb=" O PRO S 43 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL S 48 " --> pdb=" O PHE S 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU S 49 " --> pdb=" O ASN S 45 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 Proline residue: S 60 - end of helix Processing helix chain 'S' and resid 63 through 73 removed outlier: 3.771A pdb=" N ILE S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN S 73 " --> pdb=" O ARG S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 118 removed outlier: 3.693A pdb=" N ALA S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL S 115 " --> pdb=" O ARG S 111 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS S 116 " --> pdb=" O ALA S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 132 removed outlier: 3.536A pdb=" N LEU S 127 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG S 130 " --> pdb=" O GLN S 126 " (cutoff:3.500A) Proline residue: S 132 - end of helix Processing helix chain 'S' and resid 147 through 153 removed outlier: 5.731A pdb=" N ARG S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N HIS S 152 " --> pdb=" O GLU S 148 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE S 153 " --> pdb=" O ALA S 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 147 through 153' Processing helix chain 'T' and resid 4 through 16 removed outlier: 3.767A pdb=" N LYS T 8 " --> pdb=" O LEU T 4 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG T 9 " --> pdb=" O ARG T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 36 removed outlier: 3.652A pdb=" N THR T 29 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU T 31 " --> pdb=" O ASN T 27 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN T 34 " --> pdb=" O SER T 30 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA T 35 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.668A pdb=" N LYS T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY T 48 " --> pdb=" O LEU T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 77 through 82 removed outlier: 3.731A pdb=" N ARG T 81 " --> pdb=" O GLY T 77 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS T 82 " --> pdb=" O TYR T 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 77 through 82' Processing helix chain 'T' and resid 84 through 113 Proline residue: T 90 - end of helix removed outlier: 6.683A pdb=" N VAL T 93 " --> pdb=" O LEU T 89 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL T 94 " --> pdb=" O PRO T 90 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL T 101 " --> pdb=" O ARG T 97 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU T 102 " --> pdb=" O ARG T 98 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS T 108 " --> pdb=" O ARG T 104 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR T 109 " --> pdb=" O LEU T 105 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY T 113 " --> pdb=" O TYR T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 130 removed outlier: 3.747A pdb=" N TYR T 120 " --> pdb=" O ASP T 116 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS T 125 " --> pdb=" O HIS T 121 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU T 126 " --> pdb=" O VAL T 122 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS T 128 " --> pdb=" O TYR T 124 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY T 129 " --> pdb=" O LYS T 125 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN T 130 " --> pdb=" O GLU T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 187 removed outlier: 3.714A pdb=" N HIS T 141 " --> pdb=" O ALA T 137 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU T 158 " --> pdb=" O ALA T 154 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA T 159 " --> pdb=" O LEU T 155 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU T 160 " --> pdb=" O ASN T 156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG T 163 " --> pdb=" O ALA T 159 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN T 166 " --> pdb=" O ARG T 162 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG T 167 " --> pdb=" O ARG T 163 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA T 168 " --> pdb=" O LEU T 164 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA T 169 " --> pdb=" O LYS T 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG T 176 " --> pdb=" O ARG T 172 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL T 177 " --> pdb=" O ARG T 173 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU T 179 " --> pdb=" O GLN T 175 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS T 180 " --> pdb=" O ARG T 176 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP T 182 " --> pdb=" O ALA T 178 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA T 183 " --> pdb=" O GLU T 179 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU T 184 " --> pdb=" O LYS T 180 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU T 185 " --> pdb=" O ARG T 181 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS T 186 " --> pdb=" O ASP T 182 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 49 removed outlier: 3.933A pdb=" N ALA U 37 " --> pdb=" O ASN U 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE U 44 " --> pdb=" O ARG U 40 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS U 47 " --> pdb=" O TYR U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 114 removed outlier: 4.379A pdb=" N ALA U 112 " --> pdb=" O GLN U 108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG U 113 " --> pdb=" O ASP U 109 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS U 114 " --> pdb=" O MET U 110 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 145 removed outlier: 5.953A pdb=" N LYS U 141 " --> pdb=" O ARG U 137 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE U 143 " --> pdb=" O TYR U 139 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU U 144 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR U 145 " --> pdb=" O LYS U 141 " (cutoff:3.500A) Processing helix chain 'V' and resid 27 through 33 removed outlier: 3.914A pdb=" N LEU V 31 " --> pdb=" O LEU V 27 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS V 32 " --> pdb=" O SER V 28 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL V 33 " --> pdb=" O THR V 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 27 through 33' Processing helix chain 'V' and resid 92 through 97 removed outlier: 3.886A pdb=" N ILE V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS V 97 " --> pdb=" O VAL V 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 92 through 97' Processing helix chain 'V' and resid 99 through 123 removed outlier: 3.930A pdb=" N GLN V 103 " --> pdb=" O SER V 99 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU V 118 " --> pdb=" O ALA V 114 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA V 121 " --> pdb=" O ALA V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 26 removed outlier: 3.787A pdb=" N ASN W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY W 26 " --> pdb=" O PRO W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 41 removed outlier: 3.510A pdb=" N TYR W 33 " --> pdb=" O ASP W 29 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP W 39 " --> pdb=" O LYS W 35 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS W 40 " --> pdb=" O TYR W 36 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE W 41 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 88 removed outlier: 4.119A pdb=" N LEU W 76 " --> pdb=" O SER W 72 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN W 87 " --> pdb=" O TYR W 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN W 88 " --> pdb=" O LEU W 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 71 removed outlier: 3.950A pdb=" N ARG X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS X 71 " --> pdb=" O PRO X 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 66 through 71' Processing helix chain 'X' and resid 119 through 127 removed outlier: 3.508A pdb=" N ALA X 123 " --> pdb=" O GLY X 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU X 125 " --> pdb=" O GLU X 121 " (cutoff:3.500A) Proline residue: X 127 - end of helix Processing helix chain 'X' and resid 128 through 133 removed outlier: 4.007A pdb=" N ASN X 132 " --> pdb=" O ARG X 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 43 removed outlier: 3.757A pdb=" N LYS Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN Y 42 " --> pdb=" O SER Y 38 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG Y 43 " --> pdb=" O LEU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 50 removed outlier: 5.917A pdb=" N ALA Y 50 " --> pdb=" O PRO Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 60 removed outlier: 3.634A pdb=" N ARG Y 56 " --> pdb=" O THR Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 69 removed outlier: 4.544A pdb=" N ALA Y 68 " --> pdb=" O THR Y 64 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 64 through 69' Processing helix chain 'Y' and resid 86 through 93 removed outlier: 4.654A pdb=" N ILE Y 90 " --> pdb=" O SER Y 86 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Y 92 " --> pdb=" O ASP Y 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 64 removed outlier: 3.505A pdb=" N VAL Z 62 " --> pdb=" O ASP Z 58 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE Z 63 " --> pdb=" O SER Z 59 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU Z 64 " --> pdb=" O TYR Z 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 58 through 64' Processing helix chain 'Z' and resid 69 through 79 removed outlier: 3.640A pdb=" N ASP Z 78 " --> pdb=" O LYS Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 103 removed outlier: 4.394A pdb=" N LYS Z 97 " --> pdb=" O TYR Z 93 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA Z 98 " --> pdb=" O GLN Z 94 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL Z 99 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS Z 100 " --> pdb=" O LYS Z 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU Z 101 " --> pdb=" O LYS Z 97 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 140 removed outlier: 4.305A pdb=" N ASN Z 137 " --> pdb=" O LEU Z 133 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG Z 138 " --> pdb=" O ASP Z 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 21 Processing helix chain 'a' and resid 23 through 32 removed outlier: 4.099A pdb=" N ARG a 28 " --> pdb=" O SER a 24 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU a 30 " --> pdb=" O GLN a 26 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER a 32 " --> pdb=" O ARG a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 43 removed outlier: 3.764A pdb=" N ALA a 41 " --> pdb=" O LYS a 37 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 105 removed outlier: 4.207A pdb=" N LEU a 104 " --> pdb=" O HIS a 100 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL a 105 " --> pdb=" O PRO a 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 100 through 105' Processing helix chain 'a' and resid 112 through 123 removed outlier: 5.209A pdb=" N LYS a 116 " --> pdb=" O ASP a 112 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS a 122 " --> pdb=" O LEU a 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY a 123 " --> pdb=" O ILE a 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 67 removed outlier: 4.228A pdb=" N LYS b 67 " --> pdb=" O ALA b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 81 removed outlier: 4.025A pdb=" N LEU b 80 " --> pdb=" O ASN b 76 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU b 81 " --> pdb=" O TYR b 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 76 through 81' Processing helix chain 'b' and resid 92 through 97 removed outlier: 3.708A pdb=" N VAL b 96 " --> pdb=" O PHE b 92 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER b 97 " --> pdb=" O LYS b 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 92 through 97' Processing helix chain 'b' and resid 103 through 124 removed outlier: 4.370A pdb=" N GLU b 108 " --> pdb=" O PRO b 104 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU b 109 " --> pdb=" O SER b 105 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA b 110 " --> pdb=" O GLN b 106 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS b 111 " --> pdb=" O ARG b 107 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS b 112 " --> pdb=" O GLU b 108 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL b 113 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU b 120 " --> pdb=" O LYS b 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN b 123 " --> pdb=" O GLU b 119 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA b 124 " --> pdb=" O GLU b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 133 removed outlier: 5.268A pdb=" N LYS b 133 " --> pdb=" O TRP b 129 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.849A pdb=" N LYS c 10 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG c 12 " --> pdb=" O THR c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 48 removed outlier: 4.815A pdb=" N LYS c 47 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TYR c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 64 through 69 removed outlier: 4.101A pdb=" N PHE c 68 " --> pdb=" O GLN c 64 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 83 removed outlier: 5.361A pdb=" N TRP c 79 " --> pdb=" O LEU c 75 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR c 80 " --> pdb=" O ASP c 76 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU c 81 " --> pdb=" O LYS c 77 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE c 82 " --> pdb=" O LEU c 78 " (cutoff:3.500A) Proline residue: c 83 - end of helix Processing helix chain 'c' and resid 84 through 93 removed outlier: 4.370A pdb=" N ASP c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLN c 89 " --> pdb=" O ASP c 85 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER c 93 " --> pdb=" O GLN c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 108 removed outlier: 4.426A pdb=" N ALA c 107 " --> pdb=" O ASP c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 142 removed outlier: 3.607A pdb=" N GLU c 136 " --> pdb=" O LYS c 132 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS c 137 " --> pdb=" O LEU c 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 20 removed outlier: 5.068A pdb=" N LYS d 15 " --> pdb=" O ASN d 11 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN d 19 " --> pdb=" O LYS d 15 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY d 20 " --> pdb=" O ALA d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 59 removed outlier: 4.229A pdb=" N LYS d 52 " --> pdb=" O HIS d 48 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA d 57 " --> pdb=" O ALA d 53 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS d 58 " --> pdb=" O LEU d 54 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS d 59 " --> pdb=" O ALA d 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 21 removed outlier: 5.353A pdb=" N LYS e 13 " --> pdb=" O SER e 9 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS e 19 " --> pdb=" O ALA e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 26 through 37 removed outlier: 4.217A pdb=" N GLN e 36 " --> pdb=" O LYS e 32 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY e 37 " --> pdb=" O SER e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 64 removed outlier: 3.587A pdb=" N ALA e 60 " --> pdb=" O LEU e 56 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET e 61 " --> pdb=" O GLU e 57 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU e 62 " --> pdb=" O TYR e 58 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER e 63 " --> pdb=" O TYR e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 82 removed outlier: 3.608A pdb=" N VAL e 81 " --> pdb=" O LEU e 77 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY e 82 " --> pdb=" O GLY e 78 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 104 removed outlier: 4.554A pdb=" N THR e 103 " --> pdb=" O ASP e 99 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 99 through 104' Processing helix chain 'f' and resid 15 through 21 removed outlier: 3.993A pdb=" N ARG f 19 " --> pdb=" O ASN f 15 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS f 21 " --> pdb=" O HIS f 17 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 45 removed outlier: 5.175A pdb=" N ALA f 29 " --> pdb=" O PHE f 25 " (cutoff:3.500A) Proline residue: f 30 - end of helix Processing helix chain 'f' and resid 52 through 61 removed outlier: 4.067A pdb=" N LYS f 61 " --> pdb=" O GLN f 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 26 removed outlier: 4.308A pdb=" N TYR g 25 " --> pdb=" O HIS g 21 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS g 26 " --> pdb=" O SER g 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 21 through 26' Processing helix chain 'g' and resid 40 through 45 removed outlier: 3.722A pdb=" N ARG g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG g 45 " --> pdb=" O VAL g 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 40 through 45' Processing helix chain 'g' and resid 78 through 86 removed outlier: 4.034A pdb=" N LEU g 82 " --> pdb=" O ASN g 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR g 84 " --> pdb=" O LYS g 80 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU g 85 " --> pdb=" O ASP g 81 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR g 86 " --> pdb=" O LEU g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 116 removed outlier: 4.084A pdb=" N VAL g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL g 107 " --> pdb=" O LYS g 103 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA g 114 " --> pdb=" O ALA g 110 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU g 115 " --> pdb=" O ARG g 111 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 42 Processing helix chain 'i' and resid 61 through 66 removed outlier: 3.717A pdb=" N VAL i 65 " --> pdb=" O GLN i 61 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER i 66 " --> pdb=" O TYR i 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 61 through 66' Processing helix chain 'i' and resid 81 through 110 removed outlier: 4.888A pdb=" N VAL i 85 " --> pdb=" O CYS i 81 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS i 106 " --> pdb=" O LYS i 102 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU i 107 " --> pdb=" O LYS i 103 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN i 108 " --> pdb=" O VAL i 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 12 removed outlier: 5.517A pdb=" N LEU j 9 " --> pdb=" O LYS j 5 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR j 11 " --> pdb=" O TYR j 7 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS j 12 " --> pdb=" O GLU j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 39 removed outlier: 3.944A pdb=" N LEU j 17 " --> pdb=" O SER j 13 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA j 18 " --> pdb=" O LYS j 14 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER j 19 " --> pdb=" O GLU j 15 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU j 28 " --> pdb=" O LEU j 24 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA j 29 " --> pdb=" O LYS j 25 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN j 34 " --> pdb=" O GLU j 30 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU j 36 " --> pdb=" O LYS j 32 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER j 37 " --> pdb=" O VAL j 33 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG j 38 " --> pdb=" O GLN j 34 " (cutoff:3.500A) Proline residue: j 39 - end of helix Processing helix chain 'j' and resid 43 through 71 removed outlier: 4.310A pdb=" N VAL j 47 " --> pdb=" O LYS j 43 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG j 48 " --> pdb=" O ILE j 44 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL j 66 " --> pdb=" O GLN j 62 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU j 69 " --> pdb=" O ALA j 65 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 82 removed outlier: 3.574A pdb=" N ARG j 81 " --> pdb=" O PRO j 77 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA j 82 " --> pdb=" O LYS j 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 77 through 