Starting phenix.real_space_refine on Wed Mar 20 01:17:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/03_2024/6hd7_0202_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/03_2024/6hd7_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_0202/03_2024/6hd7_0202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/03_2024/6hd7_0202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/03_2024/6hd7_0202_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd7_0202/03_2024/6hd7_0202_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: {'rna2p_pur': 135, 'rna2p_pyr': 97, 'rna3p_pur': 1696, 'rna3p_pyr': 1407} Link IDs: {'rna2p': 232, 'rna3p': 3102} 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: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 60, 'rna3p_pyr': 57} Link IDs: {'rna2p': 4, 'rna3p': 116} Chain: "4" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 71, 'rna3p_pyr': 76} Link IDs: {'rna2p': 11, 'rna3p': 146} 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, 'rna2p_pyr': 1, 'rna3p_pur': 35, 'rna3p_pyr': 38} Link IDs: {'rna2p': 3, 'rna3p': 72} Chain: "B" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 35, 'rna3p_pyr': 38} Link IDs: {'rna2p': 4, 'rna3p': 72} 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: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} 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: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} 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: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} 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: 53.92, per 1000 atoms: 0.38 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: 57.38 Conformation dependent library (CDL) restraints added in 8.4 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 for structures that cannot fit in PDB format. 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: 70.32 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: 205.54 Time building geometry restraints manager: 62.11 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: 86545 35.94 - 71.88: 8735 71.88 - 107.82: 995 107.82 - 143.76: 49 143.76 - 179.70: 90 Dihedral angle restraints: 96414 sinusoidal: 73901 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 96411 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 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: 3.770 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: 0.140 Extract box with map and model: 20.150 Check model and map are aligned: 1.580 Set scattering table: 1.040 Process input model: 489.010 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 521.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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 : 22.250 179.697 81876 Min Nonbonded Distance : 0.345 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 1.86 % Allowed : 11.09 % Favored : 87.05 % Rotamer: Outliers : 0.08 % Allowed : 1.31 % Favored : 98.61 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 85 HIS 0.004 0.000 HIS F 313 PHE 0.007 0.000 PHE t 800 TYR 0.012 0.000 TYR t 507 ARG 0.003 0.000 ARG F 21 *********************** 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 : 7.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 194 ASN cc_start: 0.7585 (t0) cc_final: 0.6974 (t0) REVERT: F 224 HIS cc_start: 0.6489 (m90) cc_final: 0.6283 (m-70) REVERT: F 352 GLU cc_start: 0.5574 (tt0) cc_final: 0.5301 (tt0) REVERT: K 86 THR cc_start: 0.6672 (m) cc_final: 0.6321 (p) REVERT: L 1 MET cc_start: 0.6074 (ptm) cc_final: 0.5589 (ptt) REVERT: L 46 THR cc_start: 0.7312 (m) cc_final: 0.6994 (p) REVERT: L 49 ASN cc_start: 0.5576 (p0) cc_final: 0.5233 (p0) REVERT: L 123 ILE cc_start: 0.8676 (mt) cc_final: 0.8354 (mp) REVERT: M 31 THR cc_start: 0.7883 (p) cc_final: 0.7584 (t) REVERT: M 126 ASP cc_start: 0.6798 (m-30) cc_final: 0.6514 (t0) REVERT: N 6 ASN cc_start: 0.8002 (t0) cc_final: 0.7627 (t0) REVERT: N 16 LYS cc_start: 0.8072 (mttt) cc_final: 0.7557 (mttm) REVERT: N 93 ILE cc_start: 0.7185 (mm) cc_final: 0.6737 (mm) REVERT: N 162 ASN cc_start: 0.8005 (p0) cc_final: 0.7696 (p0) REVERT: O 113 THR cc_start: 0.6932 (t) cc_final: 0.6197 (p) REVERT: P 29 GLU cc_start: 0.6651 (tt0) cc_final: 0.6074 (tt0) REVERT: P 44 ARG cc_start: 0.5049 (mtp180) cc_final: 0.4710 (mtp180) REVERT: P 75 VAL cc_start: 0.6287 (OUTLIER) cc_final: 0.6044 (m) REVERT: P 112 ASN cc_start: 0.6969 (p0) cc_final: 0.6557 (p0) REVERT: T 91 SER cc_start: 0.8652 (m) cc_final: 0.8135 (m) REVERT: U 25 PHE cc_start: 0.5470 (m-80) cc_final: 0.5116 (m-10) REVERT: U 29 ILE cc_start: 0.7538 (mm) cc_final: 0.7155 (mm) REVERT: W 23 THR cc_start: 0.8445 (m) cc_final: 0.8232 (p) REVERT: X 53 SER cc_start: 0.8710 (p) cc_final: 0.8461 (m) REVERT: Z 139 ILE cc_start: 0.7772 (tt) cc_final: 0.7536 (mt) REVERT: a 39 LEU cc_start: 0.7274 (mt) cc_final: 0.6967 (mt) REVERT: a 80 VAL cc_start: 0.8916 (p) cc_final: 0.8644 (m) REVERT: b 40 HIS cc_start: 0.6584 (p-80) cc_final: 0.6045 (p-80) REVERT: c 19 LYS cc_start: 0.6955 (mmtm) cc_final: 0.6686 (mttt) REVERT: c 90 TYR cc_start: 0.7186 (m-10) cc_final: 0.6969 (m-80) REVERT: d 27 TYR cc_start: 0.7093 (m-80) cc_final: 0.6624 (m-80) REVERT: f 41 LYS cc_start: 0.8095 (tttt) cc_final: 0.7851 (tttt) REVERT: i 54 ILE cc_start: 0.8317 (mm) cc_final: 0.8115 (mm) REVERT: i 98 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8221 (tp40) REVERT: j 61 GLN cc_start: 0.8313 (mt0) cc_final: 0.7672 (mt0) REVERT: k 80 PHE cc_start: 0.5744 (t80) cc_final: 0.5469 (t80) REVERT: m 6 THR cc_start: 0.8606 (p) cc_final: 0.8395 (p) REVERT: p 1 MET cc_start: 0.5720 (ptm) cc_final: 0.2380 (tpp) REVERT: s 3 ARG cc_start: 0.8069 (ptp-170) cc_final: 0.7843 (ptp90) REVERT: s 59 LEU cc_start: 0.7113 (mt) cc_final: 0.6901 (mt) REVERT: s 110 LEU cc_start: 0.4511 (OUTLIER) cc_final: 0.4305 (tm) REVERT: u 127 MET cc_start: -0.1460 (ptt) cc_final: -0.1992 (ptp) outliers start: 5 outliers final: 0 residues processed: 2809 average time/residue: 1.4729 time to fit residues: 6857.7214 Evaluate side-chains 1684 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1682 time to evaluate : 7.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain s residue 110 LEU 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: 9.9990 chunk 473 optimal weight: 10.0000 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: 7.5990 ------------------------------------------------------------------------------- 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 F 3 HIS F 182 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS F 243 HIS G 43 ASN G 59 GLN ** 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 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 K 192 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 ASN L 163 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 HIS ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN P 37 HIS P 57 GLN P 87 GLN P 182 ASN P 195 ASN Q 29 ASN ** Q 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN Q 50 ASN Q 55 HIS ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 HIS R 121 GLN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 W 25 ASN ** Y 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 GLN Z 111 ASN b 127 ASN d 10 HIS ** d 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 HIS h 42 GLN ** h 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 3 GLN j 59 ASN s 58 GLN s 99 ASN s 143 ASN ** s 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 119 ASN t 172 ASN ** t 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 347 ASN t 392 GLN ** u 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 23 ASN u 163 HIS u 203 ASN v 32 GLN v 59 HIS Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.140 151811 Z= 0.547 Angle : 1.046 18.969 223438 Z= 0.525 Chirality : 0.051 0.419 28022 Planarity : 0.009 0.223 14380 Dihedral : 24.266 179.874 67063 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.68 % Favored : 92.67 % Rotamer: Outliers : 6.18 % Allowed : 13.73 % Favored : 80.09 % Cbeta Deviations : 0.01 % 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: -2.78 (0.09), residues: 7422 helix: -0.94 (0.09), residues: 2679 sheet: -1.91 (0.16), residues: 860 loop : -2.55 (0.09), residues: 3883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP h 68 HIS 0.017 0.003 HIS g 98 PHE 0.053 0.004 PHE N 26 TYR 0.057 0.004 TYR Z 60 ARG 0.022 0.002 ARG N 55 *********************** 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 2477 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 2095 time to evaluate : 7.432 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: C 43 TYR cc_start: 0.8380 (t80) cc_final: 0.7682 (t80) REVERT: D 73 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7409 (m) REVERT: E 7 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8329 (p0) REVERT: E 175 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8829 (t) REVERT: F 7 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6055 (tp30) REVERT: F 308 MET cc_start: 0.6673 (mmm) cc_final: 0.6393 (mmm) REVERT: G 307 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7829 (mm-40) REVERT: H 52 VAL cc_start: 0.8870 (t) cc_final: 0.8619 (p) REVERT: J 130 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7852 (tp) REVERT: L 177 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.6625 (t0) REVERT: M 7 ASN cc_start: 0.8336 (t0) cc_final: 0.8098 (t0) REVERT: N 64 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8394 (ttpt) REVERT: N 162 ASN cc_start: 0.7993 (p0) cc_final: 0.7790 (p0) REVERT: O 13 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5828 (ptm160) REVERT: O 54 PRO cc_start: 0.8643 (Cg_exo) cc_final: 0.8440 (Cg_endo) REVERT: P 62 TYR cc_start: 0.8586 (m-80) cc_final: 0.8260 (m-80) REVERT: P 118 SER cc_start: 0.8556 (p) cc_final: 0.8305 (p) REVERT: R 97 ASN cc_start: 0.7013 (t0) cc_final: 0.6609 (t0) REVERT: T 6 THR cc_start: 0.8835 (m) cc_final: 0.8594 (t) REVERT: T 28 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7385 (mm-30) REVERT: T 31 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8373 (tm-30) REVERT: T 134 HIS cc_start: 0.7669 (p90) cc_final: 0.7236 (p90) REVERT: T 148 ASP cc_start: 0.8368 (m-30) cc_final: 0.6016 (m-30) REVERT: T 153 LYS cc_start: 0.8885 (tppt) cc_final: 0.8664 (mmmt) REVERT: U 40 ARG cc_start: 0.7694 (mmp-170) cc_final: 0.7437 (mmp-170) REVERT: U 64 ILE cc_start: 0.8761 (mt) cc_final: 0.8447 (mt) REVERT: U 121 ILE cc_start: 0.8947 (mm) cc_final: 0.8734 (mm) REVERT: V 20 ARG cc_start: 0.7220 (ptp-170) cc_final: 0.6587 (ptt-90) REVERT: V 149 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5702 (pp30) REVERT: W 42 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8363 (mttp) REVERT: W 100 THR cc_start: 0.8723 (m) cc_final: 0.8261 (p) REVERT: X 40 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7589 (mmmm) REVERT: X 57 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7676 (tmm) REVERT: Y 35 LYS cc_start: 0.8457 (tttt) cc_final: 0.8170 (ttmm) REVERT: Z 94 GLN cc_start: 0.8000 (mt0) cc_final: 0.7780 (mt0) REVERT: Z 108 LEU cc_start: 0.8612 (mt) cc_final: 0.8358 (mt) REVERT: a 9 SER cc_start: 0.8919 (t) cc_final: 0.8191 (p) REVERT: a 56 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8287 (p) REVERT: a 81 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7292 (mm-40) REVERT: a 94 SER cc_start: 0.9035 (t) cc_final: 0.8743 (m) REVERT: b 4 PHE cc_start: 0.7597 (p90) cc_final: 0.7393 (p90) REVERT: b 55 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7919 (mttt) REVERT: b 98 THR cc_start: 0.8241 (m) cc_final: 0.7992 (t) REVERT: d 17 HIS cc_start: 0.8503 (m170) cc_final: 0.8204 (m90) REVERT: e 69 TYR cc_start: 0.8442 (m-80) cc_final: 0.8077 (m-80) REVERT: f 55 LEU cc_start: 0.9305 (tt) cc_final: 0.9102 (tp) REVERT: g 108 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8905 (tt) REVERT: h 17 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: i 51 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8539 (pp) REVERT: k 89 GLU cc_start: 0.7405 (pp20) cc_final: 0.7135 (pp20) REVERT: l 29 VAL cc_start: 0.9144 (t) cc_final: 0.8797 (m) REVERT: m 13 GLU cc_start: 0.8449 (tp30) cc_final: 0.7806 (tp30) REVERT: m 19 ASP cc_start: 0.5971 (p0) cc_final: 0.5539 (p0) REVERT: m 29 LYS cc_start: 0.8798 (mmmt) cc_final: 0.6793 (mmmt) REVERT: m 38 PHE cc_start: 0.8328 (p90) cc_final: 0.8021 (p90) REVERT: n 17 LYS cc_start: 0.9261 (ttpp) cc_final: 0.8963 (tttp) REVERT: n 38 ASN cc_start: 0.8522 (t0) cc_final: 0.8145 (t0) REVERT: o 102 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8064 (mtt90) REVERT: p 1 MET cc_start: 0.7476 (ptm) cc_final: 0.5236 (mmt) REVERT: s 12 LYS cc_start: 0.6539 (tmtt) cc_final: 0.5739 (mtmm) REVERT: t 608 MET cc_start: -0.0555 (mmm) cc_final: -0.1005 (mmt) REVERT: u 16 MET cc_start: -0.0596 (mtt) cc_final: -0.1640 (mmm) REVERT: u 30 MET cc_start: -0.1266 (tpp) cc_final: -0.2181 (tmm) REVERT: u 121 MET cc_start: -0.1994 (mtt) cc_final: -0.2602 (pmm) REVERT: u 127 MET cc_start: -0.1222 (ptt) cc_final: -0.1769 (ptp) REVERT: u 190 MET cc_start: -0.0639 (mtt) cc_final: -0.1244 (mtt) REVERT: v 89 LYS cc_start: -0.2585 (OUTLIER) cc_final: -0.2850 (tmtt) REVERT: v 105 LYS cc_start: -0.3918 (pttt) cc_final: -0.4326 (pttt) outliers start: 382 outliers final: 190 residues processed: 2304 average time/residue: 1.3270 time to fit residues: 5159.4650 Evaluate side-chains 1836 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1629 time to evaluate : 7.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 ASN Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 307 GLN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 CYS Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 230 LYS Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 157 ASN Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 162 TRP Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 83 TRP Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain R residue 144 SER Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain V residue 13 TYR Chi-restraints excluded: chain V residue 48 ILE Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 24 ASN Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 57 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Z residue 81 ILE Chi-restraints excluded: chain Z residue 82 LEU Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain Z residue 91 ASN Chi-restraints excluded: chain Z residue 105 VAL Chi-restraints excluded: chain a residue 8 VAL Chi-restraints excluded: chain a residue 21 THR Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain b residue 24 VAL Chi-restraints excluded: chain b residue 25 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 55 LYS Chi-restraints excluded: chain b residue 76 ASN Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 127 ASN Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 96 LYS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain f residue 10 ARG Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 28 VAL Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 80 LYS Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 17 GLN Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 77 ASN Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 52 GLN Chi-restraints excluded: chain i residue 68 THR Chi-restraints excluded: chain i residue 100 ILE Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 80 THR Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 ARG Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain s residue 35 LEU Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 110 LEU Chi-restraints excluded: chain s residue 128 VAL Chi-restraints excluded: chain s residue 199 LEU Chi-restraints excluded: chain s residue 216 PHE Chi-restraints excluded: chain t residue 123 THR Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 412 ASP Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 538 ASN Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain u residue 151 SER Chi-restraints excluded: chain v residue 89 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 568 optimal weight: 20.0000 chunk 317 optimal weight: 20.0000 chunk 851 optimal weight: 8.9990 chunk 696 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 1025 optimal weight: 40.0000 chunk 1107 optimal weight: 0.1980 chunk 913 optimal weight: 5.9990 chunk 1016 optimal weight: 30.0000 chunk 349 optimal weight: 5.9990 chunk 822 optimal weight: 6.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN D 25 GLN D 32 GLN E 79 ASN E 115 ASN E 139 HIS E 140 ASN F 279 ASN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 GLN H 32 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN J 52 GLN J 104 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN ** J 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN L 77 ASN L 163 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 HIS ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN N 112 ASN O 41 GLN P 11 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 ASN P 182 ASN ** P 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN Q 72 HIS ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 193 GLN R 121 GLN R 125 GLN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 HIS T 130 ASN ** T 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 ASN V 112 ASN ** Z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 HIS 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** f 105 GLN g 21 HIS h 106 ASN i 61 GLN i 69 HIS j 34 GLN j 59 ASN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 99 ASN ** s 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 347 ASN t 792 ASN t 799 ASN ** t 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 59 HIS v 166 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 151811 Z= 0.327 Angle : 0.692 11.339 223438 Z= 0.354 Chirality : 0.040 0.284 28022 Planarity : 0.005 0.124 14380 Dihedral : 24.090 179.984 67062 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.01 % Favored : 92.40 % Rotamer: Outliers : 5.81 % Allowed : 18.55 % Favored : 75.65 % 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: -2.11 (0.09), residues: 7422 helix: -0.20 (0.10), residues: 2725 sheet: -1.67 (0.16), residues: 870 loop : -2.29 (0.09), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 95 HIS 0.015 0.002 HIS g 88 PHE 0.037 0.002 PHE K 34 TYR 0.031 0.002 TYR s 180 ARG 0.027 0.001 ARG s 20 *********************** 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 2141 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 1782 time to evaluate : 7.269 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: C 87 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8320 (mtt90) REVERT: D 36 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7545 (mtp-110) REVERT: E 7 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8193 (p0) REVERT: E 140 ASN cc_start: 0.8133 (m110) cc_final: 0.7655 (m-40) REVERT: F 7 GLU cc_start: 0.6445 (mt-10) cc_final: 0.5818 (tm-30) REVERT: F 308 MET cc_start: 0.7153 (mmm) cc_final: 0.6708 (mmt) REVERT: H 111 GLN cc_start: 0.8111 (pp30) cc_final: 0.7821 (pp30) REVERT: I 84 VAL cc_start: 0.8487 (m) cc_final: 0.8240 (m) REVERT: L 177 ASP cc_start: 0.7903 (m-30) cc_final: 0.7061 (t0) REVERT: M 31 THR cc_start: 0.8038 (p) cc_final: 0.7667 (p) REVERT: N 162 ASN cc_start: 0.8106 (p0) cc_final: 0.7868 (p0) REVERT: O 115 PHE cc_start: 0.7046 (t80) cc_final: 0.6742 (t80) REVERT: P 46 ASP cc_start: 0.8662 (p0) cc_final: 0.8268 (p0) REVERT: P 86 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8766 (p0) REVERT: P 174 ILE cc_start: 0.8999 (mm) cc_final: 0.8737 (mm) REVERT: Q 87 MET cc_start: 0.8241 (mtt) cc_final: 0.8019 (mtt) REVERT: R 20 SER cc_start: 0.8695 (m) cc_final: 0.8416 (p) REVERT: R 21 TYR cc_start: 0.7726 (m-80) cc_final: 0.7445 (m-80) REVERT: R 96 GLN cc_start: 0.7242 (pp30) cc_final: 0.7020 (pp30) REVERT: S 32 LEU cc_start: 0.8545 (tt) cc_final: 0.8099 (tp) REVERT: T 136 ARG cc_start: 0.8061 (tmm-80) cc_final: 0.7758 (ttp80) REVERT: T 153 LYS cc_start: 0.8972 (tppt) cc_final: 0.8747 (mmmm) REVERT: T 175 GLN cc_start: 0.7790 (pt0) cc_final: 0.7555 (mm-40) REVERT: U 14 LEU cc_start: 0.8384 (mt) cc_final: 0.8164 (mp) REVERT: U 21 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7912 (mp0) REVERT: U 23 LYS cc_start: 0.7866 (tttt) cc_final: 0.7645 (tptm) REVERT: V 84 TYR cc_start: 0.8069 (m-80) cc_final: 0.7827 (m-80) REVERT: V 149 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5739 (pm20) REVERT: W 88 GLN cc_start: 0.8268 (mp10) cc_final: 0.8035 (mp10) REVERT: Y 35 LYS cc_start: 0.8644 (tttt) cc_final: 0.8369 (ttmt) REVERT: a 9 SER cc_start: 0.8783 (t) cc_final: 0.7993 (p) REVERT: a 81 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7372 (mm-40) REVERT: a 98 ASN cc_start: 0.8244 (p0) cc_final: 0.8006 (p0) REVERT: b 49 TYR cc_start: 0.8517 (m-10) cc_final: 0.7660 (m-10) REVERT: c 34 MET cc_start: 0.6373 (mmm) cc_final: 0.6146 (mmm) REVERT: d 23 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7651 (tppt) REVERT: e 23 TYR cc_start: 0.8478 (p90) cc_final: 0.8125 (p90) REVERT: e 103 THR cc_start: 0.3502 (OUTLIER) cc_final: 0.3293 (p) REVERT: f 55 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9060 (tt) REVERT: f 57 GLN cc_start: 0.8424 (mm110) cc_final: 0.8198 (mm110) REVERT: g 108 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8942 (tt) REVERT: i 30 LEU cc_start: 0.8863 (mp) cc_final: 0.8573 (mp) REVERT: i 51 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8211 (pp) REVERT: i 52 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: j 57 VAL cc_start: 0.9015 (t) cc_final: 0.8763 (p) REVERT: k 50 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8154 (mp) REVERT: l 11 ARG cc_start: 0.8445 (ptp-170) cc_final: 0.8193 (ptp-170) REVERT: l 29 VAL cc_start: 0.9120 (t) cc_final: 0.8890 (m) REVERT: m 28 ASN cc_start: 0.8858 (m-40) cc_final: 0.8604 (m110) REVERT: m 46 ARG cc_start: 0.7736 (tpt90) cc_final: 0.7027 (tpp80) REVERT: m 48 SER cc_start: 0.7539 (OUTLIER) cc_final: 0.7100 (p) REVERT: m 49 SER cc_start: 0.8360 (p) cc_final: 0.7807 (p) REVERT: m 56 ILE cc_start: 0.8387 (mp) cc_final: 0.8023 (mp) REVERT: m 64 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8404 (mmtt) REVERT: n 28 ARG cc_start: 0.8519 (mtp-110) cc_final: 0.8276 (mtp-110) REVERT: p 1 MET cc_start: 0.7718 (ptm) cc_final: 0.5986 (mmt) REVERT: s 12 LYS cc_start: 0.6443 (tmtt) cc_final: 0.5765 (mtmm) REVERT: t 608 MET cc_start: -0.0505 (mmm) cc_final: -0.1271 (mmt) REVERT: u 16 MET cc_start: -0.0750 (mtt) cc_final: -0.2035 (mmm) REVERT: u 127 MET cc_start: -0.1346 (ptt) cc_final: -0.1991 (ptp) REVERT: v 63 MET cc_start: 0.2968 (mmt) cc_final: 0.2687 (mmt) REVERT: v 105 LYS cc_start: -0.4840 (pttt) cc_final: -0.5095 (pttt) REVERT: v 118 LYS cc_start: -0.2262 (pttt) cc_final: -0.2486 (pttp) REVERT: v 139 LYS cc_start: -0.4129 (mmtt) cc_final: -0.4571 (mmtt) outliers start: 359 outliers final: 213 residues processed: 1976 average time/residue: 1.2768 time to fit residues: 4340.5014 Evaluate side-chains 1805 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1582 time to evaluate : 7.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 237 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 230 LYS Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 162 TRP Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 171 SER Chi-restraints excluded: chain P residue 196 THR Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 193 GLN Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 75 GLU Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 120 ASN Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 51 VAL Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain U residue 85 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain V residue 126 VAL Chi-restraints excluded: chain V residue 136 ARG Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain W residue 80 THR Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 86 VAL Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 130 TYR Chi-restraints excluded: chain a residue 8 VAL Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain b residue 72 ILE Chi-restraints excluded: chain b residue 88 ASP Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 109 GLU Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 80 LYS Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 5 HIS Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 77 ASN Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 52 GLN Chi-restraints excluded: chain i residue 68 THR Chi-restraints excluded: chain i residue 100 ILE Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 34 GLN Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 53 CYS Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 91 ASN Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain m residue 7 ASP Chi-restraints excluded: chain m residue 14 LEU Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 55 VAL Chi-restraints excluded: chain m residue 73 LEU Chi-restraints excluded: chain m residue 75 VAL Chi-restraints excluded: chain n residue 9 ILE Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 47 THR Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain s residue 199 LEU Chi-restraints excluded: chain s residue 200 SER Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 538 ASN Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain u residue 151 SER Chi-restraints excluded: chain v residue 21 LYS Chi-restraints excluded: chain v residue 159 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 1012 optimal weight: 7.9990 chunk 770 optimal weight: 10.0000 chunk 532 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 489 optimal weight: 10.0000 chunk 688 optimal weight: 10.0000 chunk 1028 optimal weight: 40.0000 chunk 1089 optimal weight: 20.0000 chunk 537 optimal weight: 6.9990 chunk 975 optimal weight: 40.0000 chunk 293 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 GLN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 GLN H 178 ASN H 274 GLN I 57 HIS J 52 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 165 GLN N 19 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 195 ASN ** Q 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN R 97 ASN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 ASN ** T 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 HIS U 108 GLN ** 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 101 ASN Z 137 ASN a 42 GLN b 36 HIS b 127 ASN c 11 HIS ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN d 43 HIS ** e 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 26 HIS ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 59 ASN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 ASN ** s 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 208 ASN ** 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 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 101 ASN v 166 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.132 151811 Z= 0.559 Angle : 0.878 12.476 223438 Z= 0.449 Chirality : 0.050 0.566 28022 Planarity : 0.007 0.109 14380 Dihedral : 24.296 179.412 67060 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.41 % Favored : 92.02 % Rotamer: Outliers : 7.76 % Allowed : 19.08 % Favored : 73.16 % 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: -2.10 (0.09), residues: 7422 helix: -0.23 (0.10), residues: 2770 sheet: -1.69 (0.16), residues: 915 loop : -2.27 (0.09), residues: 3737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP H 95 HIS 0.012 0.002 HIS g 88 PHE 0.032 0.003 PHE m 11 TYR 0.037 0.003 TYR H 198 ARG 0.021 0.001 ARG R 171 *********************** 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 2182 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 480 poor density : 1702 time to evaluate : 7.323 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: C 25 VAL cc_start: 0.9052 (t) cc_final: 0.8822 (p) REVERT: C 73 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7103 (mt-10) REVERT: E 7 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8583 (p0) REVERT: E 247 ARG cc_start: 0.6723 (mmt90) cc_final: 0.5138 (tpt90) REVERT: F 4 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8381 (ttt-90) REVERT: F 7 GLU cc_start: 0.6718 (mt-10) cc_final: 0.5631 (tm-30) REVERT: F 221 THR cc_start: 0.9273 (m) cc_final: 0.8940 (p) REVERT: G 50 TYR cc_start: 0.9002 (p90) cc_final: 0.8685 (p90) REVERT: H 17 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: H 95 TRP cc_start: 0.8190 (t60) cc_final: 0.7891 (t60) REVERT: H 111 GLN cc_start: 0.8368 (pp30) cc_final: 0.8031 (pp30) REVERT: I 84 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8267 (m) REVERT: J 52 GLN cc_start: 0.7298 (tp40) cc_final: 0.5843 (tp-100) REVERT: J 89 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8111 (pt) REVERT: J 146 GLN cc_start: 0.7623 (mt0) cc_final: 0.7346 (mt0) REVERT: J 194 HIS cc_start: 0.6862 (m170) cc_final: 0.6657 (m170) REVERT: K 54 GLU cc_start: 0.7929 (mp0) cc_final: 0.7721 (mp0) REVERT: K 57 ARG cc_start: 0.8447 (ptp90) cc_final: 0.8238 (ptp-170) REVERT: K 226 TYR cc_start: 0.7525 (t80) cc_final: 0.7138 (t80) REVERT: L 20 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7529 (mp) REVERT: L 122 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8059 (ptpp) REVERT: L 173 ARG cc_start: 0.7587 (ptt-90) cc_final: 0.7220 (ptt180) REVERT: M 65 ILE cc_start: 0.8042 (tp) cc_final: 0.7699 (tp) REVERT: N 21 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7481 (ptp-110) REVERT: N 112 ASN cc_start: 0.8170 (m-40) cc_final: 0.7957 (m110) REVERT: N 162 ASN cc_start: 0.8309 (p0) cc_final: 0.8027 (p0) REVERT: N 179 PHE cc_start: 0.8038 (m-10) cc_final: 0.7267 (m-10) REVERT: P 174 ILE cc_start: 0.8969 (mm) cc_final: 0.8753 (mm) REVERT: Q 87 MET cc_start: 0.8252 (mtt) cc_final: 0.7948 (mtt) REVERT: R 20 SER cc_start: 0.8989 (m) cc_final: 0.8758 (p) REVERT: R 21 TYR cc_start: 0.8154 (m-80) cc_final: 0.7898 (m-10) REVERT: S 32 LEU cc_start: 0.8702 (tt) cc_final: 0.8473 (tp) REVERT: S 144 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8787 (ttm170) REVERT: W 13 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8266 (tttm) REVERT: W 35 LYS cc_start: 0.9302 (mtpp) cc_final: 0.9078 (tptp) REVERT: W 88 GLN cc_start: 0.8660 (mp10) cc_final: 0.8215 (mp10) REVERT: W 101 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.7687 (m110) REVERT: Y 35 LYS cc_start: 0.8645 (tttt) cc_final: 0.8407 (ttmt) REVERT: a 81 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7453 (mm110) REVERT: b 77 TYR cc_start: 0.8408 (m-10) cc_final: 0.8171 (m-80) REVERT: b 121 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7927 (tpp80) REVERT: c 24 LYS cc_start: 0.7026 (ttmt) cc_final: 0.6132 (ptpt) REVERT: d 5 LYS cc_start: 0.8505 (tppt) cc_final: 0.8293 (tppt) REVERT: e 68 TYR cc_start: 0.8792 (t80) cc_final: 0.8572 (t80) REVERT: i 51 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8261 (pp) REVERT: i 54 ILE cc_start: 0.9189 (mm) cc_final: 0.8935 (mm) REVERT: j 59 ASN cc_start: 0.8283 (t160) cc_final: 0.8072 (t0) REVERT: j 60 GLU cc_start: 0.8127 (pp20) cc_final: 0.7924 (pp20) REVERT: m 46 ARG cc_start: 0.8026 (tpt90) cc_final: 0.7796 (tpt170) REVERT: p 1 MET cc_start: 0.7779 (ptm) cc_final: 0.6915 (mmt) REVERT: s 12 LYS cc_start: 0.6938 (tmtt) cc_final: 0.6150 (tmtt) REVERT: s 153 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6817 (ttt-90) REVERT: t 580 MET cc_start: -0.1471 (ttt) cc_final: -0.1959 (ttt) REVERT: u 16 MET cc_start: -0.0821 (mtt) cc_final: -0.2433 (mmt) REVERT: u 34 MET cc_start: 0.5223 (tpp) cc_final: 0.4671 (ttt) REVERT: u 100 MET cc_start: 0.3028 (mmm) cc_final: 0.2642 (mmm) REVERT: u 127 MET cc_start: -0.1423 (ptt) cc_final: -0.2215 (mtm) REVERT: v 118 LYS cc_start: -0.2300 (pttt) cc_final: -0.2527 (pttp) REVERT: v 139 LYS cc_start: -0.3693 (mmtt) cc_final: -0.4042 (mmtt) outliers start: 480 outliers final: 329 residues processed: 1975 average time/residue: 1.2999 time to fit residues: 4437.0759 Evaluate