82' Processing helix chain 'j' and resid 85 through 91 removed outlier: 4.531A pdb=" N ALA j 91 " --> pdb=" O ALA j 87 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 99 removed outlier: 3.628A pdb=" N GLN j 99 " --> pdb=" O PHE j 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 101 through 111 removed outlier: 3.654A pdb=" N LYS j 107 " --> pdb=" O LYS j 103 " (cutoff:3.500A) Processing helix chain 'k' and resid 34 through 49 removed outlier: 5.610A pdb=" N LYS k 38 " --> pdb=" O SER k 34 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE k 39 " --> pdb=" O ASN k 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL k 40 " --> pdb=" O ARG k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 64 removed outlier: 3.649A pdb=" N ARG k 62 " --> pdb=" O ILE k 58 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN k 63 " --> pdb=" O ASP k 59 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 77 removed outlier: 3.878A pdb=" N ALA k 69 " --> pdb=" O GLY k 65 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG k 70 " --> pdb=" O GLU k 66 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS k 71 " --> pdb=" O LYS k 67 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 98 removed outlier: 3.943A pdb=" N ALA k 83 " --> pdb=" O SER k 79 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA k 85 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS k 86 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET k 90 " --> pdb=" O LYS k 86 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN k 91 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN k 92 " --> pdb=" O GLU k 88 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER k 97 " --> pdb=" O ILE k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 12 removed outlier: 4.443A pdb=" N PHE l 8 " --> pdb=" O GLY l 4 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY l 9 " --> pdb=" O THR l 5 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS l 10 " --> pdb=" O PRO l 6 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG l 11 " --> pdb=" O SER l 7 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS l 12 " --> pdb=" O PHE l 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 4 through 12' Processing helix chain 'l' and resid 50 through 58 removed outlier: 3.916A pdb=" N HIS l 57 " --> pdb=" O ALA l 53 " (cutoff:3.500A) Processing helix chain 'l' and resid 65 through 77 removed outlier: 4.875A pdb=" N HIS l 69 " --> pdb=" O ARG l 65 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL l 70 " --> pdb=" O TYR l 66 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER l 71 " --> pdb=" O LEU l 67 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG l 72 " --> pdb=" O LYS l 68 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG l 73 " --> pdb=" O HIS l 69 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN l 76 " --> pdb=" O ARG l 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 18 removed outlier: 3.678A pdb=" N PHE m 11 " --> pdb=" O ASP m 7 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA m 18 " --> pdb=" O LEU m 14 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 69 removed outlier: 3.717A pdb=" N LYS m 64 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN m 67 " --> pdb=" O LYS m 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER m 68 " --> pdb=" O LYS m 64 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU m 69 " --> pdb=" O LEU m 65 " (cutoff:3.500A) Processing helix chain 'n' and resid 6 through 21 removed outlier: 4.024A pdb=" N LYS n 10 " --> pdb=" O SER n 6 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 30 removed outlier: 4.483A pdb=" N ARG n 28 " --> pdb=" O PRO n 24 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU n 29 " --> pdb=" O GLN n 25 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG n 30 " --> pdb=" O TRP n 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 24 through 30' Processing helix chain 'o' and resid 79 through 90 removed outlier: 4.126A pdb=" N LEU o 85 " --> pdb=" O SER o 81 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA o 86 " --> pdb=" O LEU o 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS o 88 " --> pdb=" O ALA o 84 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR o 89 " --> pdb=" O LEU o 85 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN o 90 " --> pdb=" O ALA o 86 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 25 removed outlier: 4.164A pdb=" N LYS p 8 " --> pdb=" O LYS p 4 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG p 9 " --> pdb=" O TRP p 5 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER p 24 " --> pdb=" O VAL p 20 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS p 25 " --> pdb=" O ARG p 21 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 46 removed outlier: 4.136A pdb=" N PHE s 45 " --> pdb=" O THR s 41 " (cutoff:3.500A) Proline residue: s 46 - end of helix No H-bonds generated for 'chain 's' and resid 41 through 46' Processing helix chain 's' and resid 60 through 79 removed outlier: 3.577A pdb=" N VAL s 78 " --> pdb=" O TYR s 74 " (cutoff:3.500A) Processing helix chain 's' and resid 143 through 159 removed outlier: 4.430A pdb=" N GLU s 149 " --> pdb=" O ASP s 145 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG s 152 " --> pdb=" O VAL s 148 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA s 154 " --> pdb=" O GLY s 150 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG s 155 " --> pdb=" O LEU s 151 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR s 156 " --> pdb=" O ARG s 152 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS s 157 " --> pdb=" O ARG s 153 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE s 158 " --> pdb=" O ALA s 154 " (cutoff:3.500A) Proline residue: s 159 - end of helix Processing helix chain 's' and resid 176 through 187 removed outlier: 4.085A pdb=" N TYR s 180 " --> pdb=" O ASP s 176 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU s 185 " --> pdb=" O LEU s 181 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA s 186 " --> pdb=" O LYS s 182 " (cutoff:3.500A) Processing helix chain 's' and resid 204 through 212 removed outlier: 4.580A pdb=" N ASN s 208 " --> pdb=" O SER s 204 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE s 209 " --> pdb=" O LEU s 205 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG s 210 " --> pdb=" O GLU s 206 " (cutoff:3.500A) Processing helix chain 's' and resid 213 through 218 removed outlier: 4.402A pdb=" N ALA s 217 " --> pdb=" O PRO s 213 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA s 218 " --> pdb=" O GLU s 214 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 213 through 218' Processing helix chain 't' and resid 17 through 34 removed outlier: 6.125A pdb=" N ASN t 21 " --> pdb=" O LEU t 17 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS t 29 " --> pdb=" O LEU t 25 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU t 30 " --> pdb=" O GLU t 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR t 31 " --> pdb=" O ALA t 27 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS t 34 " --> pdb=" O LEU t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 35 through 50 removed outlier: 5.179A pdb=" N SER t 39 " --> pdb=" O GLN t 35 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 68 removed outlier: 3.569A pdb=" N GLY t 68 " --> pdb=" O LEU t 64 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 85 removed outlier: 4.822A pdb=" N ALA t 73 " --> pdb=" O GLU t 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU t 85 " --> pdb=" O ILE t 81 " (cutoff:3.500A) Processing helix chain 't' and resid 90 through 105 removed outlier: 3.722A pdb=" N CYS t 94 " --> pdb=" O SER t 90 " (cutoff:3.500A) Processing helix chain 't' and resid 106 through 121 removed outlier: 3.822A pdb=" N SER t 110 " --> pdb=" O GLU t 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY t 121 " --> pdb=" O ALA t 117 " (cutoff:3.500A) Processing helix chain 't' and resid 124 through 139 removed outlier: 4.547A pdb=" N TYR t 128 " --> pdb=" O ASN t 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG t 129 " --> pdb=" O LYS t 125 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER t 136 " --> pdb=" O ALA t 132 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE t 138 " --> pdb=" O LEU t 134 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 156 removed outlier: 3.679A pdb=" N ALA t 144 " --> pdb=" O ASP t 140 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL t 146 " --> pdb=" O LYS t 142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE t 155 " --> pdb=" O TYR t 151 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU t 156 " --> pdb=" O TRP t 152 " (cutoff:3.500A) Processing helix chain 't' and resid 158 through 173 removed outlier: 3.966A pdb=" N TRP t 162 " --> pdb=" O TYR t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 174 through 190 Processing helix chain 't' and resid 195 through 217 removed outlier: 4.328A pdb=" N TYR t 199 " --> pdb=" O ASP t 195 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU t 200 " --> pdb=" O SER t 196 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER t 217 " --> pdb=" O TYR t 213 " (cutoff:3.500A) Processing helix chain 't' and resid 219 through 235 Proline residue: t 235 - end of helix Processing helix chain 't' and resid 239 through 255 removed outlier: 4.001A pdb=" N LEU t 243 " --> pdb=" O ASP t 239 " (cutoff:3.500A) Processing helix chain 't' and resid 256 through 272 removed outlier: 3.764A pdb=" N ALA t 260 " --> pdb=" O GLN t 256 " (cutoff:3.500A) Proline residue: t 272 - end of helix Processing helix chain 't' and resid 274 through 286 removed outlier: 3.579A pdb=" N TYR t 278 " --> pdb=" O ASN t 274 " (cutoff:3.500A) Processing helix chain 't' and resid 290 through 306 removed outlier: 3.989A pdb=" N LYS t 294 " --> pdb=" O ASP t 290 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN t 303 " --> pdb=" O GLY t 299 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE t 304 " --> pdb=" O LYS t 300 " (cutoff:3.500A) Proline residue: t 306 - end of helix Processing helix chain 't' and resid 308 through 319 removed outlier: 5.344A pdb=" N LYS t 312 " --> pdb=" O CYS t 308 " (cutoff:3.500A) Proline residue: t 315 - end of helix removed outlier: 4.644A pdb=" N PHE t 318 " --> pdb=" O ILE t 314 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU t 319 " --> pdb=" O PRO t 315 " (cutoff:3.500A) Processing helix chain 't' and resid 321 through 338 Proline residue: t 335 - end of helix Processing helix chain 't' and resid 343 through 355 Proline residue: t 350 - end of helix Processing helix chain 't' and resid 357 through 375 Proline residue: t 361 - end of helix removed outlier: 3.821A pdb=" N GLY t 373 " --> pdb=" O ASP t 369 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU t 374 " --> pdb=" O TYR t 370 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP t 375 " --> pdb=" O LEU t 371 " (cutoff:3.500A) Processing helix chain 't' and resid 379 through 398 Processing helix chain 't' and resid 399 through 414 removed outlier: 4.860A pdb=" N ALA t 403 " --> pdb=" O ASP t 399 " (cutoff:3.500A) Processing helix chain 't' and resid 417 through 432 removed outlier: 3.878A pdb=" N TYR t 421 " --> pdb=" O LEU t 417 " (cutoff:3.500A) Processing helix chain 't' and resid 433 through 449 removed outlier: 3.717A pdb=" N LEU t 447 " --> pdb=" O GLU t 443 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP t 448 " --> pdb=" O GLY t 444 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU t 449 " --> pdb=" O ARG t 445 " (cutoff:3.500A) Processing helix chain 't' and resid 451 through 466 removed outlier: 4.020A pdb=" N ASN t 455 " --> pdb=" O ASP t 451 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN t 466 " --> pdb=" O PHE t 462 " (cutoff:3.500A) Processing helix chain 't' and resid 467 through 480 removed outlier: 3.795A pdb=" N ALA t 471 " --> pdb=" O ASN t 467 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU t 477 " --> pdb=" O GLU t 473 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N PHE t 478 " --> pdb=" O VAL t 474 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR t 479 " --> pdb=" O ALA t 475 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS t 480 " --> pdb=" O SER t 476 " (cutoff:3.500A) Processing helix chain 't' and resid 487 through 495 removed outlier: 4.010A pdb=" N GLU t 495 " --> pdb=" O LEU t 491 " (cutoff:3.500A) Processing helix chain 't' and resid 496 through 525 removed outlier: 6.030A pdb=" N ILE t 500 " --> pdb=" O ALA t 496 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS t 515 " --> pdb=" O TYR t 511 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS t 516 " --> pdb=" O LEU t 512 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU t 524 " --> pdb=" O ASP t 520 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS t 525 " --> pdb=" O LEU t 521 " (cutoff:3.500A) Processing helix chain 't' and resid 530 through 583 removed outlier: 4.107A pdb=" N GLU t 534 " --> pdb=" O SER t 530 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE t 536 " --> pdb=" O LYS t 532 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA t 537 " --> pdb=" O SER t 533 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN t 538 " --> pdb=" O GLU t 534 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP t 539 " --> pdb=" O GLN t 535 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE t 540 " --> pdb=" O ILE t 536 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN t 559 " --> pdb=" O LEU t 555 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA t 560 " --> pdb=" O LYS t 556 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE t 561 " --> pdb=" O ARG t 557 " (cutoff:3.500A) Proline residue: t 562 - end of helix removed outlier: 4.040A pdb=" N GLN t 572 " --> pdb=" O PHE t 568 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU t 573 " --> pdb=" O GLU t 569 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP t 574 " --> pdb=" O ASP t 570 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N PHE t 575 " --> pdb=" O ASP t 571 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS t 576 " --> pdb=" O GLN t 572 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER t 577 " --> pdb=" O LEU t 573 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET t 580 " --> pdb=" O HIS t 576 " (cutoff:3.500A) Processing helix chain 't' and resid 584 through 598 Processing helix chain 't' and resid 601 through 628 removed outlier: 4.351A pdb=" N SER t 627 " --> pdb=" O LEU t 623 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP t 628 " --> pdb=" O LYS t 624 " (cutoff:3.500A) Processing helix chain 't' and resid 631 through 637 removed outlier: 3.501A pdb=" N ASP t 635 " --> pdb=" O ASP t 631 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE t 637 " --> pdb=" O ASN t 633 " (cutoff:3.500A) Processing helix chain 't' and resid 646 through 670 Processing helix chain 't' and resid 682 through 688 removed outlier: 3.564A pdb=" N ILE t 686 " --> pdb=" O GLY t 682 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU t 687 " --> pdb=" O GLU t 683 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR t 688 " --> pdb=" O LYS t 684 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 682 through 688' Processing helix chain 't' and resid 690 through 699 Processing helix chain 't' and resid 700 through 707 removed outlier: 4.125A pdb=" N VAL t 707 " --> pdb=" O TYR t 703 " (cutoff:3.500A) Processing helix chain 't' and resid 713 through 725 removed outlier: 3.596A pdb=" N ASP t 717 " --> pdb=" O ASP t 713 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG t 723 " --> pdb=" O GLU t 719 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE t 724 " --> pdb=" O PHE t 720 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY t 725 " --> pdb=" O ASN t 721 " (cutoff:3.500A) Processing helix chain 't' and resid 726 through 741 removed outlier: 4.308A pdb=" N CYS t 730 " --> pdb=" O LYS t 726 " (cutoff:3.500A) Processing helix chain 't' and resid 745 through 760 removed outlier: 3.593A pdb=" N GLY t 749 " --> pdb=" O SER t 745 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG t 760 " --> pdb=" O LEU t 756 " (cutoff:3.500A) Processing helix chain 't' and resid 766 through 781 Processing helix chain 't' and resid 796 through 805 removed outlier: 3.847A pdb=" N PHE t 800 " --> pdb=" O ASP t 796 " (cutoff:3.500A) Processing helix chain 't' and resid 809 through 820 removed outlier: 4.015A pdb=" N LEU t 813 " --> pdb=" O ASP t 809 " (cutoff:3.500A) Processing helix chain 't' and resid 826 through 839 removed outlier: 5.734A pdb=" N LEU t 830 " --> pdb=" O GLY t 826 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER t 839 " --> pdb=" O ILE t 835 " (cutoff:3.500A) Processing helix chain 't' and resid 842 through 852 Processing helix chain 't' and resid 786 through 792 removed outlier: 4.027A pdb=" N GLU t 789 " --> pdb=" O PRO t 786 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE t 790 " --> pdb=" O LEU t 787 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER t 791 " --> pdb=" O ASN t 788 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN t 792 " --> pdb=" O GLU t 789 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 786 through 792' Processing helix chain 'u' and resid 9 through 24 removed outlier: 3.946A pdb=" N ILE u 13 " --> pdb=" O THR u 9 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE u 14 " --> pdb=" O ILE u 10 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS u 15 " --> pdb=" O ASN u 11 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU u 24 " --> pdb=" O ASN u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 29 through 40 removed outlier: 3.536A pdb=" N TYR u 33 " --> pdb=" O MET u 29 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TRP u 40 " --> pdb=" O HIS u 36 " (cutoff:3.500A) Processing helix chain 'u' and resid 128 through 144 removed outlier: 5.204A pdb=" N ASN u 132 " --> pdb=" O GLY u 128 " (cutoff:3.500A) Processing helix chain 'u' and resid 158 through 166 Processing helix chain 'u' and resid 195 through 200 removed outlier: 4.457A pdb=" N LEU u 199 " --> pdb=" O LYS u 195 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN u 200 " --> pdb=" O LEU u 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 195 through 200' Processing helix chain 'v' and resid 15 through 27 removed outlier: 3.678A pdb=" N LEU v 19 " --> pdb=" O ASN v 15 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA v 23 " --> pdb=" O LEU v 19 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS v 24 " --> pdb=" O THR v 20 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL v 27 " --> pdb=" O ALA v 23 " (cutoff:3.500A) Processing helix chain 'v' and resid 32 through 41 removed outlier: 4.842A pdb=" N PHE v 36 " --> pdb=" O GLN v 32 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU v 39 " --> pdb=" O PHE v 35 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE v 40 " --> pdb=" O PHE v 36 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA v 41 " --> pdb=" O SER v 37 " (cutoff:3.500A) Processing helix chain 'v' and resid 106 through 123 removed outlier: 3.794A pdb=" N HIS v 123 " --> pdb=" O CYS v 119 " (cutoff:3.500A) Processing helix chain 'v' and resid 135 through 146 removed outlier: 4.044A pdb=" N LYS v 139 " --> pdb=" O ASP v 135 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS v 145 " --> pdb=" O TRP v 141 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY v 146 " --> pdb=" O PHE v 142 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 22 through 28 removed outlier: 7.685A pdb=" N GLN C 22 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 69 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 46 through 50 removed outlier: 8.376A pdb=" N THR D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY D 53 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS D 62 " --> pdb=" O CYS D 57 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'E' and resid 40 through 44 removed outlier: 3.599A pdb=" N ILE E 41 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 90 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 