side-chains 1907 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1566 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 237 ASN Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 134 TYR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 116 TYR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 162 TRP Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 171 SER Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 190 THR Chi-restraints excluded: chain P residue 196 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 75 GLU Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 144 SER Chi-restraints excluded: chain R residue 172 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 144 ARG Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 51 VAL Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 94 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 73 LYS Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain U residue 85 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 100 LYS Chi-restraints excluded: chain V residue 126 VAL Chi-restraints excluded: chain V residue 136 ARG Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain W residue 101 ASN Chi-restraints excluded: chain X residue 24 ASN Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 64 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 117 ASN Chi-restraints excluded: chain Z residue 130 TYR Chi-restraints excluded: chain a residue 8 VAL Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 72 ILE Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 109 GLU Chi-restraints excluded: chain b residue 127 ASN Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 73 LEU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 96 LYS Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 44 LYS Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain e residue 11 ASN Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 67 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 107 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 28 VAL Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 80 LYS Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 5 HIS Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 77 ASN Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 5 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 52 GLN Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 68 THR Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 34 GLN Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 88 GLU Chi-restraints excluded: chain k residue 91 ASN Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 80 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 7 ASP Chi-restraints excluded: chain m residue 14 LEU Chi-restraints excluded: chain m residue 19 ASP Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 54 LEU Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 47 THR Chi-restraints excluded: chain o residue 81 SER Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain s residue 35 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 153 ARG Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain s residue 200 SER Chi-restraints excluded: chain s residue 216 PHE Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 412 ASP Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 538 ASN Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain u residue 151 SER Chi-restraints excluded: chain v residue 21 LYS Chi-restraints excluded: chain v residue 159 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 907 optimal weight: 3.9990 chunk 618 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 811 optimal weight: 6.9990 chunk 449 optimal weight: 3.9990 chunk 929 optimal weight: 3.9990 chunk 753 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 556 optimal weight: 1.9990 chunk 977 optimal weight: 50.0000 chunk 274 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS E 24 GLN E 140 ASN E 194 ASN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN H 90 HIS H 178 ASN J 37 ASN J 64 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 195 ASN Q 29 ASN R 28 ASN ** 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 ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN V 131 GLN W 101 ASN Z 94 GLN a 42 GLN b 76 ASN b 78 ASN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 HIS d 12 GLN ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN ** i 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 GLN i 69 HIS j 34 GLN l 30 GLN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.8025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 151811 Z= 0.174 Angle : 0.635 11.093 223438 Z= 0.325 Chirality : 0.037 0.314 28022 Planarity : 0.004 0.059 14380 Dihedral : 24.168 179.463 67060 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.17 % Favored : 93.34 % Rotamer: Outliers : 4.58 % Allowed : 23.21 % Favored : 72.22 % 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: -1.66 (0.09), residues: 7422 helix: 0.19 (0.10), residues: 2752 sheet: -1.46 (0.16), residues: 903 loop : -2.05 (0.09), residues: 3767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 95 HIS 0.014 0.001 HIS H 90 PHE 0.028 0.002 PHE G 355 TYR 0.038 0.002 TYR t 76 ARG 0.009 0.001 ARG D 36 *********************** 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 2074 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1791 time to evaluate : 7.223 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: C 3 ASN cc_start: 0.8266 (t0) cc_final: 0.7982 (t0) REVERT: C 73 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6771 (mm-30) REVERT: C 80 ARG cc_start: 0.7126 (mtt90) cc_final: 0.6716 (mtt90) REVERT: E 7 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8050 (p0) REVERT: E 49 VAL cc_start: 0.8877 (p) cc_final: 0.8601 (m) REVERT: E 247 ARG cc_start: 0.6408 (mmt90) cc_final: 0.5164 (tpt90) REVERT: F 7 GLU cc_start: 0.6362 (mt-10) cc_final: 0.5579 (tm-30) REVERT: F 53 MET cc_start: 0.8252 (mtp) cc_final: 0.7998 (mtp) REVERT: F 221 THR cc_start: 0.9210 (m) cc_final: 0.8922 (p) REVERT: G 50 TYR cc_start: 0.9014 (p90) cc_final: 0.8659 (p90) REVERT: H 17 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: H 95 TRP cc_start: 0.8218 (t60) cc_final: 0.7905 (t60) REVERT: H 111 GLN cc_start: 0.8174 (pp30) cc_final: 0.7896 (pp30) REVERT: J 89 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7939 (pt) REVERT: J 107 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7983 (ttp-110) REVERT: M 65 ILE cc_start: 0.8123 (tp) cc_final: 0.7741 (tp) REVERT: N 21 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7403 (ptp-110) REVERT: N 162 ASN cc_start: 0.8152 (p0) cc_final: 0.7873 (p0) REVERT: P 46 ASP cc_start: 0.8586 (p0) cc_final: 0.8173 (p0) REVERT: P 197 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8458 (tp) REVERT: R 20 SER cc_start: 0.8814 (m) cc_final: 0.8563 (p) REVERT: U 6 GLU cc_start: 0.7535 (tp30) cc_final: 0.7279 (tp30) REVERT: V 83 ARG cc_start: 0.7654 (ptt90) cc_final: 0.7151 (ptt90) REVERT: V 84 TYR cc_start: 0.8289 (m-80) cc_final: 0.8077 (m-80) REVERT: W 35 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8889 (tptp) REVERT: X 57 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7249 (tmm) REVERT: X 97 ASP cc_start: 0.7690 (p0) cc_final: 0.7451 (p0) REVERT: a 40 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7300 (ttp-170) REVERT: a 81 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7400 (mm-40) REVERT: b 101 PHE cc_start: 0.8059 (m-80) cc_final: 0.7753 (m-80) REVERT: b 121 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7969 (tpp80) REVERT: b 135 ARG cc_start: 0.8443 (mmm160) cc_final: 0.8080 (mmm-85) REVERT: c 24 LYS cc_start: 0.6507 (ttmt) cc_final: 0.5946 (ptpt) REVERT: c 60 TYR cc_start: 0.8158 (t80) cc_final: 0.7918 (t80) REVERT: c 89 GLN cc_start: 0.7860 (pp30) cc_final: 0.7551 (pm20) REVERT: d 5 LYS cc_start: 0.8331 (tppt) cc_final: 0.7971 (tppt) REVERT: d 23 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7653 (tppt) REVERT: e 55 GLU cc_start: 0.7844 (pp20) cc_final: 0.7506 (pp20) REVERT: f 44 MET cc_start: 0.7898 (mmm) cc_final: 0.7606 (mmm) REVERT: f 76 SER cc_start: 0.8858 (m) cc_final: 0.8649 (m) REVERT: g 108 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8796 (tt) REVERT: i 30 LEU cc_start: 0.8919 (mt) cc_final: 0.8445 (mp) REVERT: i 34 HIS cc_start: 0.8237 (m90) cc_final: 0.7814 (m-70) REVERT: l 29 VAL cc_start: 0.9170 (t) cc_final: 0.8962 (p) REVERT: p 1 MET cc_start: 0.7668 (ptm) cc_final: 0.6684 (mmt) REVERT: t 212 MET cc_start: -0.2923 (ptt) cc_final: -0.3317 (ppp) REVERT: t 252 MET cc_start: 0.4513 (mmm) cc_final: 0.4264 (mmm) REVERT: t 580 MET cc_start: -0.1350 (ttt) cc_final: -0.1737 (ttt) REVERT: t 608 MET cc_start: -0.0800 (mmm) cc_final: -0.1144 (mmm) REVERT: u 16 MET cc_start: -0.0766 (mtt) cc_final: -0.2047 (mmm) REVERT: u 100 MET cc_start: 0.3505 (mmm) cc_final: 0.3000 (mmm) REVERT: u 121 MET cc_start: -0.1760 (OUTLIER) cc_final: -0.2167 (pmm) REVERT: u 127 MET cc_start: -0.1421 (ptt) cc_final: -0.2102 (mtm) REVERT: v 118 LYS cc_start: -0.2294 (pttt) cc_final: -0.2529 (pttp) REVERT: v 139 LYS cc_start: -0.3765 (mmtt) cc_final: -0.4147 (mmtt) outliers start: 283 outliers final: 191 residues processed: 1924 average time/residue: 1.2552 time to fit residues: 4158.8820 Evaluate side-chains 1813 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1612 time to evaluate : 7.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 237 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 240 ASN Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 116 TYR Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 171 SER Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 145 HIS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 144 GLN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 100 LYS Chi-restraints excluded: chain V residue 126 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 57 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain a residue 40 ARG Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 76 ASN Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 109 GLU Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain g residue 28 VAL Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 77 ASN Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 34 GLN Chi-restraints excluded: chain j residue 38 ARG Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain j residue 111 PHE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain k residue 90 MET Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain m residue 7 ASP Chi-restraints excluded: chain m residue 14 LEU Chi-restraints excluded: chain m residue 19 ASP Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain t residue 70 LYS Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 538 ASN Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain u residue 117 SER Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain v residue 21 LYS Chi-restraints excluded: chain v residue 159 LYS 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: 9.9990 chunk 215 optimal weight: 9.9990 chunk 639 optimal weight: 0.9980 chunk 268 optimal weight: 10.0000 chunk 1090 optimal weight: 40.0000 chunk 905 optimal weight: 1.9990 chunk 504 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 360 optimal weight: 20.0000 chunk 572 optimal weight: 3.