47 through 50 removed outlier: 4.457A pdb=" N GLN E 47 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS E 60 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E 49 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 61 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 110 through 114 removed outlier: 4.867A pdb=" N THR E 111 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE E 136 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 138 through 141 removed outlier: 4.364A pdb=" N ALA E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'F' and resid 98 through 101 removed outlier: 3.601A pdb=" N THR F 95 " --> pdb=" O GLY F 98 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 215 through 219 removed outlier: 3.520A pdb=" N ARG F 339 " --> pdb=" O ASP F 216 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 284 through 288 removed outlier: 3.940A pdb=" N ARG F 284 " --> pdb=" O MET F 323 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY F 286 " --> pdb=" O PHE F 321 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE F 321 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY F 288 " --> pdb=" O ASN F 319 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASN F 319 " --> pdb=" O GLY F 288 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 5 through 8 removed outlier: 5.486A pdb=" N ASN G 18 " --> pdb=" O VAL G 8 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 224 through 230 removed outlier: 3.707A pdb=" N GLU G 226 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G 230 " --> pdb=" O TYR G 209 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N PHE G 247 " --> pdb=" O GLY G 204 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 72 through 75 removed outlier: 6.927A pdb=" N ILE H 64 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG H 50 " --> pdb=" O ILE H 65 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 38 through 43 removed outlier: 4.270A pdb=" N THR I 38 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS I 50 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 84 through 88 removed outlier: 3.840A pdb=" N PHE J 85 " --> pdb=" O GLY J 137 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY J 137 " --> pdb=" O PHE J 85 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 112 through 115 removed outlier: 5.381A pdb=" N ASN J 112 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY J 114 " --> pdb=" O PHE J 205 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'K' and resid 177 through 180 removed outlier: 4.134A pdb=" N LEU K 150 " --> pdb=" O LEU K 200 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA K 198 " --> pdb=" O LEU K 152 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 5 through 12 removed outlier: 3.836A pdb=" N THR L 6 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL L 57 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN L 8 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL L 55 " --> pdb=" O GLN L 8 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 10 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL L 12 " --> pdb=" O GLN L 51 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLN L 51 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR L 44 " --> pdb=" O ALA L 56 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 17 through 20 Processing sheet with id= 19, first strand: chain 'L' and resid 100 through 105 removed outlier: 6.029A pdb=" N LYS L 110 " --> pdb=" O VAL L 128 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 132 through 137 removed outlier: 3.740A pdb=" N SER L 137 " --> pdb=" O GLU L 143 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU L 143 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP L 142 " --> pdb=" O TYR L 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU L 146 " --> pdb=" O TYR L 88 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY L 148 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR L 86 " --> pdb=" O GLY L 148 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 68 through 72 removed outlier: 3.676A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS M 16 " --> pdb=" O VAL M 130 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL M 130 " --> pdb=" O LYS M 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET M 125 " --> pdb=" O ILE M 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE M 106 " --> pdb=" O MET M 125 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'O' and resid 19 through 24 removed outlier: 4.164A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS O 31 " --> pdb=" O ILE O 23 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU O 45 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 6 through 10 Processing sheet with id= 24, first strand: chain 'S' and resid 100 through 103 removed outlier: 5.689A pdb=" N THR S 100 " --> pdb=" O LYS S 79 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL S 81 " --> pdb=" O THR S 100 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU S 140 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'U' and resid 24 through 31 removed outlier: 3.710A pdb=" N MET U 27 " --> pdb=" O VAL U 9 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL U 9 " --> pdb=" O MET U 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE U 29 " --> pdb=" O TYR U 7 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR U 7 " --> pdb=" O ILE U 29 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA U 31 " --> pdb=" O LYS U 5 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU U 6 " --> pdb=" O ILE U 64 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN U 62 " --> pdb=" O GLN U 8 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'U' and resid 120 through 124 removed outlier: 6.166A pdb=" N SER U 120 " --> pdb=" O ASP U 82 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG U 80 " --> pdb=" O HIS U 122 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU U 124 " --> pdb=" O TRP U 78 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TRP U 78 " --> pdb=" O LEU U 124 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'V' and resid 72 through 79 removed outlier: 3.517A pdb=" N LEU V 89 " --> pdb=" O VAL V 74 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'W' and resid 62 through 67 removed outlier: 3.684A pdb=" N SER W 67 " --> pdb=" O LYS W 13 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN W 101 " --> pdb=" O THR W 14 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR W 16 " --> pdb=" O ASN W 101 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'X' and resid 82 through 86 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'X' and resid 21 through 25 removed outlier: 6.930A pdb=" N MET X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET X 74 " --> pdb=" O ALA X 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA X 103 " --> pdb=" O PRO X 75 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'X' and resid 23 through 26 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain 'Y' and resid 3 through 6 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'Y' and resid 18 through 23 removed outlier: 3.616A pdb=" N THR Y 19 " --> pdb=" O PHE Y 31 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE Y 31 " --> pdb=" O THR Y 19 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Z' and resid 81 through 86 Processing sheet with id= 35, first strand: chain 'a' and resid 79 through 82 removed outlier: 4.875A pdb=" N ALA a 93 " --> pdb=" O LYS a 89 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL a 95 " --> pdb=" O LYS a 87 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'b' and resid 10 through 14 removed outlier: 3.721A pdb=" N LYS b 21 " --> pdb=" O VAL b 13 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL b 24 " --> pdb=" O ALA b 44 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU b 42 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU b 42 " --> pdb=" O LYS b 27 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS b 27 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'b' and resid 42 through 45 Processing sheet with id= 38, first strand: chain 'e' and resid 67 through 71 removed outlier: 3.728A pdb=" N ALA e 46 " --> pdb=" O PHE e 70 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU e 41 " --> pdb=" O ILE e 92 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'f' and resid 48 through 51 removed outlier: 3.629A pdb=" N LYS f 78 " --> pdb=" O PHE f 90 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG f 77 " --> pdb=" O VAL f 8 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL f 8 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR f 9 " --> pdb=" O VAL f 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU f 11 " --> pdb=" O VAL f 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL f 107 " --> pdb=" O GLU f 11 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'g' and resid 71 through 76 Processing sheet with id= 41, first strand: chain 'h' and resid 47 through 52 removed outlier: 4.954A pdb=" N LYS h 47 " --> pdb=" O VAL h 71 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR h 72 " --> pdb=" O ARG h 82 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG h 82 " --> pdb=" O THR h 72 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU h 29 " --> pdb=" O LEU h 14 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA h 96 " --> pdb=" O HIS h 13 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'l' and resid 26 through 29 removed outlier: 6.819A pdb=" N SER l 26 " --> pdb=" O SER l 35 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER l 35 " --> pdb=" O SER l 26 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR l 33 " --> pdb=" O HIS l 28 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'm' and resid 51 through 57 removed outlier: 3.557A pdb=" N LEU m 54 " --> pdb=" O PHE m 43 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA m 23 " --> pdb=" O LYS m 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL m 25 " --> pdb=" O ASN m 76 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 