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS E 132 ASN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 ASN P 195 ASN Q 193 GLN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN R 137 ASN ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 ASN b 127 ASN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 HIS ** c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN ** i 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 61 GLN i 69 HIS j 34 GLN j 59 ASN k 91 ASN l 30 GLN m 28 ASN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 50 HIS ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.8389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 151811 Z= 0.349 Angle : 0.700 11.365 223438 Z= 0.360 Chirality : 0.041 0.347 28022 Planarity : 0.005 0.069 14380 Dihedral : 24.119 179.659 67060 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.22 % Favored : 92.31 % Rotamer: Outliers : 5.60 % Allowed : 23.22 % Favored : 71.18 % 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: -1.54 (0.10), residues: 7422 helix: 0.26 (0.10), residues: 2764 sheet: -1.39 (0.16), residues: 938 loop : -1.96 (0.10), residues: 3720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 95 HIS 0.013 0.001 HIS H 90 PHE 0.041 0.002 PHE U 171 TYR 0.033 0.002 TYR t 76 ARG 0.010 0.001 ARG Y 48 *********************** 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 2040 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1694 time to evaluate : 7.310 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: C 73 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6893 (mt-10) REVERT: E 7 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8347 (p0) REVERT: E 49 VAL cc_start: 0.8948 (p) cc_final: 0.8636 (m) REVERT: E 247 ARG cc_start: 0.6560 (mmt90) cc_final: 0.5173 (tpt90) REVERT: F 7 GLU cc_start: 0.6503 (mt-10) cc_final: 0.5896 (tp30) REVERT: F 221 THR cc_start: 0.9250 (m) cc_final: 0.8934 (p) REVERT: F 308 MET cc_start: 0.7057 (mmm) cc_final: 0.6734 (mmt) REVERT: G 50 TYR cc_start: 0.9108 (p90) cc_final: 0.8803 (p90) REVERT: H 17 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: H 95 TRP cc_start: 0.8371 (t60) cc_final: 0.7914 (t60) REVERT: H 111 GLN cc_start: 0.8337 (pp30) cc_final: 0.8065 (pp30) REVERT: J 89 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8061 (pt) REVERT: J 107 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7986 (ttp-110) REVERT: J 110 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7822 (mtp85) REVERT: K 45 ASN cc_start: 0.7956 (t0) cc_final: 0.7653 (t0) REVERT: K 225 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6940 (ptmt) REVERT: M 65 ILE cc_start: 0.8235 (tp) cc_final: 0.7881 (tp) REVERT: N 162 ASN cc_start: 0.8262 (p0) cc_final: 0.7978 (p0) REVERT: O 16 GLU cc_start: 0.6632 (pm20) cc_final: 0.6427 (pm20) REVERT: P 46 ASP cc_start: 0.8746 (p0) cc_final: 0.8142 (p0) REVERT: P 197 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8595 (tp) REVERT: R 172 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: S 32 LEU cc_start: 0.8672 (tt) cc_final: 0.8391 (tp) REVERT: T 21 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8334 (mtpp) REVERT: U 6 GLU cc_start: 0.7653 (tp30) cc_final: 0.7225 (tp30) REVERT: U 30 PHE cc_start: 0.7571 (m-80) cc_final: 0.7112 (m-80) REVERT: U 91 TYR cc_start: 0.7209 (t80) cc_final: 0.6943 (t80) REVERT: W 35 LYS cc_start: 0.9263 (mtpp) cc_final: 0.8957 (tptp) REVERT: W 36 TYR cc_start: 0.8293 (t80) cc_final: 0.8035 (t80) REVERT: X 57 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7184 (tmm) REVERT: X 87 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7661 (mtm180) REVERT: X 98 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8486 (m110) REVERT: Y 35 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8477 (ttmm) REVERT: c 24 LYS cc_start: 0.6635 (ttmt) cc_final: 0.6199 (ttmt) REVERT: d 5 LYS cc_start: 0.8430 (tppt) cc_final: 0.8085 (tppt) REVERT: e 93 LEU cc_start: 0.8917 (mt) cc_final: 0.8631 (mp) REVERT: h 17 GLN cc_start: 0.7749 (tt0) cc_final: 0.7501 (tt0) REVERT: i 30 LEU cc_start: 0.9035 (mt) cc_final: 0.8617 (mp) REVERT: i 34 HIS cc_start: 0.8276 (m90) cc_final: 0.7764 (m-70) REVERT: i 51 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8320 (pp) REVERT: p 1 MET cc_start: 0.7737 (ptm) cc_final: 0.6901 (mmt) REVERT: p 18 ARG cc_start: 0.9133 (ttm110) cc_final: 0.8922 (ttm110) REVERT: s 12 LYS cc_start: 0.6830 (tmtt) cc_final: 0.6176 (tmtt) REVERT: t 252 MET cc_start: 0.4986 (mmm) cc_final: 0.4698 (mmm) REVERT: t 580 MET cc_start: -0.1398 (ttt) cc_final: -0.1672 (ttt) REVERT: t 608 MET cc_start: -0.0551 (mmm) cc_final: -0.0922 (mmm) REVERT: u 16 MET cc_start: -0.0540 (mtt) cc_final: -0.2563 (mmt) REVERT: u 100 MET cc_start: 0.3576 (mmm) cc_final: 0.3094 (mmm) REVERT: u 127 MET cc_start: -0.1151 (ptt) cc_final: -0.2352 (mtm) REVERT: v 118 LYS cc_start: -0.2134 (pttt) cc_final: -0.2395 (pttp) REVERT: v 139 LYS cc_start: -0.3679 (mmtt) cc_final: -0.4090 (mmtt) outliers start: 346 outliers final: 253 residues processed: 1871 average time/residue: 1.2559 time to fit residues: 4061.2479 Evaluate side-chains 1887 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1622 time to evaluate : 7.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 237 ASN Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 225 LYS Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 116 TYR Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 171 SER Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 172 GLN Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 144 GLN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 88 HIS Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 100 LYS Chi-restraints excluded: chain V residue 126 VAL Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 24 ASN Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 57 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 80 ASN Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain a residue 9 SER Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 109 GLU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain e residue 11 ASN Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 36 GLN Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 107 VAL Chi-restraints excluded: chain g residue 28 VAL Chi-restraints excluded: chain g residue 36 LYS Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 77 ASN Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 101 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 80 THR Chi-restraints excluded: chain m residue 7 ASP Chi-restraints excluded: chain m residue 14 LEU Chi-restraints excluded: chain m residue 19 ASP Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain n residue 29 LEU Chi-restraints excluded: chain n residue 49 MET Chi-restraints excluded: chain o residue 81 SER Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 165 ILE Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain t residue 70 LYS Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 412 ASP Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 538 ASN Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain v residue 21 LYS Chi-restraints excluded: chain v residue 110 LYS Chi-restraints excluded: chain v residue 159 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 1051 optimal weight: 40.0000 chunk 122 optimal weight: 30.0000 chunk 621 optimal weight: 7.9990 chunk 796 optimal weight: 0.9980 chunk 616 optimal weight: 4.9990 chunk 917 optimal weight: 0.9990 chunk 608 optimal weight: 9.9990 chunk 1086 optimal weight: 20.0000 chunk 679 optimal weight: 10.0000 chunk 662 optimal weight: 6.9990 chunk 501 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS E 47 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS H 178 ASN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN L 51 GLN ** L 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 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 193 GLN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN R 145 HIS ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN V 131 GLN Z 65 GLN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 HIS ** e 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN ** i 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 61 GLN j 34 GLN j 59 ASN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 50 HIS ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 20 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.8549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 151811 Z= 0.291 Angle : 0.663 11.422 223438 Z= 0.342 Chirality : 0.039 0.330 28022 Planarity : 0.005 0.069 14380 Dihedral : 24.137 179.621 67060 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.91 % Favored : 92.66 % Rotamer: Outliers : 5.58 % Allowed : 23.58 % Favored : 70.84 % 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: -1.46 (0.10), residues: 7422 helix: 0.32 (0.10), residues: 2763 sheet: -1.35 (0.16), residues: 935 loop : -1.90 (0.10), residues: 3724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 95 HIS 0.018 0.001 HIS H 90 PHE 0.040 0.002 PHE U 171 TYR 0.032 0.002 TYR t 76 ARG 0.013 0.001 ARG N 174 *********************** 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 2047 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1702 time to evaluate : 9.592 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: E 7 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8243 (p0) REVERT: E 49 VAL cc_start: 0.8920 (p) cc_final: 0.8666 (m) REVERT: E 247 ARG cc_start: 0.6553 (mmt90) cc_final: 0.5130 (tpt90) REVERT: F 7 GLU cc_start: 0.6453 (mt-10) cc_final: 0.5594 (tm-30) REVERT: F 221 THR cc_start: 0.9236 (m) cc_final: 0.8948 (p) REVERT: G 50 TYR cc_start: 0.9105 (p90) cc_final: 0.8792 (p90) REVERT: G 99 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7944 (ppp) REVERT: G 107 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7890 (ttm110) REVERT: H 17 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: H 95 TRP cc_start: 0.8420 (t60) cc_final: 0.7924 (t60) REVERT: H 111 GLN cc_start: 0.8338 (pp30) cc_final: 0.8083 (pp30) REVERT: J 89 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8018 (pt) REVERT: J 107 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8047 (ttp-110) REVERT: K 45 ASN cc_start: 0.8028 (t0) cc_final: 0.7780 (t0) REVERT: K 221 ASN cc_start: 0.7938 (p0) cc_final: 0.7376 (t0) REVERT: L 156 GLN cc_start: 0.8106 (tp40) cc_final: 0.7798 (tp-100) REVERT: M 65 ILE cc_start: 0.8312 (tp) cc_final: 0.7952 (tp) REVERT: M 77 GLU cc_start: 0.8624 (mp0) cc_final: 0.8249 (pm20) REVERT: N 162 ASN cc_start: 0.8204 (p0) cc_final: 0.7902 (p0) REVERT: O 16 GLU cc_start: 0.6567 (pm20) cc_final: 0.6328 (pm20) REVERT: P 46 ASP cc_start: 0.8651 (p0) cc_final: 0.8028 (p0) REVERT: P 197 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8566 (tp) REVERT: R 135 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7600 (mtt180) REVERT: T 21 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8345 (mtpp) REVERT: U 6 GLU cc_start: 0.7734 (tp30) cc_final: 0.7069 (tp30) REVERT: U 172 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7528 (t80) REVERT: W 35 LYS cc_start: 0.9272 (mtpp) cc_final: 0.8956 (tptp) REVERT: X 24 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7585 (p0) REVERT: X 57 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7121 (tmm) REVERT: X 87 ARG cc_start: 0.7909 (mpt-90) cc_final: 0.7663 (mtm180) REVERT: X 98 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8137 (m110) REVERT: Y 35 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8323 (ttmm) REVERT: c 85 ASP cc_start: 0.8440 (p0) cc_final: 0.8212 (p0) REVERT: c 89 GLN cc_start: 0.7987 (pp30) cc_final: 0.7472 (pm20) REVERT: d 5 LYS cc_start: 0.8419 (tppt) cc_final: 0.8052 (tppt) REVERT: e 55 GLU cc_start: 0.7858 (pp20) cc_final: 0.7054 (pp20) REVERT: i 30 LEU cc_start: 0.9004 (mt) cc_final: 0.8614 (mp) REVERT: i 51 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8297 (pp) REVERT: n 50 ASN cc_start: 0.8396 (m-40) cc_final: 0.8139 (m-40) REVERT: o 82 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8425 (mt) REVERT: p 1 MET cc_start: 0.7737 (ptm) cc_final: 0.6906 (mmt) REVERT: s 12 LYS cc_start: 0.6790 (tmtt) cc_final: 0.5948 (mtmm) REVERT: s 65 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7037 (mm-30) REVERT: s 120 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7657 (mmtt) REVERT: t 252 MET cc_start: 0.4962 (mmm) cc_final: 0.4694 (mmm) REVERT: t 580 MET cc_start: -0.1372 (ttt) cc_final: -0.1995 (ttt) REVERT: t 608 MET cc_start: -0.0387 (mmm) cc_final: -0.0812 (mmm) REVERT: u 16 MET cc_start: 0.0019 (mtt) cc_final: -0.2068 (mmt) REVERT: u 100 MET cc_start: 0.3777 (mmm) cc_final: 0.3249 (mmm) REVERT: u 127 MET cc_start: -0.1098 (ptt) cc_final: -0.2263 (mtm) REVERT: v 118 LYS cc_start: -0.2419 (pttt) cc_final: -0.2715 (pttp) REVERT: v 139 LYS cc_start: -0.3637 (mmtt) cc_final: -0.4088 (mmtt) outliers start: 345 outliers final: 274 residues processed: 1880 average time/residue: 1.2411 time to fit residues: 4041.9833 Evaluate side-chains 1926 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1638 time to evaluate : 7.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 237 ASN Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 116 TYR Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 171 SER Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 75 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 144 GLN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 88 HIS Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 172 TYR Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 100 LYS Chi-restraints excluded: chain V residue 126 VAL Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 29 ASP Chi-restraints excluded: chain W residue 33 TYR Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 11 PHE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 24 ASN Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 57 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 80 ASN Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 129 ASP Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain a residue 9 SER Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain c residue 3 SER Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 107 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 28 VAL Chi-restraints excluded: chain g residue 36 LYS Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 77 ASN Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 89 ILE Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 34 GLN Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 101 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 80 THR Chi-restraints excluded: chain m residue 7 ASP Chi-restraints excluded: chain m residue 14 LEU Chi-restraints excluded: chain m residue 19 ASP Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 75 VAL Chi-restraints excluded: chain o residue 81 SER Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain s residue 216 PHE Chi-restraints excluded: chain t residue 70 LYS Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 412 ASP Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 538 ASN Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain v residue 21 LYS Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 89 LYS Chi-restraints excluded: chain v residue 110 LYS Chi-restraints excluded: chain v residue 159 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 672 optimal weight: 4.9990 chunk 433 optimal weight: 9.9990 chunk 648 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 690 optimal weight: 3.9990 chunk 740 optimal weight: 0.7980 chunk 537 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 853 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 195 ASN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN V 131 GLN ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 HIS ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN ** i 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 34 GLN m 28 ASN ** 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 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS t 347 ASN ** t 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.8858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 151811 Z= 0.376 Angle : 0.720 11.849 223438 Z= 0.371 Chirality : 0.042 0.360 28022 Planarity : 0.005 0.073 14380 Dihedral : 24.180 179.875 67060 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.65 % Favored : 91.96 % Rotamer: Outliers : 5.71 % Allowed : 24.26 % Favored : 70.04 % 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: -1.49 (0.10), residues: 7422 helix: 0.29 (0.10), residues: 2768 sheet: -1.40 (0.16), residues: 954 loop : -1.90 (0.10), residues: 3700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP t 385 HIS 0.026 0.001 HIS c 49 PHE 0.041 0.002 PHE U 171 TYR 0.034 0.002 TYR t 76 ARG 0.017 0.001 ARG F 146 *********************** 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 2028 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 1675 time to evaluate : 7.478 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: E 7 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8354 (p0) REVERT: E 49 VAL cc_start: 0.9034 (p) cc_final: 0.8767 (m) REVERT: E 247 ARG cc_start: 0.6593 (mmt90) cc_final: 0.5061 (tpt90) REVERT: F 7 GLU cc_start: 0.6493 (mt-10) cc_final: 0.5782 (tm-30) REVERT: F 221 THR cc_start: 0.9237 (m) cc_final: 0.8954 (p) REVERT: F 308 MET cc_start: 0.7006 (mmm) cc_final: 0.6685 (mmt) REVERT: G 50 TYR cc_start: 0.9118 (p90) cc_final: 0.8892 (p90) REVERT: G 99 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8028 (ppp) REVERT: G 107 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7939 (ttm110) REVERT: G 212 ASP cc_start: 0.7977 (t0) cc_final: 0.7650 (t0) REVERT: H 17 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: H 95 TRP cc_start: 0.8495 (t60) cc_final: 0.7895 (t60) REVERT: H 111 GLN cc_start: 0.8443 (pp30) cc_final: 0.8146 (pp30) REVERT: J 89 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8066 (pt) REVERT: J 107 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7978 (ttp-110) REVERT: K 45 ASN cc_start: 0.8133 (t0) cc_final: 0.7900 (t0) REVERT: K 79 GLN cc_start: 0.7219 (pt0) cc_final: 0.6675 (pt0) REVERT: L 156 GLN cc_start: 0.8173 (tp40) cc_final: 0.7871 (tp-100) REVERT: M 65 ILE cc_start: 0.8453 (tp) cc_final: 0.8092 (tp) REVERT: M 75 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8357 (tttt) REVERT: N 162 ASN cc_start: 0.8191 (p0) cc_final: 0.7886 (p0) REVERT: O 16 GLU cc_start: 0.6957 (pm20) cc_final: 0.6613 (pm20) REVERT: P 46 ASP cc_start: 0.8789 (p0) cc_final: 0.8100 (p0) REVERT: P 197 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8660 (tp) REVERT: Q 81 TYR cc_start: 0.7451 (t80) cc_final: 0.6991 (t80) REVERT: R 135 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7538 (mtt180) REVERT: S 32 LEU cc_start: 0.8783 (tt) cc_final: 0.8482 (tp) REVERT: T 21 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8431 (mtpp) REVERT: U 106 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8679 (tp) REVERT: V 83 ARG cc_start: 0.7760 (ptt90) cc_final: 0.7394 (ptt90) REVERT: V 156 TYR cc_start: 0.8047 (t80) cc_final: 0.7805 (t80) REVERT: W 35 LYS cc_start: 0.9314 (mtpp) cc_final: 0.9009 (tptp) REVERT: X 57 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7213 (tmm) REVERT: X 87 ARG cc_start: 0.8042 (mpt-90) cc_final: 0.7795 (mtm180) REVERT: X 98 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8253 (m110) REVERT: Y 30 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7989 (mpp80) REVERT: Y 35 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8636 (ttmt) REVERT: a 81 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7676 (mm-40) REVERT: c 24 LYS cc_start: 0.6733 (ttmt) cc_final: 0.6384 (ttmt) REVERT: c 60 TYR cc_start: 0.8323 (t80) cc_final: 0.7999 (t80) REVERT: c 85 ASP cc_start: 0.8666 (p0) cc_final: 0.8248 (p0) REVERT: c 89 GLN cc_start: 0.8029 (pp30) cc_final: 0.7526 (pm20) REVERT: d 5 LYS cc_start: 0.8415 (tppt) cc_final: 0.8073 (tppt) REVERT: d 23 LYS cc_start: 0.8560 (mmmm) cc_final: 0.7967 (tppt) REVERT: h 17 GLN cc_start: 0.7799 (tt0) cc_final: 0.7575 (tt0) REVERT: h 67 MET cc_start: 0.8052 (mtp) cc_final: 0.7837 (mtt) REVERT: i 34 HIS cc_start: 0.8332 (m90) cc_final: 0.7938 (m-70) REVERT: i 51 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8348 (pp) REVERT: i 106 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8964 (mttt) REVERT: j 34 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8591 (pp30) REVERT: l 43 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8203 (mtpp) REVERT: n 42 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7695 (tmm-80) REVERT: p 1 MET cc_start: 0.7716 (ptm) cc_final: 0.6964 (mmt) REVERT: p 23 ARG cc_start: 0.8919 (ttt-90) cc_final: 0.8580 (ttt-90) REVERT: s 12 LYS cc_start: 0.6909 (tmtt) cc_final: 0.6021 (mtmm) REVERT: t 212 MET cc_start: -0.2773 (ptt) cc_final: -0.3415 (ppp) REVERT: t 252 MET cc_start: 0.4972 (mmm) cc_final: 0.4754 (mmm) REVERT: t 580 MET cc_start: -0.1710 (ttt) cc_final: -0.2331 (ttt) REVERT: t 608 MET cc_start: -0.0219 (mmm) cc_final: -0.0665 (mmm) REVERT: u 16 MET cc_start: 0.0084 (mtt) cc_final: -0.1915 (mmt) REVERT: u 100 MET cc_start: 0.3842 (mmm) cc_final: 0.3258 (mmm) REVERT: u 127 MET cc_start: -0.1144 (ptt) cc_final: -0.2142 (mtm) REVERT: v 118 LYS cc_start: -0.2304 (pttt) cc_final: -0.2626 (pttp) REVERT: v 139 LYS cc_start: -0.3589 (mmtt) cc_final: -0.4054 (mmtt) outliers start: 353 outliers final: 297 residues processed: 1855 average time/residue: 1.2542 time to fit residues: 4027.9557 Evaluate side-chains 1934 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1620 time to evaluate : 7.