's' and resid 33 through 36 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'u' and resid 3 through 7 removed outlier: 6.708A pdb=" N ALA u 47 " --> pdb=" O VAL u 93 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS u 91 " --> pdb=" O THR u 49 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY u 89 " --> pdb=" O THR u 51 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'u' and resid 117 through 120 removed outlier: 6.705A pdb=" N LEU u 97 " --> pdb=" O THR u 116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS u 114 " --> pdb=" O LYS u 99 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS u 153 " --> pdb=" O ILE u 115 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLU u 148 " --> pdb=" O LEU u 194 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA u 189 " --> pdb=" O LEU u 174 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU u 172 " --> pdb=" O LYS u 191 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'u' and resid 43 through 47 removed outlier: 5.613A pdb=" N ALA u 43 " --> pdb=" O VAL u 98 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL u 98 " --> pdb=" O ALA u 43 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'u' and resid 175 through 178 Processing sheet with id= 49, first strand: chain 'v' and resid 7 through 11 removed outlier: 4.073A pdb=" N VAL v 58 " --> pdb=" O LEU v 78 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL v 75 " --> pdb=" O GLU v 94 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N HIS v 125 " --> pdb=" O ILE v 175 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE v 175 " --> pdb=" O HIS v 125 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP v 167 " --> pdb=" O ALA v 133 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU v 170 " --> pdb=" O VAL v 150 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'v' and resid 72 through 75 1922 hydrogen bonds defined for protein. 5726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2763 hydrogen bonds 4482 hydrogen bond angles 0 basepair planarities 1118 basepair parallelities 1738 stacking parallelities Total time for adding SS restraints: 260.62 Time building geometry restraints manager: 58.84 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: 25723 1.33 - 1.45: 56493 1.45 - 1.57: 61858 1.57 - 1.69: 7523 1.69 - 1.81: 214 Bond restraints: 151811 Sorted by residual: bond pdb=" O 3HE 13401 " pdb=" C4 3HE 13401 " ideal model delta sigma weight residual 1.210 1.405 -0.195 2.00e-02 2.50e+03 9.50e+01 bond pdb=" C11 3HE 13401 " pdb=" O1 3HE 13401 " ideal model delta sigma weight residual 1.212 1.395 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C12 3HE 13401 " pdb=" O2 3HE 13401 " ideal model delta sigma weight residual 1.212 1.389 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N 3HE 13401 " pdb=" C12 3HE 13401 " ideal model delta sigma weight residual 1.379 1.507 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" N 3HE 13401 " pdb=" C11 3HE 13401 " ideal model delta sigma weight residual 1.378 1.492 -0.114 2.00e-02 2.50e+03 3.24e+01 ... (remaining 151806 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 23076 106.88 - 113.66: 90485 113.66 - 120.44: 56271 120.44 - 127.22: 45299 127.22 - 134.01: 8307 Bond angle restraints: 223438 Sorted by residual: angle pdb=" C ASN t 643 " pdb=" CA ASN t 643 " pdb=" CB ASN t 643 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 angle pdb=" C10 3HE 13401 " pdb=" C11 3HE 13401 " pdb=" O1 3HE 13401 " ideal model delta sigma weight residual 123.70 108.81 14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C13 3HE 13401 " pdb=" C12 3HE 13401 " pdb=" O2 3HE 13401 " ideal model delta sigma weight residual 123.47 108.82 14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C11 3HE 13401 " pdb=" N 3HE 13401 " pdb=" C12 3HE 13401 " ideal model delta sigma weight residual 127.39 113.38 14.01 3.00e+00 1.11e-01 2.18e+01 angle pdb=" O 3HE 13401 " pdb=" C4 3HE 13401 " pdb=" C5 3HE 13401 " ideal model delta sigma weight residual 122.73 109.08 13.65 3.00e+00 1.11e-01 2.07e+01 ... (remaining 223433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 80438 35.94 - 71.88: 2310 71.88 - 107.82: 239 107.82 - 143.76: 47 143.76 - 179.70: 90 Dihedral angle restraints: 83124 sinusoidal: 60611 harmonic: 22513 Sorted by residual: dihedral pdb=" C4' U 1 764 " pdb=" C3' U 1 764 " pdb=" C2' U 1 764 " pdb=" C1' U 1 764 " ideal model delta sinusoidal sigma weight residual -35.00 34.82 -69.82 1 8.00e+00 1.56e-02 9.83e+01 dihedral pdb=" C4' G B 17A" pdb=" C3' G B 17A" pdb=" C2' G B 17A" pdb=" C1' G B 17A" ideal model delta sinusoidal sigma weight residual -35.00 34.80 -69.80 1 8.00e+00 1.56e-02 9.82e+01 dihedral pdb=" C4' U 12514 " pdb=" C3' U 12514 " pdb=" C2' U 12514 " pdb=" C1' U 12514 " ideal model delta sinusoidal sigma weight residual -35.00 34.70 -69.70 1 8.00e+00 1.56e-02 9.80e+01 ... (remaining 83121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 27114 0.073 - 0.146: 861 0.146 - 0.219: 25 0.219 - 0.292: 15 0.292 - 0.365: 7 Chirality restraints: 28022 Sorted by residual: chirality pdb=" C3' U 13078 " pdb=" C4' U 13078 " pdb=" O3' U 13078 " pdb=" C2' U 13078 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C3' U 11241 " pdb=" C4' U 11241 " pdb=" O3' U 11241 " pdb=" C2' U 11241 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C3' A 12593 " pdb=" C4' A 12593 " pdb=" O3' A 12593 " pdb=" C2' A 12593 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 28019 not shown) Planarity restraints: 14380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 3HE 13401 " -0.000 2.00e-02 2.50e+03 1.99e-01 4.96e+02 pdb=" C11 3HE 13401 " 0.090 2.00e-02 2.50e+03 pdb=" C12 3HE 13401 " -0.376 2.00e-02 2.50e+03 pdb=" C13 3HE 13401 " 0.081 2.00e-02 2.50e+03 pdb=" O2 3HE 13401 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O 3HE 13401 " 0.127 2.00e-02 2.50e+03 2.09e-01 4.37e+02 pdb=" C3 3HE 13401 " 0.117 2.00e-02 2.50e+03 pdb=" C4 3HE 13401 " -0.362 2.00e-02 2.50e+03 pdb=" C5 3HE 13401 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 3HE 13401 " -0.118 2.00e-02 2.50e+03 2.06e-01 4.23e+02 pdb=" C10 3HE 13401 " -0.115 2.00e-02 2.50e+03 pdb=" C11 3HE 13401 " 0.356 2.00e-02 2.50e+03 pdb=" O1 3HE 13401 " -0.123 2.00e-02 2.50e+03 ... (remaining 14377 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 85 1.26 - 2.17: 830 2.17 - 3.08: 89005 3.08 - 3.99: 414250 3.99 - 4.90: 694543 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1198713 Sorted by model distance: nonbonded pdb=" N6 A 1 108 " pdb=" NH2 ARG N 55 " model vdw 0.345 3.200 nonbonded pdb=" OP1 U 1 382 " pdb=" CE LYS t 37 " model vdw 0.402 3.440 nonbonded pdb=" N1 G 12012 " pdb=" N GLN t 176 " model vdw 0.513 3.200 nonbonded pdb=" OP2 A 1 123 " pdb=" NZ LYS K 105 " model vdw 0.517 2.520 nonbonded pdb=" C4' G 1 450 " pdb=" CB GLN v 83 " model vdw 0.551 3.870 ... (remaining 1198708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3766 5.49 5 S 134 5.16 5 C 74338 2.51 5 N 25871 2.21 5 O 37044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.77 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 24.180 Check model and map are aligned: 1.640 Convert atoms to be neutral: 0.920 Process input model: 541.190 Find NCS groups from input model: 3.550 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 579.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 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 0.195 151811 Z= 0.104 Angle : 0.432 14.889 223438 Z= 0.231 Chirality : 0.027 0.365 28022 Planarity : 0.004 0.209 14380 Dihedral : 14.927 179.697 68586 Min Nonbonded Distance : 0.345 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 1.86 % Allowed : 11.09 % Favored : 87.05 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -3.26 (0.08), residues: 7422 helix: -1.20 (0.09), residues: 2598 sheet: -2.30 (0.19), residues: 649 loop : -2.90 (0.08), residues: 4175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2811 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2806 time to evaluate : 7.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 2809 average time/residue: 1.5816 time to fit residues: 7456.8106 Evaluate side-chains 1671 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1671 time to evaluate : 7.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 951 optimal weight: 5.9990 chunk 854 optimal weight: 6.9990 chunk 473 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 576 optimal weight: 10.0000 chunk 456 optimal weight: 30.0000 chunk 883 optimal weight: 7.9990 chunk 341 optimal weight: 10.0000 chunk 537 optimal weight: 5.9990 chunk 657 optimal weight: 7.9990 chunk 1023 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN C 82 GLN E 140 ASN E 209 HIS E 218 HIS E 233 GLN F 3 HIS F 182 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 HIS F 231 HIS F 243 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 43 ASN G 213 ASN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 HIS ** G 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 GLN G 304 GLN G 307 GLN ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 61 ASN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 GLN K 61 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 ASN L 163 GLN M 39 GLN M 68 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 132 ASN N 19 GLN N 112 ASN P 37 HIS P 57 GLN P 87 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 ASN ** Q 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN Q 55 HIS ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 HIS R 97 ASN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 GLN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 HIS ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 HIS T 156 ASN U 3 HIS U 62 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 122 HIS ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 157 GLN V 98 HIS ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN Z 85 GLN Z 111 ASN b 127 ASN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 HIS ** d 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 HIS h 39 GLN h 42 GLN ** h 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 3 GLN j 34 GLN j 59 ASN n 19 GLN s 58 GLN s 143 ASN ** s 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 119 ASN t 172 ASN t 347 ASN t 392 GLN t 799 ASN ** u 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 163 HIS u 203 ASN v 32 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.121 151811 Z= 0.493 Angle : 0.953 15.098 223438 Z= 0.481 Chirality : 0.048 0.364 28022 Planarity : 0.009 0.190 14380 Dihedral : 16.955 179.770 53770 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.47 % Favored : 92.86 % Rotamer Outliers : 5.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -2.59 (0.09), residues: 7422 helix: -0.66 (0.10), residues: 2689 sheet: -1.87 (0.17), residues: 835 loop : -2.51 (0.09), residues: 3898 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2413 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 2051 time to evaluate : 7.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 362 outliers final: 190 residues processed: 2251 average time/residue: 1.5179 time to fit residues: 5920.2928 Evaluate side-chains 1763 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1573 time to evaluate : 7.559 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 190 outliers final: 1 residues processed: 190 average time/residue: 1.2375 time to fit residues: 455.0100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 568 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 851 optimal weight: 7.9990 chunk 696 optimal weight: 0.9980 chunk 282 optimal weight: 6.9990 chunk 1025 optimal weight: 10.0000 chunk 1107 optimal weight: 30.0000 chunk 913 optimal weight: 0.0370 chunk 1016 optimal weight: 10.0000 chunk 349 optimal weight: 7.9990 chunk 822 optimal weight: 6.9990 overall best weight: 4.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 GLN D 32 GLN E 79 ASN E 115 ASN E 139 HIS E 140 ASN F 279 ASN G 59 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN J 52 GLN J 104 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN L 58 HIS L 77 ASN ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 ASN L 163 GLN M 109 HIS ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN P 11 GLN P 86 ASN P 182 ASN ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 ASN Q 31 GLN Q 50 ASN Q 72 HIS Q 193 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 GLN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 HIS T 130 ASN T 156 ASN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 HIS V 77 ASN V 146 ASN V 149 GLN a 66 GLN b 36 HIS b 127 ASN c 49 HIS c 64 GLN c 74 ASN d 12 GLN ** d 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 HIS h 106 ASN i 61 GLN i 69 HIS ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 347 ASN t 503 GLN t 792 ASN ** t 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 20 ASN u 23 ASN v 166 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.225 151811 Z= 0.329 Angle : 0.679 10.879 223438 Z= 0.348 Chirality : 0.039 0.346 28022 Planarity : 0.006 0.118 14380 Dihedral : 16.654 179.958 53770 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.15 % Favored : 92.28 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -2.00 (0.09), residues: 7422 helix: -0.02 (0.10), residues: 2704 sheet: -1.63 (0.16), residues: 899 loop : -2.28 (0.09), residues: 3819 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1761 time to evaluate : 7.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 235 outliers final: 116 residues processed: 1882 average time/residue: 1.3719 time to fit residues: 4498.3965 Evaluate side-chains 1657 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1541 time to evaluate : 7.660 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 0 residues processed: 116 average time/residue: 1.2139 time to fit residues: 276.2806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 1012 optimal weight: 30.0000 chunk 770 optimal weight: 0.9990 chunk 532 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 489 optimal weight: 9.9990 chunk 688 optimal weight: 10.0000 chunk 1028 optimal weight: 9.9990 chunk 1089 optimal weight: 20.0000 chunk 537 optimal weight: 5.9990 chunk 975 optimal weight: 40.0000 chunk 293 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 GLN E 233 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN H 32 GLN H 178 ASN I 57 HIS J 52 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 ASN L 183 HIS N 112 ASN N 114 GLN N 160 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 86 ASN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN R 72 GLN R 96 GLN R 97 ASN ** R 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 GLN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 ASN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 HIS U 108 GLN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 ASN Z 65 GLN a 42 GLN ** c 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN ** e 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN i 83 ASN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 ASN ** s 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS t 503 GLN ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 101 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.7968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.145 151811 Z= 0.480 Angle : 0.840 18.642 223438 Z= 0.431 Chirality : 0.047 0.399 28022 Planarity : 0.007 0.115 14380 Dihedral : 17.226 179.958 53770 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.44 % Favored : 92.00 % Rotamer Outliers : 5.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.94 (0.09), residues: 7422 helix: -0.04 (0.10), residues: 2747 sheet: -1.54 (0.16), residues: 910 loop : -2.23 (0.09), residues: 3765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2095 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1768 time to evaluate : 7.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 327 outliers final: 194 residues processed: 1942 average time/residue: 1.3477 time to fit residues: 4569.1999 Evaluate side-chains 1797 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1603 time to evaluate : 7.705 Switching outliers to nearest non-outliers outliers start: 194 outliers final: 0 residues processed: 194 average time/residue: 1.0405 time to fit residues: 393.9186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 907 optimal weight: 2.9990 chunk 618 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 811 optimal weight: 2.9990 chunk 449 optimal weight: 0.7980 chunk 929 optimal weight: 3.9990 chunk 753 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 556 optimal weight: 4.9990 chunk 977 optimal weight: 50.0000 chunk 274 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN E 139 HIS F 165 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN J 146 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN L 183 HIS ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN O 41 GLN ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 138 GLN ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN R 97 ASN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 156 ASN U 62 ASN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 66 GLN ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 HIS d 12 GLN d 43 HIS ** i 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 GLN i 83 ASN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 ASN s 143 ASN ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 503 GLN ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.7970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.106 151811 Z= 0.221 Angle : 0.637 13.192 223438 Z= 0.328 Chirality : 0.038 0.287 28022 Planarity : 0.005 0.101 14380 Dihedral : 16.913 179.925 53770 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.48 % Favored : 93.02 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.59 (0.09), residues: 7422 helix: 0.28 (0.10), residues: 2720 sheet: -1.30 (0.16), residues: 935 loop : -2.05 (0.09), residues: 3767 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1897 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1765 time to evaluate : 7.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 56 residues processed: 1824 average time/residue: 1.3595 time to fit residues: 4325.3258 Evaluate side-chains 1676 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1620 time to evaluate : 7.296 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 1.1132 time to fit residues: 127.4015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 366 optimal weight: 20.0000 chunk 981 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 639 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 1090 optimal weight: 50.0000 chunk 905 optimal weight: 0.1980 chunk 504 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 360 optimal weight: 20.0000 chunk 572 optimal weight: 0.5980 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS E 86 GLN F 165 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 GLN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 ASN L 156 GLN L 183 HIS ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN O 119 GLN P 86 ASN P 112 ASN P 117 ASN ** P 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN R 97 ASN R 137 ASN ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 131 GLN ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 GLN a 66 GLN b 76 ASN c 49 HIS d 45 HIS h 42 GLN i 83 ASN j 34 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 GLN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 ASN s 50 HIS ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 503 GLN ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.8219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.130 151811 Z= 0.309 Angle : 0.664 12.093 223438 Z= 0.342 Chirality : 0.040 0.287 28022 Planarity : 0.005 0.085 14380 Dihedral : 16.916 179.914 53770 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.94 % Favored : 92.59 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.49 (0.10), residues: 7422 helix: 0.34 (0.10), residues: 2726 sheet: -1.28 (0.17), residues: 935 loop : -1.97 (0.09), residues: 3761 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1842 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1681 time to evaluate : 7.