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 237 ASN Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 116 TYR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 171 SER Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 88 HIS Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 100 LYS Chi-restraints excluded: chain V residue 126 VAL Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 29 ASP Chi-restraints excluded: chain W residue 33 TYR Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain X residue 11 PHE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 57 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 80 ASN Chi-restraints excluded: chain Z residue 129 ASP Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain a residue 9 SER Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain c residue 3 SER Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 105 LEU Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain e residue 11 ASN Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 66 LYS Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 107 VAL Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 28 VAL Chi-restraints excluded: chain g residue 36 LYS Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 77 ASN Chi-restraints excluded: chain i residue 5 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 34 GLN Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 101 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 80 THR Chi-restraints excluded: chain m residue 7 ASP Chi-restraints excluded: chain m residue 14 LEU Chi-restraints excluded: chain m residue 19 ASP Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 75 VAL Chi-restraints excluded: chain n residue 29 LEU Chi-restraints excluded: chain n residue 42 ARG Chi-restraints excluded: chain o residue 81 SER Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain s residue 216 PHE Chi-restraints excluded: chain t residue 70 LYS Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 412 ASP Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 538 ASN Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain u residue 117 SER Chi-restraints excluded: chain v residue 21 LYS Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 89 LYS Chi-restraints excluded: chain v residue 159 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 988 optimal weight: 7.9990 chunk 1040 optimal weight: 50.0000 chunk 949 optimal weight: 2.9990 chunk 1012 optimal weight: 40.0000 chunk 609 optimal weight: 20.0000 chunk 440 optimal weight: 7.9990 chunk 794 optimal weight: 0.2980 chunk 310 optimal weight: 20.0000 chunk 914 optimal weight: 8.9990 chunk 957 optimal weight: 0.9990 chunk 1008 optimal weight: 7.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS E 47 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 ASN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 HIS J 225 GLN K 59 GLN K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 ASN L 37 ASN L 40 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 ASN P 195 ASN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN ** V 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN ** c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN i 34 HIS ** j 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 28 ASN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 ASN ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS t 347 ASN ** t 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.8928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 151811 Z= 0.280 Angle : 0.672 12.999 223438 Z= 0.347 Chirality : 0.040 0.331 28022 Planarity : 0.005 0.073 14380 Dihedral : 24.179 179.884 67060 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.09 % Favored : 92.52 % Rotamer: Outliers : 5.53 % Allowed : 24.90 % Favored : 69.57 % 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: -1.39 (0.10), residues: 7422 helix: 0.38 (0.10), residues: 2763 sheet: -1.36 (0.16), residues: 948 loop : -1.84 (0.10), residues: 3711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP t 385 HIS 0.025 0.001 HIS c 49 PHE 0.042 0.002 PHE U 171 TYR 0.037 0.002 TYR t 76 ARG 0.014 0.001 ARG N 174 *********************** 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 2040 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1698 time to evaluate : 7.340 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: E 7 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8240 (p0) REVERT: E 49 VAL cc_start: 0.8903 (p) cc_final: 0.8693 (m) REVERT: E 247 ARG cc_start: 0.6562 (mmt90) cc_final: 0.4926 (tpt90) REVERT: F 7 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5676 (tm-30) REVERT: F 221 THR cc_start: 0.9230 (m) cc_final: 0.8972 (p) REVERT: F 308 MET cc_start: 0.6916 (mmm) cc_final: 0.6679 (mmt) REVERT: G 50 TYR cc_start: 0.9069 (p90) cc_final: 0.8863 (p90) REVERT: G 99 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7943 (ppp) REVERT: G 107 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7894 (ttm110) REVERT: G 212 ASP cc_start: 0.7912 (t0) cc_final: 0.7554 (t0) REVERT: H 17 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: H 95 TRP cc_start: 0.8477 (t60) cc_final: 0.7874 (t60) REVERT: H 111 GLN cc_start: 0.8416 (pp30) cc_final: 0.8128 (pp30) REVERT: J 89 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7976 (pt) REVERT: J 107 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7984 (ttp-110) REVERT: K 221 ASN cc_start: 0.7805 (p0) cc_final: 0.7439 (t0) REVERT: L 156 GLN cc_start: 0.8106 (tp40) cc_final: 0.7823 (tp-100) REVERT: M 65 ILE cc_start: 0.8468 (tp) cc_final: 0.8148 (tp) REVERT: N 162 ASN cc_start: 0.8205 (p0) cc_final: 0.7898 (p0) REVERT: O 16 GLU cc_start: 0.6763 (pm20) cc_final: 0.6448 (pm20) REVERT: O 39 ILE cc_start: 0.8976 (mt) cc_final: 0.8751 (mt) REVERT: P 46 ASP cc_start: 0.8705 (p0) cc_final: 0.8019 (p0) REVERT: R 28 ASN cc_start: 0.8996 (m-40) cc_final: 0.8783 (m110) REVERT: R 135 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7492 (mtt180) REVERT: S 32 LEU cc_start: 0.8702 (tt) cc_final: 0.8434 (tp) REVERT: S 144 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7566 (mtt-85) REVERT: V 156 TYR cc_start: 0.8026 (t80) cc_final: 0.7824 (t80) REVERT: W 13 LYS cc_start: 0.8712 (tttm) cc_final: 0.8502 (tttm) REVERT: W 35 LYS cc_start: 0.9296 (mtpp) cc_final: 0.8962 (tptp) REVERT: X 57 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7211 (tmm) REVERT: X 98 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8266 (m110) REVERT: Y 30 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8045 (mpp80) REVERT: Y 35 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8622 (ttmt) REVERT: c 24 LYS cc_start: 0.6535 (ttmt) cc_final: 0.5230 (ttmt) REVERT: c 85 ASP cc_start: 0.8646 (p0) cc_final: 0.8305 (p0) REVERT: c 89 GLN cc_start: 0.7987 (pp30) cc_final: 0.7478 (pm20) REVERT: h 67 MET cc_start: 0.8053 (mtp) cc_final: 0.7827 (mtt) REVERT: i 51 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8269 (pp) REVERT: i 106 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8989 (mttt) REVERT: l 43 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8189 (mtpp) REVERT: n 42 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7469 (tmm-80) REVERT: n 50 ASN cc_start: 0.8302 (m-40) cc_final: 0.8073 (m-40) REVERT: p 1 MET cc_start: 0.7662 (ptm) cc_final: 0.6930 (mmt) REVERT: p 23 ARG cc_start: 0.8938 (ttt-90) cc_final: 0.8193 (ttt-90) REVERT: s 12 LYS cc_start: 0.6939 (tmtt) cc_final: 0.6214 (tmtt) REVERT: s 185 GLU cc_start: 0.8635 (mp0) cc_final: 0.8250 (pp20) REVERT: t 212 MET cc_start: -0.2706 (ptt) cc_final: -0.3313 (ppp) REVERT: t 580 MET cc_start: -0.1702 (ttt) cc_final: -0.2337 (ttt) REVERT: t 608 MET cc_start: -0.0014 (mmm) cc_final: -0.0508 (mmm) REVERT: u 16 MET cc_start: 0.0046 (mtt) cc_final: -0.1854 (mmt) REVERT: u 100 MET cc_start: 0.3986 (mmm) cc_final: 0.3400 (mmm) REVERT: u 127 MET cc_start: -0.1216 (ptt) cc_final: -0.3663 (mtm) REVERT: v 118 LYS cc_start: -0.2565 (pttt) cc_final: -0.2855 (pttp) REVERT: v 139 LYS cc_start: -0.3815 (mmtt) cc_final: -0.4266 (mmtt) outliers start: 342 outliers final: 291 residues processed: 1864 average time/residue: 1.3710 time to fit residues: 4471.7938 Evaluate side-chains 1960 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1656 time to evaluate : 7.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 237 ASN Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 116 TYR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 171 SER Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain R residue 144 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 144 ARG Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain T residue 144 GLN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 88 HIS Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 100 LYS Chi-restraints excluded: chain V residue 126 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 33 TYR Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain X residue 11 PHE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 57 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 64 LYS Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 80 ASN Chi-restraints excluded: chain Z residue 129 ASP Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain a residue 9 SER Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain c residue 3 SER Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 105 LEU Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 66 LYS Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 107 VAL Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 28 VAL Chi-restraints excluded: chain g residue 36 LYS Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 126 LEU Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 77 ASN Chi-restraints excluded: chain i residue 5 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 101 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 80 THR Chi-restraints excluded: chain m residue 7 ASP Chi-restraints excluded: chain m residue 14 LEU Chi-restraints excluded: chain m residue 19 ASP Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 75 VAL Chi-restraints excluded: chain n residue 29 LEU Chi-restraints excluded: chain n residue 42 ARG Chi-restraints excluded: chain o residue 81 SER Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain p residue 19 LYS Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain s residue 216 PHE Chi-restraints excluded: chain t residue 70 LYS Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 412 ASP Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 538 ASN Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 89 LYS Chi-restraints excluded: chain v residue 110 LYS Chi-restraints excluded: chain v residue 159 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 664 optimal weight: 0.1980 chunk 1070 optimal weight: 1.9990 chunk 653 optimal weight: 2.9990 chunk 507 optimal weight: 0.4980 chunk 744 optimal weight: 0.7980 chunk 1122 optimal weight: 8.9990 chunk 1033 optimal weight: 10.0000 chunk 894 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 690 optimal weight: 2.9990 chunk 548 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS E 24 GLN E 47 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN H 57 ASN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 195 ASN ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN Q 193 GLN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN i 52 GLN i 69 HIS j 34 GLN m 28 ASN ** m 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.8809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 151811 Z= 0.160 Angle : 0.632 18.390 223438 Z= 0.322 Chirality : 0.036 0.442 28022 Planarity : 0.004 0.104 14380 Dihedral : 24.097 179.830 67060 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.47 % Favored : 93.17 % Rotamer: Outliers : 3.54 % Allowed : 26.99 % Favored : 69.47 % 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: -1.24 (0.10), residues: 7422 helix: 0.44 (0.10), residues: 2739 sheet: -1.19 (0.16), residues: 934 loop : -1.71 (0.10), residues: 3749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP t 385 HIS 0.021 0.001 HIS c 49 PHE 0.040 0.002 PHE U 171 TYR 0.038 0.001 TYR t 76 ARG 0.028 0.001 ARG H 179 ********************** 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 1988 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1769 time to evaluate : 7.306 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: D 40 SER cc_start: 0.8916 (m) cc_final: 0.8645 (p) REVERT: D 88 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: E 7 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7843 (p0) REVERT: E 49 VAL cc_start: 0.8792 (p) cc_final: 0.8563 (m) REVERT: E 158 ILE cc_start: 0.8573 (mp) cc_final: 0.8092 (tt) REVERT: E 247 ARG cc_start: 0.6506 (mmt90) cc_final: 0.4999 (tpt90) REVERT: F 7 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5930 (tp30) REVERT: F 221 THR cc_start: 0.9174 (m) cc_final: 0.8973 (p) REVERT: G 50 TYR cc_start: 0.9069 (p90) cc_final: 0.8859 (p90) REVERT: G 99 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7756 (ppp) REVERT: H 95 TRP cc_start: 0.8383 (t60) cc_final: 0.7901 (t60) REVERT: J 89 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7793 (pt) REVERT: J 107 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7978 (ttp-110) REVERT: K 221 ASN cc_start: 0.7732 (p0) cc_final: 0.7421 (t0) REVERT: L 156 GLN cc_start: 0.7922 (tp40) cc_final: 0.7655 (tp-100) REVERT: M 65 ILE cc_start: 0.8400 (tp) cc_final: 0.8106 (tp) REVERT: N 162 ASN cc_start: 0.8152 (p0) cc_final: 0.7807 (p0) REVERT: O 16 GLU cc_start: 0.6703 (pm20) cc_final: 0.6415 (pm20) REVERT: O 39 ILE cc_start: 0.8946 (mt) cc_final: 0.8706 (mt) REVERT: P 46 ASP cc_start: 0.8564 (p0) cc_final: 0.8005 (p0) REVERT: Q 87 MET cc_start: 0.7911 (mtt) cc_final: 0.7658 (mtt) REVERT: R 28 ASN cc_start: 0.8864 (m-40) cc_final: 0.8657 (m110) REVERT: R 55 GLN cc_start: 0.8781 (mm110) cc_final: 0.8442 (mp10) REVERT: S 144 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7475 (mtt-85) REVERT: U 124 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7856 (mm) REVERT: V 13 TYR cc_start: 0.8732 (m-80) cc_final: 0.8510 (m-80) REVERT: W 13 LYS cc_start: 0.8684 (tttm) cc_final: 0.8481 (tttm) REVERT: W 35 LYS cc_start: 0.9282 (mtpp) cc_final: 0.8950 (tptp) REVERT: X 57 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7647 (ttp) REVERT: X 66 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8390 (mmtt) REVERT: X 98 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8172 (m110) REVERT: Y 9 SER cc_start: 0.9437 (p) cc_final: 0.9012 (p) REVERT: Y 35 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8218 (ttmm) REVERT: Z 94 GLN cc_start: 0.8168 (mt0) cc_final: 0.7951 (mt0) REVERT: c 24 LYS cc_start: 0.6254 (ttmt) cc_final: 0.5969 (ptpt) REVERT: c 85 ASP cc_start: 0.8557 (p0) cc_final: 0.8147 (p0) REVERT: c 89 GLN cc_start: 0.7952 (pp30) cc_final: 0.7388 (pm20) REVERT: e 55 GLU cc_start: 0.7653 (pp20) cc_final: 0.7054 (pp20) REVERT: h 67 MET cc_start: 0.8057 (mtp) cc_final: 0.7852 (mtt) REVERT: i 51 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8232 (pp) REVERT: n 42 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7421 (tmm-80) REVERT: p 1 MET cc_start: 0.7810 (ptm) cc_final: 0.6883 (mmt) REVERT: s 12 LYS cc_start: 0.6499 (tmtt) cc_final: 0.5817 (tmtt) REVERT: s 185 GLU cc_start: 0.8573 (mp0) cc_final: 0.8249 (pp20) REVERT: t 580 MET cc_start: -0.1704 (ttt) cc_final: -0.2329 (ttt) REVERT: u 16 MET cc_start: -0.0078 (mtt) cc_final: -0.1811 (mmt) REVERT: u 100 MET cc_start: 0.3846 (mmm) cc_final: 0.3265 (mmm) REVERT: u 127 MET cc_start: -0.1221 (ptt) cc_final: -0.3650 (mtm) REVERT: v 63 MET cc_start: 0.2007 (mmt) cc_final: 0.1736 (mmt) REVERT: v 118 LYS cc_start: -0.2567 (pttt) cc_final: -0.2822 (pttp) REVERT: v 139 LYS cc_start: -0.3628 (mmtt) cc_final: -0.4079 (mmtt) outliers start: 219 outliers final: 177 residues processed: 1876 average time/residue: 1.2744 time to fit residues: 4145.7991 Evaluate side-chains 1858 residues out of total 6338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1670 time to evaluate : 7.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 116 TYR Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 171 SER Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 75 GLU Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 144 ARG Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 173 GLU Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain T residue 144 GLN Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 88 HIS Chi-restraints excluded: chain U residue 92 LYS Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 126 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 57 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 80 ASN Chi-restraints excluded: chain Z residue 129 ASP Chi-restraints excluded: chain a residue 9 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 107 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 28 VAL Chi-restraints excluded: chain g residue 36 LYS Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 126 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 89 ILE Chi-restraints excluded: chain j residue 16 GLN Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 101 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain m residue 7 ASP Chi-restraints excluded: chain m residue 14 LEU Chi-restraints excluded: chain m residue 19 ASP Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 75 VAL Chi-restraints excluded: chain n residue 42 ARG Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain p residue 13 LEU Chi-restraints excluded: chain p residue 19 LYS Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain s residue 216 PHE Chi-restraints excluded: chain t residue 70 LYS Chi-restraints excluded: chain t residue 146 VAL Chi-restraints excluded: chain t residue 449 LEU Chi-restraints excluded: chain t residue 788 ASN Chi-restraints excluded: chain u residue 96 VAL Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 89 LYS Chi-restraints excluded: chain v residue 110 LYS Chi-restraints excluded: chain v residue 159 LYS 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: 10.0000 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: 4.9990 chunk 374 optimal weight: 7.9990 chunk 919 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 ASN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN K 61 GLN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 ASN P 195 ASN ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 45 ASN ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 GLN U 62 ASN V 90 ASN ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 ASN ** c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN ** e 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN ** h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 34 HIS i 61 GLN i 69 HIS l 30 GLN m 28 ASN ** 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 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 23 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.103249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.070941 restraints weight = 427109.503| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.06 r_work: 0.2906 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.9208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 151811 Z= 0.450 Angle : 0.778 13.424 223438 Z= 0.398 Chirality : 0.045 0.350 28022 Planarity : 0.005 0.078 14380 Dihedral : 24.177 179.972 67060 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.79 % Favored : 91.85 % Rotamer: Outliers : 4.19 % Allowed : 27.07 % Favored : 68.74 % 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: -1.43 (0.10), residues: 7422 helix: 0.28 (0.10), residues: 2763 sheet: -1.35 (0.16), residues: 941 loop : -1.81 (0.10), residues: 3718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP t 385 HIS 0.023 0.002 HIS c 49 PHE 0.036 0.002 PHE U 171 TYR 0.048 0.002 TYR V 156 ARG 0.012 0.001 ARG Y 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 60090.14 seconds wall clock time: 1037 minutes 33.62 seconds (62253.62 seconds total)