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 101 residues processed: 1756 average time/residue: 1.4002 time to fit residues: 4281.2901 Evaluate side-chains 1705 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1604 time to evaluate : 7.660 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 0 residues processed: 101 average time/residue: 1.1111 time to fit residues: 223.3943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 1051 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 621 optimal weight: 10.0000 chunk 796 optimal weight: 0.9990 chunk 616 optimal weight: 2.9990 chunk 917 optimal weight: 0.5980 chunk 608 optimal weight: 0.0770 chunk 1086 optimal weight: 50.0000 chunk 679 optimal weight: 2.9990 chunk 662 optimal weight: 10.0000 chunk 501 optimal weight: 0.9980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS F 165 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 ASN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN S 45 ASN ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 ASN U 122 HIS U 138 GLN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 131 GLN W 101 ASN ** X 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 ASN ** a 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 ASN f 87 ASN h 42 GLN i 69 HIS j 34 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 GLN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 209 ASN t 347 ASN ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 166 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.8144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.142 151811 Z= 0.165 Angle : 0.607 17.203 223438 Z= 0.310 Chirality : 0.035 0.287 28022 Planarity : 0.005 0.105 14380 Dihedral : 16.755 179.893 53770 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.13 % Favored : 93.44 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.34 (0.10), residues: 7422 helix: 0.42 (0.10), residues: 2732 sheet: -1.27 (0.16), residues: 934 loop : -1.81 (0.10), residues: 3756 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1849 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1752 time to evaluate : 7.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 46 residues processed: 1789 average time/residue: 1.3600 time to fit residues: 4234.0273 Evaluate side-chains 1638 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1592 time to evaluate : 7.582 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 1.1786 time to fit residues: 110.0512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 672 optimal weight: 5.9990 chunk 433 optimal weight: 6.9990 chunk 648 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 690 optimal weight: 0.6980 chunk 740 optimal weight: 7.9990 chunk 537 optimal weight: 2.9990 chunk 101 optimal weight: 30.0000 chunk 853 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 233 GLN F 165 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 HIS ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN O 41 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN R 97 ASN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 61 GLN i 69 HIS k 91 ASN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 ASN ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 23 ASN v 166 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.8451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.136 151811 Z= 0.316 Angle : 0.668 14.397 223438 Z= 0.344 Chirality : 0.039 0.287 28022 Planarity : 0.005 0.101 14380 Dihedral : 16.845 179.947 53770 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.03 % Favored : 92.54 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.33 (0.10), residues: 7422 helix: 0.41 (0.10), residues: 2741 sheet: -1.21 (0.16), residues: 942 loop : -1.82 (0.10), residues: 3739 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1740 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1634 time to evaluate : 7.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 68 residues processed: 1667 average time/residue: 1.3475 time to fit residues: 3922.6326 Evaluate side-chains 1639 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1571 time to evaluate : 7.467 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 1.0923 time to fit residues: 148.7597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 988 optimal weight: 6.9990 chunk 1040 optimal weight: 50.0000 chunk 949 optimal weight: 3.9990 chunk 1012 optimal weight: 7.9990 chunk 609 optimal weight: 20.0000 chunk 440 optimal weight: 3.9990 chunk 794 optimal weight: 0.0970 chunk 310 optimal weight: 20.0000 chunk 914 optimal weight: 7.9990 chunk 957 optimal weight: 9.9990 chunk 1008 optimal weight: 7.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 ASN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 131 GLN ** X 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 61 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.8728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.154 151811 Z= 0.310 Angle : 0.678 13.910 223438 Z= 0.349 Chirality : 0.040 0.295 28022 Planarity : 0.005 0.136 14380 Dihedral : 16.962 179.893 53770 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.02 % Favored : 92.52 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.35 (0.10), residues: 7422 helix: 0.41 (0.10), residues: 2730 sheet: -1.19 (0.16), residues: 941 loop : -1.84 (0.10), residues: 3751 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1717 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1660 time to evaluate : 7.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 34 residues processed: 1680 average time/residue: 1.3131 time to fit residues: 3862.0572 Evaluate side-chains 1618 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1584 time to evaluate : 7.518 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 1.0672 time to fit residues: 77.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 664 optimal weight: 8.9990 chunk 1070 optimal weight: 30.0000 chunk 653 optimal weight: 5.9990 chunk 507 optimal weight: 3.9990 chunk 744 optimal weight: 0.8980 chunk 1122 optimal weight: 10.0000 chunk 1033 optimal weight: 8.9990 chunk 894 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 690 optimal weight: 0.6980 chunk 548 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN E 24 GLN E 47 GLN E 79 ASN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 HIS V 58 GLN ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN ** j 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 347 ASN ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 145 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.8851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.168 151811 Z= 0.272 Angle : 0.665 14.163 223438 Z= 0.343 Chirality : 0.039 0.319 28022 Planarity : 0.005 0.135 14380 Dihedral : 16.951 179.733 53770 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.88 % Favored : 92.71 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.31 (0.10), residues: 7422 helix: 0.43 (0.10), residues: 2731 sheet: -1.13 (0.16), residues: 943 loop : -1.81 (0.10), residues: 3748 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1683 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1638 time to evaluate : 7.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 30 residues processed: 1649 average time/residue: 1.3545 time to fit residues: 3904.7159 Evaluate side-chains 1635 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1605 time to evaluate : 7.615 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 1.1340 time to fit residues: 73.2413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 710 optimal weight: 4.9990 chunk 952 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 chunk 824 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 895 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 919 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 ASN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 GLN K 61 GLN K 79 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 ASN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN j 34 GLN ** j 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.105052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.072880 restraints weight = 424731.737| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.01 r_work: 0.3058 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3040 rms_B_bonded: 1.94 restraints_weight: 0.1250 r_work: 0.3031 rms_B_bonded: 2.00 restraints_weight: 0.0625 r_work: 0.3022 rms_B_bonded: 2.09 restraints_weight: 0.0312 r_work: 0.3012 rms_B_bonded: 2.21 restraints_weight: 0.0156 r_work: 0.3002 rms_B_bonded: 2.34 restraints_weight: 0.0078 r_work: 0.2991 rms_B_bonded: 2.50 restraints_weight: 0.0039 r_work: 0.2980 rms_B_bonded: 2.68 restraints_weight: 0.0020 r_work: 0.2968 rms_B_bonded: 2.88 restraints_weight: 0.0010 r_work: 0.2955 rms_B_bonded: 3.11 restraints_weight: 0.0005 r_work: 0.2942 rms_B_bonded: 3.37 restraints_weight: 0.0002 r_work: 0.2927 rms_B_bonded: 3.67 restraints_weight: 0.0001 r_work: 0.2911 rms_B_bonded: 3.99 restraints_weight: 0.0001 r_work: 0.2894 rms_B_bonded: 4.36 restraints_weight: 0.0000 r_work: 0.2876 rms_B_bonded: 4.77 restraints_weight: 0.0000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.9076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.154 151811 Z= 0.340 Angle : 0.708 15.752 223438 Z= 0.365 Chirality : 0.041 0.305 28022 Planarity : 0.006 0.137 14380 Dihedral : 17.066 179.599 53770 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.32 % Favored : 92.29 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.37 (0.10), residues: 7422 helix: 0.34 (0.10), residues: 2743 sheet: -1.17 (0.16), residues: 938 loop : -1.83 (0.10), residues: 3741 =============================================================================== Job complete usr+sys time: 59597.60 seconds wall clock time: 1017 minutes 15.98 seconds (61035.98 seconds total)